diff --git a/R/v4.1.2/contracted/v1.0/Dockerfile b/R/v4.1.2/contracted/v1.0/Dockerfile
index 20ecc5f7a33706e613ce27da7da3c04d23388070..7f5359f0f6a82f24e32ccbc4599f402d847f4a09 100644
--- a/R/v4.1.2/contracted/v1.0/Dockerfile
+++ b/R/v4.1.2/contracted/v1.0/Dockerfile
@@ -77,9 +77,11 @@ RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n
           value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)),  \
           warning = W \
         ) ; \
-        return(if(is.null(output\$warning)){NULL}else{as.character(output\$warning)}) \
+        return(if(is.null(output$warning)){NULL}else{as.character(output$warning)}) \
       } ; \
-      message(paste0('\n\n\n\n================\n\nR PACKAGE REMOVAL ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n')) ; \
+      tempo <- paste0('\n\n\n\n================\n\nR PACKAGE REMOVAL ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n') ; \
+      message(tempo) ; \
+      print(tempo) ; \
       remove.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library') \
     " ; \
   done \
diff --git a/R/v4.1.2/extended/v3.0/Dockerfile b/R/v4.1.2/extended/v3.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..587339fe6ed3f6409f4ed3fb2762aca10e499c31
--- /dev/null
+++ b/R/v4.1.2/extended/v3.0/Dockerfile
@@ -0,0 +1,209 @@
+#########################################################################
+##                                                                     ##
+##     Dockerfile                                                      ##
+##     R extended                                                      ##
+##                                                                     ##
+##     Gael A. Millot                                                  ##
+##     Bioinformatics and Biostatistics Hub                            ##
+##     Computational Biology Department                                ##
+##     Institut Pasteur Paris                                          ##
+##                                                                     ##
+#########################################################################
+
+
+
+# to see the log of the building:
+# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
+# cat building.log
+
+# to export the log file of the image building from the container:
+# sudo docker images
+# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
+# exit
+# sudo docker container ls -a # to get all the active containers
+# sudo docker cp <containerNAMES>:/building.log </host/path/target>
+# sudo docker cp <containerNAMES>:/installed_r_packages.csv </host/path/target>
+
+# base image:
+FROM gmillot/r-base_v4.1.2:gitlab_v8.2
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. Here, the image is present locally, or distantly on the gmillot repo. Thus, gmillot/r-base:4.0.5 is correct.
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+ENV APT_GET_LINUX_LIB="\
+    procps \
+    libfontconfig1-dev \
+    ghostscript \
+    lmodern \
+    pandoc \
+    pandoc-citeproc \
+    qpdf \
+    texinfo \
+    texlive-fonts-extra \
+    texlive-fonts-recommended \
+    texlive-latex-extra \
+    texlive-latex-recommended \
+    texlive-luatex \
+    texlive-plain-generic \
+    texlive-science \
+    texlive-xetex \
+    libpoppler-cpp-dev \
+"
+
+ENV APT_LINUX_LIB="\
+    build-essential \
+    libcurl4-gnutls-dev \
+    libxml2-dev \
+    libssl-dev \
+    libgit2-dev \
+    libcairo2-dev \
+    libxt-dev \
+"
+
+ENV CRANREPO="'https://cran.irsn.fr/'"
+
+ENV BIOCONDUCTOR_REPO="'https://cloud.r-project.org'"
+
+ENV RLIB="\
+  'BiocManager' \
+  'devtools' \
+  'Cairo' \
+  'dplyr' \
+  'data.table' \
+  'gridExtra' \
+  'mgcv' \
+  'InteractionSet' \
+  'GenomicRanges' \
+  'IRanges' \
+  'BiocParallel' \
+  'QDNAseq' \
+  'GenomeInfoDbData' \
+  'ggplot2' \
+  'HiCcompare' \
+  'lubridate' \
+  'parallel' \
+  'reshape2' \
+  'binb' \
+  'linl' \
+  'pinp' \
+  'tint' \
+  'pdftools' \
+  'qqman' \
+"
+
+
+
+
+# fun.warning.capture from fun_get_message() of the cute package.
+# I used a first loop because I cannot use array in dockerfiles.
+# Inactivate sink(file = tempo, append = TRUE, type = 'message') for debbuging.
+RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n" > building.log \
+  && add-apt-repository -y ppa:cran/poppler \
+  && apt-get update \
+    | tee -a building.log ; echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> building.log \
+  && apt-get install -y $APT_GET_LINUX_LIB \
+    | tee -a building.log ; echo "\n\n\n\n================\n\napt install\n\n================\n\n\n\n" >> building.log \
+  && apt -y install $APT_LINUX_LIB \
+    | tee -a building.log \
+  && RLIB_LENGTH=0 \
+  && for i2 in $RLIB ; do RLIB_LENGTH=$((RLIB_LENGTH+1)) ; done \
+  && COUNT=0 \
+  && for i2 in $RLIB ; do \
+    COUNT=$((COUNT+1)) ; \
+    Rscript --vanilla -e " \
+      options(warn = 1, verbose = TRUE) ; \
+      tempo <- file('building.log', open = 'a+b') ; \
+      sink(file = tempo, append = TRUE, type = 'message') ; \
+      fun.warning.capture <- function(expr){ \
+        W <- NULL ; \
+        w.handler <- function(w){ \
+          W <<- w ; \
+          invokeRestart('muffleWarning') \
+        } ; \
+        output <- list( \
+          value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)),  \
+          warning = W \
+        ) ; \
+        return(if(is.null(output\$warning)){NULL}else{as.character(output\$warning)}) \
+      } ; \
+      message(paste0('\n\n\n\n================\n\nR PACKAGE INSTALLATION ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n')) ; \
+      if( ! ($i2 %in% c('ggplot2', 'SARTools'))){ \
+        tempo.warn <- fun.warning.capture(exp = install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO)) ; \
+        if(is.null(tempo.warn)){ \
+            tempo <- paste0('STANDARD INSTALLATION ATTEMPT FOR ', $i2) ; \
+            message(paste0('\n\n', tempo, '\n\n')) ; \
+            cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
+            install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO) \
+        }else{ \
+            tempo <- paste0('BiocManager INSTALLATION ATTEMPT FOR ', $i2) ; \
+            message(paste0('\n\n', tempo, '\n\n')) ; \
+            cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
+            BiocManager::install(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, update = FALSE, site_repository = $BIOCONDUCTOR_REPO) \
+        } \
+      }else if($i2 == 'ggplot2'){ \
+        devtools::install_version(package = 'ggplot2', version = '3.3.3', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repos = $CRANREPO) \
+      }else if($i2 == 'SARTools'){ \
+        devtools::install_github('PF2-pasteur-fr/SARTools', build_opts='--no-resave-data', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, upgrade = "always") \
+      } \
+    " ; \
+  done \
+  && Rscript --vanilla -e  " \
+    options(warn = 1, verbose = TRUE) ; \
+    args <- commandArgs(trailingOnly = TRUE) ; \
+    if(any(is.na(args))){ \
+        stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE args OBJECT HAS NA\n\n================\n\n'), call. = FALSE) \
+    } ; \
+    tempo.arg.names <- c( \
+        'RLIB' \
+    ) ; \
+    if(length(args) != length(tempo.arg.names)){ \
+        stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE NUMBER OF ELEMENTS IN args (', length(args),') IS DIFFERENT FROM THE NUMBER OF ELEMENTS IN tempo.arg.names (', length(tempo.arg.names),')\nargs:', paste0(args, collapse = ','), '\ntempo.arg.names:', paste0(tempo.arg.names, collapse = ','), '\n\n================\n\n'), call. = FALSE) \
+    } ; \
+    for(i1 in 1:length(tempo.arg.names)){ \
+        assign(tempo.arg.names[i1], args[i1]) \
+    } ; \
+    RLIB <- strsplit(RLIB, split = ',')[[1]] ; \
+    RLIB <- RLIB[RLIB != ''] ; \
+    if(file.exists('installed_r_packages.csv')){ \
+      file.remove('installed_r_packages.csv') \
+    } ; \
+    if(file.exists('not_installed_r_packages.txt')){ \
+      file.remove('not_installed_r_packages.txt') \
+    } ; \
+    tempo <- file('building.log', open = 'a+b') ; \
+    sink(file = tempo, append = TRUE, type = 'message') ; \
+    message(paste0('\n\n\n\n================\n\nR PACKAGES INSTALLED\n\n================\n\n\n\n')) ; \
+    message('SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
+    capture.output(as.data.frame(installed.packages())[1:4], file = tempo, append = TRUE, type = 'output') ; \
+    df <- as.data.frame(installed.packages()) ; \
+    for (i2 in 1:length(df)){ \
+      df[, i2] <- gsub(x = df[, i2], replacement = '', pattern = '\n', fixed = TRUE) \
+    } ; \
+    write.table(x = df, file = 'installed_r_packages.csv', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
+    message(paste0('\n\n\n\n================\n\nR PACKAGES NOT INSTALLED\n\n================\n\n\n\n')) ; \
+    df2 <- as.data.frame(RLIB[ ! RLIB %in% df[ , 'Package']]) ; \
+    if(nrow(df2) == 0){ \
+      message('ALL THE PACKAGES HAVE BEEN INSTALLED\n\n') \
+    }else{ \
+      message('SEE ALSO THE not_installed_r_packages.txt TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
+      names(df2) <- 'Name' ; \
+      capture.output(df2, file = tempo, append = TRUE, type = 'output') ; \
+      write.table(x = df2, file = 'not_installed_r_packages.txt', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
+    } \
+  " $(echo "$RLIB" | sed 's/ \{1,\}/,/g' | sed "s/'//g") \
+  && echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n\n\n" >> building.log \
+  && apt-get autoremove -y \
+    | tee -a building.log ; echo "\n\n\n\n================\n\napt-get clean\n\n================\n\n\n\n" >> building.log \
+  && apt-get clean \
+    | tee -a building.log ; echo "\n\n\n\n================\n\nrm\n\n================\n\n\n\n" >> building.log \
+  && rm -rf /var/lib/apt/lists/* \
+    | tee -a building.log \
+  && echo "\n\n\n\n================\n\nLINUX PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \
+  && apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB \
+    >> /building.log
+
+# dependencies=NA means c("Depends", "Imports", "LinkingTo"). Do no use TRUE -> install suggesting packages which inflates tremendously the image.
+
+ENTRYPOINT ["/usr/bin/R"]
diff --git a/R/v4.1.2/extended/v3.0/building.log b/R/v4.1.2/extended/v3.0/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..b13384e9dcc0205f82de85cbef9d3f5a0dd09f8f
--- /dev/null
+++ b/R/v4.1.2/extended/v3.0/building.log
@@ -0,0 +1,3860 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Hit:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease
+Hit:2 http://security.ubuntu.com/ubuntu focal-security InRelease
+Hit:3 http://ppa.launchpad.net/cran/poppler/ubuntu focal InRelease
+Hit:4 http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal InRelease
+Hit:5 http://archive.ubuntu.com/ubuntu focal InRelease
+Hit:6 http://archive.ubuntu.com/ubuntu focal-updates InRelease
+Hit:7 http://archive.ubuntu.com/ubuntu focal-backports InRelease
+Reading package lists...
+
+
+
+
+================
+
+apt-get install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+procps is already the newest version (2:3.3.16-1ubuntu2.3).
+The following additional packages will be installed:
+  dvisvgm fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius
+  fonts-adf-universalis fonts-cabin fonts-cantarell fonts-comfortaa
+  fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito
+  fonts-dejavu-extra fonts-droid-fallback fonts-ebgaramond
+  fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf
+  fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-baskerville
+  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
+  fonts-gfs-porson fonts-gfs-solomos fonts-go fonts-junicode fonts-lato
+  fonts-linuxlibertine fonts-lmodern fonts-lobster fonts-lobstertwo
+  fonts-noto-core fonts-noto-mono fonts-oflb-asana-math fonts-open-sans
+  fonts-roboto-unhinted fonts-sil-gentium fonts-sil-gentium-basic
+  fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix fonts-texgyre
+  fonts-urw-base35 javascript-common libapache-pom-java libauthen-sasl-perl
+  libavahi-client3 libavahi-common-data libavahi-common3 libbibutils6
+  libcommons-logging-java libcommons-parent-java libcups2 libdata-dump-perl
+  libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
+  libdrm2 libedit2 libencode-locale-perl libexpat1 libexpat1-dev
+  libfile-listing-perl libfont-afm-perl libfontbox-java libfontenc1
+  libfreetype-dev libfreetype6 libfreetype6-dev libghc-pandoc-citeproc-data
+  libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgs9
+  libgs9-common libharfbuzz-icu0 libhtml-form-perl libhtml-format-perl
+  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl
+  libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
+  libhttp-message-perl libhttp-negotiate-perl libidn11 libijs-0.35
+  libio-html-perl libio-socket-ssl-perl libjbig2dec0 libjs-jquery libkpathsea6
+  liblcms2-2 libllvm12 liblwp-mediatypes-perl liblwp-protocol-https-perl
+  libmailtools-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl
+  libnspr4 libnss3 libopenjp2-7 libpciaccess0 libpdfbox-java libpoppler-cpp0v5
+  libpoppler-dev libpoppler118 libptexenc1 libqpdf26 libruby2.7
+  libsensors-config libsensors5 libsynctex2 libteckit0 libtexlua53
+  libtexluajit2 libtext-unidecode-perl libtimedate-perl libtry-tiny-perl
+  liburi-perl libutempter0 libuuid1 libvulkan1 libwayland-client0 libwoff1
+  libwww-perl libwww-robotrules-perl libx11-xcb1 libxaw7 libxcb-dri2-0
+  libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-shape0
+  libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxfixes3 libxi6 libxinerama1
+  libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl
+  libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl
+  libxml-sax-perl libxmu6 libxpm4 libxrandr2 libxshmfence1 libxtst6 libxv1
+  libxxf86dga1 libxxf86vm1 libzzip-0-13 mesa-vulkan-drivers netbase
+  pandoc-data perl-openssl-defaults poppler-data preview-latex-style rake ruby
+  ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc
+  ruby2.7 rubygems-integration t1utils tcl tcl8.6 teckit tex-common tex-gyre
+  texlive-base texlive-binaries texlive-fonts-extra-links texlive-lang-greek
+  texlive-latex-base texlive-pictures tipa tk tk8.6 uuid-dev x11-utils
+  xbitmaps xfonts-encodings xfonts-utils xterm
+Suggested packages:
+  fonts-noto fontforge ghostscript-x apache2 | lighttpd | httpd
+  libdigest-hmac-perl libgssapi-perl libavalon-framework-java
+  libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java
+  cups-common freetype2-doc liblcms2-utils libcrypt-ssleay-perl pciutils
+  lm-sensors libauthen-ntlm-perl libxml-sax-expatxs-perl context wkhtmltopdf
+  librsvg2-bin groff ghc nodejs php python libjs-mathjax node-katex
+  poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho
+  fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai
+  fonts-arphic-uming fonts-nanum ri ruby-dev bundler tcl-tclreadline debhelper
+  perl-tk xpdf | pdf-viewer xzdec cm-super texlive-fonts-extra-doc
+  texlive-fonts-recommended-doc texlive-latex-base-doc python3-pygments
+  icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl
+  texlive-latex-extra-doc texlive-latex-recommended-doc texlive-pstricks
+  dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex
+  default-jre-headless texlive-science-doc mesa-utils xfonts-cyrillic
+Recommended packages:
+  uuid-runtime
+The following NEW packages will be installed:
+  dvisvgm fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius
+  fonts-adf-universalis fonts-cabin fonts-cantarell fonts-comfortaa
+  fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito
+  fonts-dejavu-extra fonts-droid-fallback fonts-ebgaramond
+  fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf
+  fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-baskerville
+  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
+  fonts-gfs-porson fonts-gfs-solomos fonts-go fonts-junicode fonts-lato
+  fonts-linuxlibertine fonts-lmodern fonts-lobster fonts-lobstertwo
+  fonts-noto-core fonts-noto-mono fonts-oflb-asana-math fonts-open-sans
+  fonts-roboto-unhinted fonts-sil-gentium fonts-sil-gentium-basic
+  fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix fonts-texgyre
+  fonts-urw-base35 ghostscript javascript-common libapache-pom-java
+  libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3
+  libbibutils6 libcommons-logging-java libcommons-parent-java libcups2
+  libdata-dump-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2
+  libdrm-radeon1 libdrm2 libedit2 libencode-locale-perl libexpat1-dev
+  libfile-listing-perl libfont-afm-perl libfontbox-java libfontconfig1-dev
+  libfontenc1 libfreetype-dev libfreetype6-dev libghc-pandoc-citeproc-data
+  libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgs9
+  libgs9-common libharfbuzz-icu0 libhtml-form-perl libhtml-format-perl
+  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl
+  libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
+  libhttp-message-perl libhttp-negotiate-perl libidn11 libijs-0.35
+  libio-html-perl libio-socket-ssl-perl libjbig2dec0 libjs-jquery libkpathsea6
+  liblcms2-2 libllvm12 liblwp-mediatypes-perl liblwp-protocol-https-perl
+  libmailtools-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl
+  libnspr4 libnss3 libopenjp2-7 libpciaccess0 libpdfbox-java
+  libpoppler-cpp-dev libpoppler-cpp0v5 libpoppler-dev libpoppler118
+  libptexenc1 libqpdf26 libruby2.7 libsensors-config libsensors5 libsynctex2
+  libteckit0 libtexlua53 libtexluajit2 libtext-unidecode-perl libtimedate-perl
+  libtry-tiny-perl liburi-perl libutempter0 libvulkan1 libwayland-client0
+  libwoff1 libwww-perl libwww-robotrules-perl libx11-xcb1 libxaw7
+  libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0
+  libxcb-shape0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxfixes3 libxi6
+  libxinerama1 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl
+  libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl
+  libxml-sax-perl libxmu6 libxpm4 libxrandr2 libxshmfence1 libxtst6 libxv1
+  libxxf86dga1 libxxf86vm1 libzzip-0-13 lmodern mesa-vulkan-drivers netbase
+  pandoc pandoc-citeproc pandoc-data perl-openssl-defaults poppler-data
+  preview-latex-style qpdf rake ruby ruby-minitest ruby-net-telnet
+  ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
+  t1utils tcl tcl8.6 teckit tex-common tex-gyre texinfo texlive-base
+  texlive-binaries texlive-fonts-extra texlive-fonts-extra-links
+  texlive-fonts-recommended texlive-lang-greek texlive-latex-base
+  texlive-latex-extra texlive-latex-recommended texlive-luatex
+  texlive-pictures texlive-plain-generic texlive-science texlive-xetex tipa tk
+  tk8.6 uuid-dev x11-utils xbitmaps xfonts-encodings xfonts-utils xterm
+The following packages will be upgraded:
+  libexpat1 libfreetype6 libuuid1
+3 upgraded, 215 newly installed, 0 to remove and 115 not upgraded.
+Need to get 834 MB of archives.
+After this operation, 2,899 MB of additional disk space will be used.
+Get:1 http://ppa.launchpad.net/cran/poppler/ubuntu focal/main amd64 libpoppler118 amd64 22.02.0-focal0 [999 kB]
+Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 fonts-droid-fallback all 1:6.0.1r16-1.1 [1,805 kB]
+Get:3 http://ppa.launchpad.net/cran/poppler/ubuntu focal/main amd64 libpoppler-cpp0v5 amd64 22.02.0-focal0 [55.0 kB]
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+Preparing to unpack .../193-libpdfbox-java_1%3a1.8.16-2_all.deb ...
+Unpacking libpdfbox-java (1:1.8.16-2) ...
+Selecting previously unselected package texlive-latex-recommended.
+Preparing to unpack .../194-texlive-latex-recommended_2019.20200218-1_all.deb ...
+Unpacking texlive-latex-recommended (2019.20200218-1) ...
+Selecting previously unselected package texlive-pictures.
+Preparing to unpack .../195-texlive-pictures_2019.20200218-1_all.deb ...
+Unpacking texlive-pictures (2019.20200218-1) ...
+Selecting previously unselected package texlive-latex-extra.
+Preparing to unpack .../196-texlive-latex-extra_2019.202000218-1_all.deb ...
+Unpacking texlive-latex-extra (2019.202000218-1) ...
+Selecting previously unselected package texlive-luatex.
+Preparing to unpack .../197-texlive-luatex_2019.20200218-1_all.deb ...
+Unpacking texlive-luatex (2019.20200218-1) ...
+Selecting previously unselected package texlive-plain-generic.
+Preparing to unpack .../198-texlive-plain-generic_2019.202000218-1_all.deb ...
+Unpacking texlive-plain-generic (2019.202000218-1) ...
+Selecting previously unselected package texlive-science.
+Preparing to unpack .../199-texlive-science_2019.202000218-1_all.deb ...
+Unpacking texlive-science (2019.202000218-1) ...
+Selecting previously unselected package tipa.
+Preparing to unpack .../200-tipa_2%3a1.3-20_all.deb ...
+Unpacking tipa (2:1.3-20) ...
+Selecting previously unselected package texlive-xetex.
+Preparing to unpack .../201-texlive-xetex_2019.20200218-1_all.deb ...
+Unpacking texlive-xetex (2019.20200218-1) ...
+Selecting previously unselected package tk8.6.
+Preparing to unpack .../202-tk8.6_8.6.10-1_amd64.deb ...
+Unpacking tk8.6 (8.6.10-1) ...
+Selecting previously unselected package tk.
+Preparing to unpack .../203-tk_8.6.9+1_amd64.deb ...
+Unpacking tk (8.6.9+1) ...
+Selecting previously unselected package libglvnd0:amd64.
+Preparing to unpack .../204-libglvnd0_1.3.2-1~ubuntu0.20.04.2_amd64.deb ...
+Unpacking libglvnd0:amd64 (1.3.2-1~ubuntu0.20.04.2) ...
+Selecting previously unselected package libglx0:amd64.
+Preparing to unpack .../205-libglx0_1.3.2-1~ubuntu0.20.04.2_amd64.deb ...
+Unpacking libglx0:amd64 (1.3.2-1~ubuntu0.20.04.2) ...
+Selecting previously unselected package libgl1:amd64.
+Preparing to unpack .../206-libgl1_1.3.2-1~ubuntu0.20.04.2_amd64.deb ...
+Unpacking libgl1:amd64 (1.3.2-1~ubuntu0.20.04.2) ...
+Selecting previously unselected package x11-utils.
+Preparing to unpack .../207-x11-utils_7.7+5_amd64.deb ...
+Unpacking x11-utils (7.7+5) ...
+Selecting previously unselected package xbitmaps.
+Preparing to unpack .../208-xbitmaps_1.1.1-2_all.deb ...
+Unpacking xbitmaps (1.1.1-2) ...
+Selecting previously unselected package xterm.
+Preparing to unpack .../209-xterm_353-1ubuntu1.20.04.2_amd64.deb ...
+Unpacking xterm (353-1ubuntu1.20.04.2) ...
+Selecting previously unselected package libauthen-sasl-perl.
+Preparing to unpack .../210-libauthen-sasl-perl_2.1600-1_all.deb ...
+Unpacking libauthen-sasl-perl (2.1600-1) ...
+Selecting previously unselected package libghc-pandoc-citeproc-data.
+Preparing to unpack .../211-libghc-pandoc-citeproc-data_0.15.0.1-1build4_all.deb ...
+Unpacking libghc-pandoc-citeproc-data (0.15.0.1-1build4) ...
+Selecting previously unselected package pandoc-citeproc.
+Preparing to unpack .../212-pandoc-citeproc_0.15.0.1-1build4_amd64.deb ...
+Unpacking pandoc-citeproc (0.15.0.1-1build4) ...
+Setting up libexpat1:amd64 (2.2.9-1ubuntu0.4) ...
+Setting up javascript-common (11) ...
+Setting up tk8.6 (8.6.10-1) ...
+Setting up libxcb-dri3-0:amd64 (1.14-2) ...
+Setting up liblcms2-2:amd64 (2.9-4) ...
+Setting up fonts-gfs-didot (1.1-6) ...
+Setting up fonts-gfs-artemisia (1.1-5) ...
+Setting up fonts-sil-gentium-basic (1.102-1) ...
+Setting up libx11-xcb1:amd64 (2:1.6.9-2ubuntu1.2) ...
+Setting up libpciaccess0:amd64 (0.16-0ubuntu1) ...
+Setting up fonts-cantarell (0.111-2) ...
+Setting up tcl8.6 (8.6.10+dfsg-1) ...
+Setting up libxmu6:amd64 (2:1.1.3-0ubuntu1) ...
+Setting up fonts-ebgaramond (0.016-1ubuntu1) ...
+Setting up libharfbuzz-icu0:amd64 (2.6.4-1ubuntu4.2) ...
+Setting up fonts-lato (2.0-2) ...
+Setting up fonts-junicode (1.002-2) ...
+Setting up libxcb-xfixes0:amd64 (1.14-2) ...
+Setting up fonts-noto-mono (20200323-1build1~ubuntu20.04.1) ...
+Setting up libxpm4:amd64 (1:3.5.12-1) ...
+Setting up libqpdf26:amd64 (9.1.1-1ubuntu0.1) ...
+Setting up fonts-gfs-porson (1.1-6) ...
+Setting up libxi6:amd64 (2:1.7.10-0ubuntu1) ...
+Setting up libfont-afm-perl (1.20-2) ...
+Setting up libwoff1:amd64 (1.0.2-1build2) ...
+Setting up ruby-power-assert (1.1.7-1) ...
+Setting up libtexlua53:amd64 (2019.20190605.51237-3build2) ...
+Setting up libglvnd0:amd64 (1.3.2-1~ubuntu0.20.04.2) ...
+Setting up fonts-adf-berenis (0.20190904-1.1) ...
+Setting up libxtst6:amd64 (2:1.2.3-1) ...
+Setting up libhtml-tagset-perl (3.20-4) ...
+Setting up libijs-0.35:amd64 (0.35-15) ...
+Setting up libauthen-sasl-perl (2.1600-1) ...
+Setting up libxcb-glx0:amd64 (1.14-2) ...
+Setting up libtexluajit2:amd64 (2019.20190605.51237-3build2) ...
+Setting up libfontbox-java (1:1.8.16-2) ...
+Setting up libedit2:amd64 (3.1-20191231-1) ...
+Setting up liblwp-mediatypes-perl (6.04-1) ...
+Setting up fonts-freefont-otf (20120503-10) ...
+Setting up libxcb-shape0:amd64 (1.14-2) ...
+Setting up libtry-tiny-perl (0.30-1) ...
+Setting up libsensors-config (1:3.6.0-2ubuntu1.1) ...
+Setting up libxxf86dga1:amd64 (2:1.1.5-0ubuntu1) ...
+Setting up perl-openssl-defaults:amd64 (4) ...
+Setting up fonts-freefont-ttf (20120503-10) ...
+Setting up fonts-gfs-solomos (1.1-5) ...
+Setting up libxml-namespacesupport-perl (1.12-1) ...
+Setting up fonts-comfortaa (3.001-3) ...
+Setting up libencode-locale-perl (1.05-1) ...
+Setting up rubygems-integration (1.16) ...
+Setting up libzzip-0-13:amd64 (0.13.62-3.2ubuntu1) ...
+Setting up fonts-sil-gentiumplus-compact (5.000-2) ...
+Setting up libxaw7:amd64 (2:1.0.13-1) ...
+Setting up libghc-pandoc-citeproc-data (0.15.0.1-1build4) ...
+Setting up fonts-roboto-unhinted (2:0~20170802-3) ...
+Setting up fonts-urw-base35 (20170801.1-3) ...
+Setting up fonts-open-sans (1.11-1) ...
+Setting up fonts-sil-gentiumplus (5.000-2) ...
+Setting up fonts-gfs-neohellenic (1.1-6) ...
+Setting up fonts-gfs-olga (1.1-5) ...
+Setting up fonts-oflb-asana-math (000.907-6) ...
+Setting up libxxf86vm1:amd64 (1:1.1.4-1build1) ...
+Setting up poppler-data (0.4.9-2) ...
+Setting up libxcb-present0:amd64 (1.14-2) ...
+Setting up fonts-crosextra-carlito (20130920-1) ...
+Setting up ruby-minitest (5.13.0-1) ...
+Setting up fonts-adf-accanthis (0.20190904-1.1) ...
+Setting up tex-common (6.13) ...
+update-language: texlive-base not installed and configured, doing nothing!
+Setting up fonts-sil-gentium (20081126:1.03-2) ...
+Setting up libxml-sax-base-perl (1.09-1) ...
+Setting up fonts-adf-universalis (0.20190904-1.1) ...
+Setting up libbibutils6 (6.2-1) ...
+Setting up libfontenc1:amd64 (1:1.1.4-0ubuntu1) ...
+Setting up libexpat1-dev:amd64 (2.2.9-1ubuntu0.4) ...
+Setting up fonts-stix (1.1.1-4) ...
+Setting up libfreetype6:amd64 (2.10.1-2ubuntu0.2) ...
+Setting up ruby-test-unit (3.3.5-1) ...
+Setting up libdata-dump-perl (1.23-1) ...
+Setting up libnspr4:amd64 (2:4.25-1) ...
+Setting up libxfixes3:amd64 (1:5.0.3-2) ...
+Setting up libxcb-sync1:amd64 (1.14-2) ...
+Setting up libjbig2dec0:amd64 (0.18-1ubuntu1) ...
+Setting up fonts-go (0~20170330-1) ...
+Setting up libidn11:amd64 (1.33-2.2ubuntu2) ...
+Setting up libteckit0:amd64 (2.5.8+ds2-5ubuntu2) ...
+Setting up uuid-dev:amd64 (2.34-0.1ubuntu9.3) ...
+Setting up libapache-pom-java (18-1) ...
+Setting up libavahi-common-data:amd64 (0.7-4ubuntu7.1) ...
+Setting up libllvm12:amd64 (1:12.0.0-3ubuntu1~20.04.5) ...
+Setting up qpdf (9.1.1-1ubuntu0.1) ...
+Setting up ruby-net-telnet (0.1.1-2) ...
+Setting up fonts-cabin (1.5-3) ...
+Setting up xfonts-encodings (1:1.0.5-0ubuntu1) ...
+Setting up t1utils (1.41-3) ...
+Setting up libxinerama1:amd64 (2:1.1.4-2) ...
+Setting up libxv1:amd64 (2:1.0.11-1) ...
+Setting up libio-html-perl (1.001-1) ...
+Setting up libxrandr2:amd64 (2:1.5.2-0ubuntu1) ...
+Setting up fonts-texgyre (20180621-3) ...
+Setting up libsensors5:amd64 (1:3.6.0-2ubuntu1.1) ...
+Setting up fonts-linuxlibertine (5.3.0-4) ...
+Setting up libglapi-mesa:amd64 (21.2.6-0ubuntu0.1~20.04.2) ...
+Setting up libkpathsea6:amd64 (2019.20190605.51237-3build2) ...
+Setting up libvulkan1:amd64 (1.2.131.2-1) ...
+Setting up libtimedate-perl (2.3200-1) ...
+Setting up fonts-croscore (20200323-1build1~ubuntu20.04.1) ...
+Setting up libutempter0:amd64 (1.1.6-4) ...
+Setting up libxcb-dri2-0:amd64 (1.14-2) ...
+Setting up fonts-dejavu-extra (2.37-1) ...
+Setting up fonts-gfs-baskerville (1.1-5) ...
+Setting up libxshmfence1:amd64 (1.3-1) ...
+Setting up libxcb-randr0:amd64 (1.14-2) ...
+Setting up tcl (8.6.9+1) ...
+Setting up fonts-gfs-complutum (1.1-6) ...
+Setting up fonts-crosextra-caladea (20130214-2) ...
+Setting up fonts-lmodern (2.004.5-6) ...
+Setting up libopenjp2-7:amd64 (2.3.1-1ubuntu4.20.04.1) ...
+Setting up netbase (6.1) ...
+Setting up fonts-ebgaramond-extra (0.016-1ubuntu1) ...
+Setting up fonts-lobster (2.0-2) ...
+Setting up fonts-droid-fallback (1:6.0.1r16-1.1) ...
+Setting up libxkbfile1:amd64 (1:1.1.0-1) ...
+Setting up pandoc-data (2.5-3build2) ...
+Setting up libjs-jquery (3.3.1~dfsg-3) ...
+Setting up libtext-unidecode-perl (1.30-1) ...
+Setting up tk (8.6.9+1) ...
+Setting up libdrm-common (2.4.107-8ubuntu1~20.04.2) ...
+Setting up libxcomposite1:amd64 (1:0.4.5-1) ...
+Setting up fonts-adf-gillius (0.20190904-1.1) ...
+Setting up ruby-xmlrpc (0.3.0-2) ...
+Setting up fonts-noto-core (20200323-1build1~ubuntu20.04.1) ...
+Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-1) ...
+Setting up liburi-perl (1.76-2) ...
+Setting up xbitmaps (1.1.1-2) ...
+Setting up libsynctex2:amd64 (2019.20190605.51237-3build2) ...
+Setting up libwayland-client0:amd64 (1.18.0-1ubuntu0.1) ...
+Setting up libnet-ssleay-perl (1.88-2ubuntu1) ...
+Setting up libgs9-common (9.50~dfsg-5ubuntu4.6) ...
+Setting up teckit (2.5.8+ds2-5ubuntu2) ...
+Setting up libhttp-date-perl (6.05-1) ...
+Setting up pandoc-citeproc (0.15.0.1-1build4) ...
+Setting up libfile-listing-perl (6.04-1) ...
+Setting up libpdfbox-java (1:1.8.16-2) ...
+Setting up preview-latex-style (11.91-2ubuntu2) ...
+Setting up libcommons-parent-java (43-1) ...
+Setting up libavahi-common3:amd64 (0.7-4ubuntu7.1) ...
+Setting up libcommons-logging-java (1.2-2) ...
+Setting up libnet-http-perl (6.19-1) ...
+Setting up libnss3:amd64 (2:3.49.1-1ubuntu1.8) ...
+Setting up xfonts-utils (1:7.7+6) ...
+Setting up libxml-sax-perl (1.02+dfsg-1) ...
+update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
+update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
+
+Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
+Setting up fonts-lobstertwo (2.0-2) ...
+Setting up libfreetype-dev:amd64 (2.10.1-2ubuntu0.2) ...
+Setting up libpoppler118:amd64 (22.02.0-focal0) ...
+Setting up libptexenc1:amd64 (2019.20190605.51237-3build2) ...
+Setting up pandoc (2.5-3build2) ...
+Setting up texlive-fonts-extra-links (2019.202000218-1) ...
+Setting up libxml-libxml-perl (2.0134+dfsg-1build1) ...
+update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
+update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
+update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
+Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
+Setting up libwww-robotrules-perl (6.02-1) ...
+Setting up libdrm2:amd64 (2.4.107-8ubuntu1~20.04.2) ...
+Setting up texlive-binaries (2019.20190605.51237-3build2) ...
+update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
+update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/bibtex.1.gz because associated file /usr/share/man/man1/bibtex.original.1.gz (of link group bibtex) doesn't exist
+Setting up lmodern (2.004.5-6) ...
+Setting up libhtml-parser-perl (3.72-5) ...
+Setting up xterm (353-1ubuntu1.20.04.2) ...
+update-alternatives: using /usr/bin/xterm to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/x-terminal-emulator.1.gz because associated file /usr/share/man/man1/xterm.1.gz (of link group x-terminal-emulator) doesn't exist
+update-alternatives: using /usr/bin/lxterm to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode
+update-alternatives: warning: skip creation of /usr/share/man/man1/x-terminal-emulator.1.gz because associated file /usr/share/man/man1/lxterm.1.gz (of link group x-terminal-emulator) doesn't exist
+Setting up libpoppler-cpp0v5:amd64 (22.02.0-focal0) ...
+Setting up texlive-base (2019.20200218-1) ...
+tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
+tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
+tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
+tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
+tl-paper: setting paper size for dvipdfmx to letter: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
+tl-paper: setting paper size for dvips to letter: /var/lib/texmf/dvips/config/config-paper.ps
+tl-paper: setting paper size for pdftex to letter: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
+tl-paper: setting paper size for xdvi to letter: /var/lib/texmf/xdvi/XDvi-paper
+Setting up tex-gyre (20180621-3) ...
+Setting up libavahi-client3:amd64 (0.7-4ubuntu7.1) ...
+Setting up libio-socket-ssl-perl (2.067-1) ...
+Setting up libhttp-message-perl (6.22-1) ...
+Setting up libdrm-amdgpu1:amd64 (2.4.107-8ubuntu1~20.04.2) ...
+Setting up libhtml-form-perl (6.07-1) ...
+Setting up libpoppler-dev:amd64 (22.02.0-focal0) ...
+Setting up mesa-vulkan-drivers:amd64 (21.2.6-0ubuntu0.1~20.04.2) ...
+Setting up libhttp-negotiate-perl (6.01-1) ...
+Setting up libdrm-nouveau2:amd64 (2.4.107-8ubuntu1~20.04.2) ...
+Setting up libhttp-cookies-perl (6.08-1) ...
+Setting up texlive-luatex (2019.20200218-1) ...
+Setting up libdrm-radeon1:amd64 (2.4.107-8ubuntu1~20.04.2) ...
+Setting up libpoppler-cpp-dev:amd64 (22.02.0-focal0) ...
+Setting up libhtml-tree-perl (5.07-2) ...
+Setting up libdrm-intel1:amd64 (2.4.107-8ubuntu1~20.04.2) ...
+Setting up libgl1-mesa-dri:amd64 (21.2.6-0ubuntu0.1~20.04.2) ...
+Setting up texlive-plain-generic (2019.202000218-1) ...
+Setting up texlive-lang-greek (2019.20200218-1) ...
+Setting up libhtml-format-perl (2.12-1) ...
+Setting up libfreetype6-dev:amd64 (2.10.1-2ubuntu0.2) ...
+Setting up libnet-smtp-ssl-perl (1.04-1) ...
+Setting up texlive-latex-base (2019.20200218-1) ...
+Setting up libmailtools-perl (2.21-1) ...
+Setting up texlive-fonts-extra (2019.202000218-1) ...
+Setting up texlive-latex-recommended (2019.20200218-1) ...
+Setting up texinfo (6.7.0.dfsg.2-5) ...
+Running mktexlsr. This may take some time. ... done.
+Setting up texlive-pictures (2019.20200218-1) ...
+Setting up libcups2:amd64 (2.3.1-9ubuntu1.2) ...
+Setting up libhttp-daemon-perl (6.06-1ubuntu0.1) ...
+Setting up texlive-fonts-recommended (2019.20200218-1) ...
+Setting up tipa (2:1.3-20) ...
+Regenerating '/var/lib/texmf/fmtutil.cnf-DEBIAN'... done.
+Regenerating '/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST'... done.
+update-fmtutil has updated the following file(s):
+	/var/lib/texmf/fmtutil.cnf-DEBIAN
+	/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST
+If you want to activate the changes in the above file(s),
+you should run fmtutil-sys or fmtutil.
+Setting up libfontconfig1-dev:amd64 (2.13.1-2ubuntu3) ...
+Setting up libglx-mesa0:amd64 (21.2.6-0ubuntu0.1~20.04.2) ...
+Setting up libgs9:amd64 (9.50~dfsg-5ubuntu4.6) ...
+Setting up libglx0:amd64 (1.3.2-1~ubuntu0.20.04.2) ...
+Setting up texlive-science (2019.202000218-1) ...
+Setting up dvisvgm (2.8.1-1build1) ...
+Setting up texlive-latex-extra (2019.202000218-1) ...
+Setting up ghostscript (9.50~dfsg-5ubuntu4.6) ...
+Setting up libgl1:amd64 (1.3.2-1~ubuntu0.20.04.2) ...
+Setting up x11-utils (7.7+5) ...
+Setting up texlive-xetex (2019.20200218-1) ...
+Setting up ruby (1:2.7+1) ...
+Setting up rake (13.0.1-4) ...
+Setting up liblwp-protocol-https-perl (6.07-2ubuntu2) ...
+Setting up libwww-perl (6.43-1) ...
+Setting up libruby2.7:amd64 (2.7.0-5ubuntu1.7) ...
+Setting up libxml-parser-perl (2.46-1) ...
+Setting up ruby2.7 (2.7.0-5ubuntu1.7) ...
+Setting up libxml-sax-expat-perl (0.51-1) ...
+update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50...
+update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
+Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
+Processing triggers for fontconfig (2.13.1-2ubuntu3) ...
+Processing triggers for mime-support (3.64ubuntu1) ...
+Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
+Processing triggers for tex-common (6.13) ...
+Running updmap-sys. This may take some time... done.
+Running mktexlsr /var/lib/texmf ... done.
+Building format(s) --all.
+	This may take some time... done.
+
+
+
+
+================
+
+apt install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+build-essential is already the newest version (12.8ubuntu1.1).
+build-essential set to manually installed.
+The following additional packages will be installed:
+  libblkid-dev libblkid1 libcairo-gobject2 libcairo-script-interpreter2
+  libcurl3-gnutls libffi-dev libgcrypt20-dev libgit2-28 libglib2.0-dev
+  libglib2.0-dev-bin libgpg-error-dev libhttp-parser-dev libhttp-parser2.9
+  libice-dev liblzo2-2 libmbedcrypto3 libmbedtls-dev libmbedtls12
+  libmbedx509-0 libmount-dev libmount1 libpixman-1-dev libpthread-stubs0-dev
+  libselinux1-dev libsepol1 libsepol1-dev libsm-dev libssh2-1 libssh2-1-dev
+  libssl1.1 libx11-dev libxau-dev libxcb-render0-dev libxcb-shm0-dev
+  libxcb1-dev libxdmcp-dev libxext-dev libxml2 libxrender-dev
+  python3-distutils python3-lib2to3 x11proto-core-dev x11proto-dev
+  x11proto-xext-dev xorg-sgml-doctools xtrans-dev
+Suggested packages:
+  libcairo2-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev
+  libldap2-dev librtmp-dev libgcrypt20-doc libgirepository1.0-dev
+  libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils
+  libice-doc libmbedtls-doc libsm-doc libssl-doc libx11-doc libxcb-doc
+  libxext-doc libxt-doc
+The following NEW packages will be installed:
+  libblkid-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2-dev
+  libcurl3-gnutls libcurl4-gnutls-dev libffi-dev libgcrypt20-dev libgit2-28
+  libgit2-dev libglib2.0-dev libglib2.0-dev-bin libgpg-error-dev
+  libhttp-parser-dev libhttp-parser2.9 libice-dev liblzo2-2 libmbedcrypto3
+  libmbedtls-dev libmbedtls12 libmbedx509-0 libmount-dev libpixman-1-dev
+  libpthread-stubs0-dev libselinux1-dev libsepol1-dev libsm-dev libssh2-1
+  libssh2-1-dev libssl-dev libx11-dev libxau-dev libxcb-render0-dev
+  libxcb-shm0-dev libxcb1-dev libxdmcp-dev libxext-dev libxml2-dev
+  libxrender-dev libxt-dev python3-distutils python3-lib2to3 x11proto-core-dev
+  x11proto-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev
+The following packages will be upgraded:
+  libblkid1 libmount1 libsepol1 libssl1.1 libxml2
+5 upgraded, 47 newly installed, 0 to remove and 110 not upgraded.
+Need to get 13.9 MB of archives.
+After this operation, 55.1 MB of additional disk space will be used.
+Get:1 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libblkid1 amd64 2.34-0.1ubuntu9.3 [136 kB]
+Get:2 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libmount1 amd64 2.34-0.1ubuntu9.3 [149 kB]
+Get:3 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsepol1 amd64 3.0-1ubuntu0.1 [252 kB]
+Get:4 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu2.16 [1,321 kB]
+Get:5 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libxml2 amd64 2.9.10+dfsg-5ubuntu0.20.04.4 [640 kB]
+Get:6 http://archive.ubuntu.com/ubuntu focal/main amd64 libcairo-gobject2 amd64 1.16.0-4ubuntu1 [17.2 kB]
+Get:7 http://archive.ubuntu.com/ubuntu focal/main amd64 liblzo2-2 amd64 2.10-2 [50.8 kB]
+Get:8 http://archive.ubuntu.com/ubuntu focal/main amd64 libcairo-script-interpreter2 amd64 1.16.0-4ubuntu1 [54.2 kB]
+Get:9 http://archive.ubuntu.com/ubuntu focal/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB]
+Get:10 http://archive.ubuntu.com/ubuntu focal/main amd64 x11proto-dev all 2019.2-1ubuntu1 [594 kB]
+Get:11 http://archive.ubuntu.com/ubuntu focal/main amd64 x11proto-core-dev all 2019.2-1ubuntu1 [2,620 B]
+Get:12 http://archive.ubuntu.com/ubuntu focal/main amd64 libxau-dev amd64 1:1.0.9-0ubuntu1 [9,552 B]
+Get:13 http://archive.ubuntu.com/ubuntu focal/main amd64 libxdmcp-dev amd64 1:1.1.3-0ubuntu1 [25.3 kB]
+Get:14 http://archive.ubuntu.com/ubuntu focal/main amd64 xtrans-dev all 1.4.0-1 [68.9 kB]
+Get:15 http://archive.ubuntu.com/ubuntu focal/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5,384 B]
+Get:16 http://archive.ubuntu.com/ubuntu focal/main amd64 libxcb1-dev amd64 1.14-2 [80.5 kB]
+Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libx11-dev amd64 2:1.6.9-2ubuntu1.2 [647 kB]
+Get:18 http://archive.ubuntu.com/ubuntu focal/main amd64 libxrender-dev amd64 1:0.9.10-1 [24.9 kB]
+Get:19 http://archive.ubuntu.com/ubuntu focal/main amd64 x11proto-xext-dev all 2019.2-1ubuntu1 [2,616 B]
+Get:20 http://archive.ubuntu.com/ubuntu focal/main amd64 libxext-dev amd64 2:1.3.4-0ubuntu1 [82.2 kB]
+Get:21 http://archive.ubuntu.com/ubuntu focal/main amd64 libice-dev amd64 2:1.0.10-0ubuntu1 [47.8 kB]
+Get:22 http://archive.ubuntu.com/ubuntu focal/main amd64 libsm-dev amd64 2:1.2.3-1 [17.0 kB]
+Get:23 http://archive.ubuntu.com/ubuntu focal/main amd64 libpixman-1-dev amd64 0.38.4-0ubuntu1 [243 kB]
+Get:24 http://archive.ubuntu.com/ubuntu focal/main amd64 libxcb-render0-dev amd64 1.14-2 [18.4 kB]
+Get:25 http://archive.ubuntu.com/ubuntu focal/main amd64 libxcb-shm0-dev amd64 1.14-2 [6,716 B]
+Get:26 http://archive.ubuntu.com/ubuntu focal/main amd64 libffi-dev amd64 3.3-4 [57.0 kB]
+Get:27 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-lib2to3 all 3.8.10-0ubuntu1~20.04 [76.3 kB]
+Get:28 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-distutils all 3.8.10-0ubuntu1~20.04 [141 kB]
+Get:29 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libglib2.0-dev-bin amd64 2.64.6-1~ubuntu20.04.4 [109 kB]
+Get:30 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libblkid-dev amd64 2.34-0.1ubuntu9.3 [167 kB]
+Get:31 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libmount-dev amd64 2.34-0.1ubuntu9.3 [176 kB]
+Get:32 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsepol1-dev amd64 3.0-1ubuntu0.1 [325 kB]
+Get:33 http://archive.ubuntu.com/ubuntu focal/main amd64 libselinux1-dev amd64 3.0-1build2 [151 kB]
+Get:34 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libglib2.0-dev amd64 2.64.6-1~ubuntu20.04.4 [1,506 kB]
+Get:35 http://archive.ubuntu.com/ubuntu focal/main amd64 libcairo2-dev amd64 1.16.0-4ubuntu1 [627 kB]
+Get:36 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcurl3-gnutls amd64 7.68.0-1ubuntu2.13 [233 kB]
+Get:37 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcurl4-gnutls-dev amd64 7.68.0-1ubuntu2.13 [320 kB]
+Get:38 http://archive.ubuntu.com/ubuntu focal/main amd64 libgpg-error-dev amd64 1.37-1 [109 kB]
+Get:39 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgcrypt20-dev amd64 1.8.5-5ubuntu1.1 [471 kB]
+Get:40 http://archive.ubuntu.com/ubuntu focal/universe amd64 libhttp-parser2.9 amd64 2.9.2-2 [21.8 kB]
+Get:41 http://archive.ubuntu.com/ubuntu focal/universe amd64 libmbedcrypto3 amd64 2.16.4-1ubuntu2 [150 kB]
+Get:42 http://archive.ubuntu.com/ubuntu focal/universe amd64 libmbedx509-0 amd64 2.16.4-1ubuntu2 [42.3 kB]
+Get:43 http://archive.ubuntu.com/ubuntu focal/universe amd64 libmbedtls12 amd64 2.16.4-1ubuntu2 [71.8 kB]
+Get:44 http://archive.ubuntu.com/ubuntu focal/universe amd64 libssh2-1 amd64 1.8.0-2.1build1 [75.4 kB]
+Get:45 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgit2-28 amd64 0.28.4+dfsg.1-2 [403 kB]
+Get:46 http://archive.ubuntu.com/ubuntu focal/universe amd64 libmbedtls-dev amd64 2.16.4-1ubuntu2 [444 kB]
+Get:47 http://archive.ubuntu.com/ubuntu focal/universe amd64 libssh2-1-dev amd64 1.8.0-2.1build1 [244 kB]
+Get:48 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl-dev amd64 1.1.1f-1ubuntu2.16 [1,584 kB]
+Get:49 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libxml2-dev amd64 2.9.10+dfsg-5ubuntu0.20.04.4 [736 kB]
+Get:50 http://archive.ubuntu.com/ubuntu focal/main amd64 libxt-dev amd64 1:1.1.5-1 [395 kB]
+Get:51 http://archive.ubuntu.com/ubuntu focal/universe amd64 libhttp-parser-dev amd64 2.9.2-2 [20.2 kB]
+Get:52 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgit2-dev amd64 0.28.4+dfsg.1-2 [691 kB]
+Fetched 13.9 MB in 20s (699 kB/s)
+(Reading database ... 
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(Reading database ... 147709 files and directories currently installed.)
+Preparing to unpack .../libblkid1_2.34-0.1ubuntu9.3_amd64.deb ...
+Unpacking libblkid1:amd64 (2.34-0.1ubuntu9.3) over (2.34-0.1ubuntu9.1) ...
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(Reading database ... 147709 files and directories currently installed.)
+Preparing to unpack .../libmount1_2.34-0.1ubuntu9.3_amd64.deb ...
+Unpacking libmount1:amd64 (2.34-0.1ubuntu9.3) over (2.34-0.1ubuntu9.1) ...
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+(Reading database ... 
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(Reading database ... 147709 files and directories currently installed.)
+Preparing to unpack .../libsepol1_3.0-1ubuntu0.1_amd64.deb ...
+Unpacking libsepol1:amd64 (3.0-1ubuntu0.1) over (3.0-1) ...
+Setting up libsepol1:amd64 (3.0-1ubuntu0.1) ...
+(Reading database ... 
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(Reading database ... 147709 files and directories currently installed.)
+Preparing to unpack .../00-libssl1.1_1.1.1f-1ubuntu2.16_amd64.deb ...
+Unpacking libssl1.1:amd64 (1.1.1f-1ubuntu2.16) over (1.1.1f-1ubuntu2.10) ...
+Preparing to unpack .../01-libxml2_2.9.10+dfsg-5ubuntu0.20.04.4_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.10+dfsg-5ubuntu0.20.04.4) over (2.9.10+dfsg-5ubuntu0.20.04.1) ...
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+Preparing to unpack .../03-liblzo2-2_2.10-2_amd64.deb ...
+Unpacking liblzo2-2:amd64 (2.10-2) ...
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+Preparing to unpack .../04-libcairo-script-interpreter2_1.16.0-4ubuntu1_amd64.deb ...
+Unpacking libcairo-script-interpreter2:amd64 (1.16.0-4ubuntu1) ...
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+Preparing to unpack .../05-xorg-sgml-doctools_1%3a1.11-1_all.deb ...
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+Unpacking x11proto-core-dev (2019.2-1ubuntu1) ...
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+Preparing to unpack .../08-libxau-dev_1%3a1.0.9-0ubuntu1_amd64.deb ...
+Unpacking libxau-dev:amd64 (1:1.0.9-0ubuntu1) ...
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+Preparing to unpack .../09-libxdmcp-dev_1%3a1.1.3-0ubuntu1_amd64.deb ...
+Unpacking libxdmcp-dev:amd64 (1:1.1.3-0ubuntu1) ...
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+Unpacking libxcb1-dev:amd64 (1.14-2) ...
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+Preparing to unpack .../15-x11proto-xext-dev_2019.2-1ubuntu1_all.deb ...
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+Preparing to unpack .../16-libxext-dev_2%3a1.3.4-0ubuntu1_amd64.deb ...
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+Selecting previously unselected package libice-dev:amd64.
+Preparing to unpack .../17-libice-dev_2%3a1.0.10-0ubuntu1_amd64.deb ...
+Unpacking libice-dev:amd64 (2:1.0.10-0ubuntu1) ...
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+Preparing to unpack .../18-libsm-dev_2%3a1.2.3-1_amd64.deb ...
+Unpacking libsm-dev:amd64 (2:1.2.3-1) ...
+Selecting previously unselected package libpixman-1-dev:amd64.
+Preparing to unpack .../19-libpixman-1-dev_0.38.4-0ubuntu1_amd64.deb ...
+Unpacking libpixman-1-dev:amd64 (0.38.4-0ubuntu1) ...
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+Preparing to unpack .../20-libxcb-render0-dev_1.14-2_amd64.deb ...
+Unpacking libxcb-render0-dev:amd64 (1.14-2) ...
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+Unpacking libxcb-shm0-dev:amd64 (1.14-2) ...
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+Unpacking libffi-dev:amd64 (3.3-4) ...
+Selecting previously unselected package python3-lib2to3.
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+Setting up libpixman-1-dev:amd64 (0.38.4-0ubuntu1) ...
+Setting up libssl1.1:amd64 (1.1.1f-1ubuntu2.16) ...
+Setting up libsepol1-dev:amd64 (3.0-1ubuntu0.1) ...
+Setting up liblzo2-2:amd64 (2.10-2) ...
+Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu2.13) ...
+Setting up libcurl4-gnutls-dev:amd64 (7.68.0-1ubuntu2.13) ...
+Setting up libffi-dev:amd64 (3.3-4) ...
+Setting up libpthread-stubs0-dev:amd64 (0.4-1) ...
+Setting up xtrans-dev (1.4.0-1) ...
+Setting up libgpg-error-dev (1.37-1) ...
+Setting up libssl-dev:amd64 (1.1.1f-1ubuntu2.16) ...
+Setting up libmbedcrypto3:amd64 (2.16.4-1ubuntu2) ...
+Setting up libssh2-1:amd64 (1.8.0-2.1build1) ...
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+================
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+R PACKAGE INSTALLATION 1 / 24: BiocManager
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+================
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+================
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+downloaded 365 KB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpHBh0rr/downloaded_packages’
+BiocManager INSTALLATION ATTEMPT FOR devtools
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'BiocVersion', 'devtools'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+also installing the dependencies ‘textshaping’, ‘ragg’, ‘pkgdown’
+
+trying URL 'https://cloud.r-project.org/src/contrib/textshaping_0.3.6.tar.gz'
+Content type 'application/x-gzip' length 35722 bytes (34 KB)
+==================================================
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+
+trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.3.tar.gz'
+Content type 'application/x-gzip' length 427529 bytes (417 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/pkgdown_2.0.6.tar.gz'
+Content type 'application/x-gzip' length 871371 bytes (850 KB)
+==================================================
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+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/BiocVersion_3.14.0.tar.gz'
+Content type 'application/octet-stream' length 969 bytes
+==================================================
+downloaded 969 bytes
+
+trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.4.5.tar.gz'
+Content type 'application/x-gzip' length 374718 bytes (365 KB)
+==================================================
+downloaded 365 KB
+
+foundpkgs: textshaping, ragg, pkgdown, BiocVersion, devtools, /tmp/RtmpHBh0rr/downloaded_packages/textshaping_0.3.6.tar.gz, /tmp/RtmpHBh0rr/downloaded_packages/ragg_1.2.3.tar.gz, /tmp/RtmpHBh0rr/downloaded_packages/pkgdown_2.0.6.tar.gz, /tmp/RtmpHBh0rr/downloaded_packages/BiocVersion_3.14.0.tar.gz, /tmp/RtmpHBh0rr/downloaded_packages/devtools_2.4.5.tar.gz
+files: /tmp/RtmpHBh0rr/downloaded_packages/textshaping_0.3.6.tar.gz, 
+	/tmp/RtmpHBh0rr/downloaded_packages/ragg_1.2.3.tar.gz, 
+	/tmp/RtmpHBh0rr/downloaded_packages/pkgdown_2.0.6.tar.gz, 
+	/tmp/RtmpHBh0rr/downloaded_packages/BiocVersion_3.14.0.tar.gz, 
+	/tmp/RtmpHBh0rr/downloaded_packages/devtools_2.4.5.tar.gz
+Warning in install.packages(...) :
+  installation of package ‘textshaping’ had non-zero exit status
+2): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpHBh0rr/downloaded_packages/BiocVersion_3.14.0.tar.gz''
+Warning in install.packages(...) :
+  installation of package ‘ragg’ had non-zero exit status
+Warning in install.packages(...) :
+  installation of package ‘pkgdown’ had non-zero exit status
+Warning in install.packages(...) :
+  installation of package ‘devtools’ had non-zero exit status
+
+The downloaded source packages are in
+	‘/tmp/RtmpHBh0rr/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 3 / 24: Cairo
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/Cairo_1.6-0.tar.gz'
+Content type 'application/x-gzip' length 98278 bytes (95 KB)
+==================================================
+downloaded 95 KB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmp2mIJBI/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR Cairo
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/Cairo_1.6-0.tar.gz'
+Content type 'application/x-gzip' length 98278 bytes (95 KB)
+==================================================
+downloaded 95 KB
+
+foundpkgs: Cairo, /tmp/Rtmp2mIJBI/downloaded_packages/Cairo_1.6-0.tar.gz
+files: /tmp/Rtmp2mIJBI/downloaded_packages/Cairo_1.6-0.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp2mIJBI/downloaded_packages/Cairo_1.6-0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmp2mIJBI/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 4 / 24: dplyr
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/generics_0.1.3.tar.gz'
+Content type 'application/x-gzip' length 172201 bytes (168 KB)
+==================================================
+downloaded 168 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/tidyselect_1.2.0.tar.gz'
+Content type 'application/x-gzip' length 101498 bytes (99 KB)
+==================================================
+downloaded 99 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/dplyr_1.0.10.tar.gz'
+Content type 'application/x-gzip' length 884984 bytes (864 KB)
+==================================================
+downloaded 864 KB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmpio0vQC/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR dplyr
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/dplyr_1.0.10.tar.gz'
+Content type 'application/x-gzip' length 884984 bytes (864 KB)
+==================================================
+downloaded 864 KB
+
+foundpkgs: dplyr, /tmp/Rtmpio0vQC/downloaded_packages/dplyr_1.0.10.tar.gz
+files: /tmp/Rtmpio0vQC/downloaded_packages/dplyr_1.0.10.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpio0vQC/downloaded_packages/dplyr_1.0.10.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmpio0vQC/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 5 / 24: data.table
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/data.table_1.14.2.tar.gz'
+Content type 'application/x-gzip' length 5301817 bytes (5.1 MB)
+==================================================
+downloaded 5.1 MB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmpn1S9A8/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR data.table
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/data.table_1.14.2.tar.gz'
+Content type 'application/x-gzip' length 5301817 bytes (5.1 MB)
+==================================================
+downloaded 5.1 MB
+
+foundpkgs: data.table, /tmp/Rtmpn1S9A8/downloaded_packages/data.table_1.14.2.tar.gz
+files: /tmp/Rtmpn1S9A8/downloaded_packages/data.table_1.14.2.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpn1S9A8/downloaded_packages/data.table_1.14.2.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmpn1S9A8/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 6 / 24: gridExtra
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/gtable_0.3.1.tar.gz'
+Content type 'application/x-gzip' length 92733 bytes (90 KB)
+==================================================
+downloaded 90 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/gridExtra_2.3.tar.gz'
+Content type 'application/x-gzip' length 1062844 bytes (1.0 MB)
+==================================================
+downloaded 1.0 MB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpoMYigu/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR gridExtra
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/gridExtra_2.3.tar.gz'
+Content type 'application/x-gzip' length 1062844 bytes (1.0 MB)
+==================================================
+downloaded 1.0 MB
+
+foundpkgs: gridExtra, /tmp/RtmpoMYigu/downloaded_packages/gridExtra_2.3.tar.gz
+files: /tmp/RtmpoMYigu/downloaded_packages/gridExtra_2.3.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpoMYigu/downloaded_packages/gridExtra_2.3.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpoMYigu/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 7 / 24: mgcv
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/mgcv_1.8-40.tar.gz'
+Content type 'application/x-gzip' length 1175920 bytes (1.1 MB)
+==================================================
+downloaded 1.1 MB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmpf3hx1G/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR mgcv
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/mgcv_1.8-40.tar.gz'
+Content type 'application/x-gzip' length 1175920 bytes (1.1 MB)
+==================================================
+downloaded 1.1 MB
+
+foundpkgs: mgcv, /tmp/Rtmpf3hx1G/downloaded_packages/mgcv_1.8-40.tar.gz
+files: /tmp/Rtmpf3hx1G/downloaded_packages/mgcv_1.8-40.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpf3hx1G/downloaded_packages/mgcv_1.8-40.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmpf3hx1G/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 8 / 24: InteractionSet
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR InteractionSet
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'InteractionSet'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+also installing the dependencies ‘zlibbioc’, ‘matrixStats’, ‘bitops’, ‘XVector’, ‘MatrixGenerics’, ‘Biobase’, ‘DelayedArray’, ‘RCurl’, ‘GenomeInfoDbData’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/zlibbioc_1.40.0.tar.gz'
+Content type 'application/octet-stream' length 257409 bytes (251 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/matrixStats_0.62.0.tar.gz'
+Content type 'application/x-gzip' length 201651 bytes (196 KB)
+==================================================
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+
+trying URL 'https://cloud.r-project.org/src/contrib/bitops_1.0-7.tar.gz'
+Content type 'application/x-gzip' length 10809 bytes (10 KB)
+==================================================
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+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/XVector_0.34.0.tar.gz'
+Content type 'application/octet-stream' length 67783 bytes (66 KB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/MatrixGenerics_1.6.0.tar.gz'
+Content type 'application/octet-stream' length 28270 bytes (27 KB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biobase_2.54.0.tar.gz'
+Content type 'application/octet-stream' length 1641111 bytes (1.6 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DelayedArray_0.20.0.tar.gz'
+Content type 'application/octet-stream' length 676428 bytes (660 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
+Content type 'application/x-gzip' length 731611 bytes (714 KB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz'
+Content type 'application/octet-stream' length 11193674 bytes (10.7 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicRanges_1.46.1.tar.gz'
+Content type 'application/octet-stream' length 1171939 bytes (1.1 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SummarizedExperiment_1.24.0.tar.gz'
+Content type 'application/octet-stream' length 1524667 bytes (1.5 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/BiocGenerics_0.40.0.tar.gz'
+Content type 'application/octet-stream' length 45969 bytes (44 KB)
+==================================================
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+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/S4Vectors_0.32.4.tar.gz'
+Content type 'application/octet-stream' length 668558 bytes (652 KB)
+==================================================
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+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/IRanges_2.28.0.tar.gz'
+Content type 'application/octet-stream' length 455647 bytes (444 KB)
+==================================================
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+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz'
+Content type 'application/octet-stream' length 3457147 bytes (3.3 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/InteractionSet_1.22.0.tar.gz'
+Content type 'application/octet-stream' length 385508 bytes (376 KB)
+==================================================
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+
+foundpkgs: zlibbioc, matrixStats, bitops, XVector, MatrixGenerics, Biobase, DelayedArray, RCurl, GenomeInfoDbData, GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, InteractionSet, /tmp/Rtmpr6c8wR/downloaded_packages/zlibbioc_1.40.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/matrixStats_0.62.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/bitops_1.0-7.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/XVector_0.34.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/MatrixGenerics_1.6.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/Biobase_2.54.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/DelayedArray_0.20.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/RCurl_1.98-1.9.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/GenomeInfoDbData_1.2.7.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/GenomicRanges_1.46.1.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/SummarizedExperiment_1.24.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/BiocGenerics_0.40.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/S4Vectors_0.32.4.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/IRanges_2.28.0.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/GenomeInfoDb_1.30.1.tar.gz, /tmp/Rtmpr6c8wR/downloaded_packages/InteractionSet_1.22.0.tar.gz
+files: /tmp/Rtmpr6c8wR/downloaded_packages/zlibbioc_1.40.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/matrixStats_0.62.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/bitops_1.0-7.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/XVector_0.34.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/MatrixGenerics_1.6.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/Biobase_2.54.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/DelayedArray_0.20.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/RCurl_1.98-1.9.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/GenomeInfoDbData_1.2.7.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/GenomicRanges_1.46.1.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/SummarizedExperiment_1.24.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/BiocGenerics_0.40.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/S4Vectors_0.32.4.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/IRanges_2.28.0.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/GenomeInfoDb_1.30.1.tar.gz, 
+	/tmp/Rtmpr6c8wR/downloaded_packages/InteractionSet_1.22.0.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/zlibbioc_1.40.0.tar.gz''
+2): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/matrixStats_0.62.0.tar.gz''
+3): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/bitops_1.0-7.tar.gz''
+4): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/GenomeInfoDbData_1.2.7.tar.gz''
+5): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/BiocGenerics_0.40.0.tar.gz''
+6): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/MatrixGenerics_1.6.0.tar.gz''
+7): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/Biobase_2.54.0.tar.gz''
+8): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/RCurl_1.98-1.9.tar.gz''
+9): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/S4Vectors_0.32.4.tar.gz''
+10): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/IRanges_2.28.0.tar.gz''
+11): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/XVector_0.34.0.tar.gz''
+12): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/DelayedArray_0.20.0.tar.gz''
+13): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/GenomeInfoDb_1.30.1.tar.gz''
+14): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/GenomicRanges_1.46.1.tar.gz''
+15): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/SummarizedExperiment_1.24.0.tar.gz''
+16): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmpr6c8wR/downloaded_packages/InteractionSet_1.22.0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmpr6c8wR/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 9 / 24: GenomicRanges
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR GenomicRanges
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
+  re-install: 'GenomicRanges'
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 10 / 24: IRanges
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR IRanges
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
+  re-install: 'IRanges'
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 11 / 24: BiocParallel
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR BiocParallel
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'BiocParallel'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+also installing the dependencies ‘formatR’, ‘lambda.r’, ‘futile.options’, ‘futile.logger’, ‘snow’, ‘BH’
+
+trying URL 'https://cloud.r-project.org/src/contrib/formatR_1.12.tar.gz'
+Content type 'application/x-gzip' length 95944 bytes (93 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/lambda.r_1.2.4.tar.gz'
+Content type 'application/x-gzip' length 25666 bytes (25 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/futile.options_1.0.1.tar.gz'
+Content type 'application/x-gzip' length 3919 bytes
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz'
+Content type 'application/x-gzip' length 17456 bytes (17 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/snow_0.4-4.tar.gz'
+Content type 'application/x-gzip' length 20464 bytes (19 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/BH_1.78.0-0.tar.gz'
+Content type 'application/x-gzip' length 13269768 bytes (12.7 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/BiocParallel_1.28.3.tar.gz'
+Content type 'application/octet-stream' length 883999 bytes (863 KB)
+==================================================
+downloaded 863 KB
+
+foundpkgs: formatR, lambda.r, futile.options, futile.logger, snow, BH, BiocParallel, /tmp/Rtmp9Y6cyE/downloaded_packages/formatR_1.12.tar.gz, /tmp/Rtmp9Y6cyE/downloaded_packages/lambda.r_1.2.4.tar.gz, /tmp/Rtmp9Y6cyE/downloaded_packages/futile.options_1.0.1.tar.gz, /tmp/Rtmp9Y6cyE/downloaded_packages/futile.logger_1.4.3.tar.gz, /tmp/Rtmp9Y6cyE/downloaded_packages/snow_0.4-4.tar.gz, /tmp/Rtmp9Y6cyE/downloaded_packages/BH_1.78.0-0.tar.gz, /tmp/Rtmp9Y6cyE/downloaded_packages/BiocParallel_1.28.3.tar.gz
+files: /tmp/Rtmp9Y6cyE/downloaded_packages/formatR_1.12.tar.gz, 
+	/tmp/Rtmp9Y6cyE/downloaded_packages/lambda.r_1.2.4.tar.gz, 
+	/tmp/Rtmp9Y6cyE/downloaded_packages/futile.options_1.0.1.tar.gz, 
+	/tmp/Rtmp9Y6cyE/downloaded_packages/futile.logger_1.4.3.tar.gz, 
+	/tmp/Rtmp9Y6cyE/downloaded_packages/snow_0.4-4.tar.gz, 
+	/tmp/Rtmp9Y6cyE/downloaded_packages/BH_1.78.0-0.tar.gz, 
+	/tmp/Rtmp9Y6cyE/downloaded_packages/BiocParallel_1.28.3.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/formatR_1.12.tar.gz''
+2): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/futile.options_1.0.1.tar.gz''
+3): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/snow_0.4-4.tar.gz''
+4): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/BH_1.78.0-0.tar.gz''
+5): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/lambda.r_1.2.4.tar.gz''
+6): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/futile.logger_1.4.3.tar.gz''
+7): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp9Y6cyE/downloaded_packages/BiocParallel_1.28.3.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmp9Y6cyE/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 12 / 24: QDNAseq
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR QDNAseq
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'QDNAseq'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+also installing the dependencies ‘limma’, ‘listenv’, ‘parallelly’, ‘marray’, ‘impute’, ‘snowfall’, ‘R.oo’, ‘R.methodsS3’, ‘Biostrings’, ‘Rhtslib’, ‘future’, ‘globals’, ‘CGHbase’, ‘CGHcall’, ‘DNAcopy’, ‘R.utils’, ‘Rsamtools’, ‘future.apply’
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/limma_3.50.3.tar.gz'
+Content type 'application/octet-stream' length 1559281 bytes (1.5 MB)
+==================================================
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+
+trying URL 'https://cloud.r-project.org/src/contrib/listenv_0.8.0.tar.gz'
+Content type 'application/x-gzip' length 36762 bytes (35 KB)
+==================================================
+downloaded 35 KB
+
+trying URL 'https://cloud.r-project.org/src/contrib/parallelly_1.32.1.tar.gz'
+Content type 'application/x-gzip' length 124853 bytes (121 KB)
+==================================================
+downloaded 121 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/marray_1.72.0.tar.gz'
+Content type 'application/octet-stream' length 5160434 bytes (4.9 MB)
+==================================================
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+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/impute_1.68.0.tar.gz'
+Content type 'application/octet-stream' length 641569 bytes (626 KB)
+==================================================
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+
+trying URL 'https://cloud.r-project.org/src/contrib/snowfall_1.84-6.2.tar.gz'
+Content type 'application/x-gzip' length 176212 bytes (172 KB)
+==================================================
+downloaded 172 KB
+
+trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.25.0.tar.gz'
+Content type 'application/x-gzip' length 384384 bytes (375 KB)
+==================================================
+downloaded 375 KB
+
+trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz'
+Content type 'application/x-gzip' length 24131 bytes (23 KB)
+==================================================
+downloaded 23 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz'
+Content type 'application/octet-stream' length 12645827 bytes (12.1 MB)
+==================================================
+downloaded 12.1 MB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rhtslib_1.26.0.tar.gz'
+Content type 'application/octet-stream' length 1470165 bytes (1.4 MB)
+==================================================
+downloaded 1.4 MB
+
+trying URL 'https://cloud.r-project.org/src/contrib/future_1.28.0.tar.gz'
+Content type 'application/x-gzip' length 366473 bytes (357 KB)
+==================================================
+downloaded 357 KB
+
+trying URL 'https://cloud.r-project.org/src/contrib/globals_0.16.1.tar.gz'
+Content type 'application/x-gzip' length 35152 bytes (34 KB)
+==================================================
+downloaded 34 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/CGHbase_1.54.0.tar.gz'
+Content type 'application/octet-stream' length 868353 bytes (848 KB)
+==================================================
+downloaded 848 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/CGHcall_2.56.0.tar.gz'
+Content type 'application/octet-stream' length 379558 bytes (370 KB)
+==================================================
+downloaded 370 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DNAcopy_1.68.0.tar.gz'
+Content type 'application/octet-stream' length 319512 bytes (312 KB)
+==================================================
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+
+trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.0.tar.gz'
+Content type 'application/x-gzip' length 363986 bytes (355 KB)
+==================================================
+downloaded 355 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rsamtools_2.10.0.tar.gz'
+Content type 'application/octet-stream' length 2870706 bytes (2.7 MB)
+==================================================
+downloaded 2.7 MB
+
+trying URL 'https://cloud.r-project.org/src/contrib/future.apply_1.9.1.tar.gz'
+Content type 'application/x-gzip' length 65416 bytes (63 KB)
+==================================================
+downloaded 63 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/QDNAseq_1.30.0.tar.gz'
+Content type 'application/octet-stream' length 1057078 bytes (1.0 MB)
+==================================================
+downloaded 1.0 MB
+
+foundpkgs: limma, listenv, parallelly, marray, impute, snowfall, R.oo, R.methodsS3, Biostrings, Rhtslib, future, globals, CGHbase, CGHcall, DNAcopy, R.utils, Rsamtools, future.apply, QDNAseq, /tmp/RtmpKFc7yt/downloaded_packages/limma_3.50.3.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/listenv_0.8.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/parallelly_1.32.1.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/marray_1.72.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/impute_1.68.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/snowfall_1.84-6.2.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/R.oo_1.25.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/R.methodsS3_1.8.2.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/Biostrings_2.62.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/Rhtslib_1.26.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/future_1.28.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/globals_0.16.1.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/CGHbase_1.54.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/CGHcall_2.56.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/DNAcopy_1.68.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/R.utils_2.12.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/Rsamtools_2.10.0.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/future.apply_1.9.1.tar.gz, /tmp/RtmpKFc7yt/downloaded_packages/QDNAseq_1.30.0.tar.gz
+files: /tmp/RtmpKFc7yt/downloaded_packages/limma_3.50.3.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/listenv_0.8.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/parallelly_1.32.1.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/marray_1.72.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/impute_1.68.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/snowfall_1.84-6.2.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/R.oo_1.25.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/R.methodsS3_1.8.2.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/Biostrings_2.62.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/Rhtslib_1.26.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/future_1.28.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/globals_0.16.1.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/CGHbase_1.54.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/CGHcall_2.56.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/DNAcopy_1.68.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/R.utils_2.12.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/Rsamtools_2.10.0.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/future.apply_1.9.1.tar.gz, 
+	/tmp/RtmpKFc7yt/downloaded_packages/QDNAseq_1.30.0.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/limma_3.50.3.tar.gz''
+2): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/listenv_0.8.0.tar.gz''
+3): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/parallelly_1.32.1.tar.gz''
+4): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/impute_1.68.0.tar.gz''
+5): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/snowfall_1.84-6.2.tar.gz''
+6): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/R.methodsS3_1.8.2.tar.gz''
+7): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/Biostrings_2.62.0.tar.gz''
+8): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/Rhtslib_1.26.0.tar.gz''
+9): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/globals_0.16.1.tar.gz''
+10): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/DNAcopy_1.68.0.tar.gz''
+11): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/marray_1.72.0.tar.gz''
+12): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/R.oo_1.25.0.tar.gz''
+13): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/future_1.28.0.tar.gz''
+14): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/Rsamtools_2.10.0.tar.gz''
+15): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/CGHbase_1.54.0.tar.gz''
+16): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/R.utils_2.12.0.tar.gz''
+17): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/future.apply_1.9.1.tar.gz''
+18): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/CGHcall_2.56.0.tar.gz''
+19): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpKFc7yt/downloaded_packages/QDNAseq_1.30.0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpKFc7yt/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 13 / 24: GenomeInfoDbData
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR GenomeInfoDbData
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
+  re-install: 'GenomeInfoDbData'
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 14 / 24: ggplot2
+
+================
+
+
+
+
+Error in loadNamespace(x) : there is no package called ‘devtools’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 15 / 24: HiCcompare
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR HiCcompare
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'HiCcompare'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+also installing the dependencies ‘colorspace’, ‘farver’, ‘labeling’, ‘munsell’, ‘viridisLite’, ‘isoband’, ‘scales’, ‘RColorBrewer’, ‘Rhdf5lib’, ‘rhdf5filters’, ‘ggplot2’, ‘pheatmap’, ‘gtools’, ‘rhdf5’
+
+trying URL 'https://cloud.r-project.org/src/contrib/colorspace_2.0-3.tar.gz'
+Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/farver_2.1.1.tar.gz'
+Content type 'application/x-gzip' length 1274363 bytes (1.2 MB)
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+trying URL 'https://cloud.r-project.org/src/contrib/labeling_0.4.2.tar.gz'
+Content type 'application/x-gzip' length 10156 bytes
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/munsell_0.5.0.tar.gz'
+Content type 'application/x-gzip' length 182653 bytes (178 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/viridisLite_0.4.1.tar.gz'
+Content type 'application/x-gzip' length 1267090 bytes (1.2 MB)
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+trying URL 'https://cloud.r-project.org/src/contrib/isoband_0.2.6.tar.gz'
+Content type 'application/x-gzip' length 1672253 bytes (1.6 MB)
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+trying URL 'https://cloud.r-project.org/src/contrib/scales_1.2.1.tar.gz'
+Content type 'application/x-gzip' length 270609 bytes (264 KB)
+==================================================
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+trying URL 'https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-3.tar.gz'
+Content type 'application/x-gzip' length 11638 bytes (11 KB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rhdf5lib_1.16.0.tar.gz'
+Content type 'application/octet-stream' length 9989467 bytes (9.5 MB)
+==================================================
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+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/rhdf5filters_1.6.0.tar.gz'
+Content type 'application/octet-stream' length 854552 bytes (834 KB)
+==================================================
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+
+trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.6.tar.gz'
+Content type 'application/x-gzip' length 3061989 bytes (2.9 MB)
+==================================================
+downloaded 2.9 MB
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+trying URL 'https://cloud.r-project.org/src/contrib/pheatmap_1.0.12.tar.gz'
+Content type 'application/x-gzip' length 15071 bytes (14 KB)
+==================================================
+downloaded 14 KB
+
+trying URL 'https://cloud.r-project.org/src/contrib/gtools_3.9.3.tar.gz'
+Content type 'application/x-gzip' length 240614 bytes (234 KB)
+==================================================
+downloaded 234 KB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/rhdf5_2.38.1.tar.gz'
+Content type 'application/octet-stream' length 1231762 bytes (1.2 MB)
+==================================================
+downloaded 1.2 MB
+
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/HiCcompare_1.16.0.tar.gz'
+Content type 'application/octet-stream' length 3714564 bytes (3.5 MB)
+==================================================
+downloaded 3.5 MB
+
+foundpkgs: colorspace, farver, labeling, munsell, viridisLite, isoband, scales, RColorBrewer, Rhdf5lib, rhdf5filters, ggplot2, pheatmap, gtools, rhdf5, HiCcompare, /tmp/RtmpeWDUMj/downloaded_packages/colorspace_2.0-3.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/farver_2.1.1.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/labeling_0.4.2.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/munsell_0.5.0.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/viridisLite_0.4.1.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/isoband_0.2.6.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/scales_1.2.1.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/RColorBrewer_1.1-3.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/Rhdf5lib_1.16.0.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/rhdf5filters_1.6.0.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/ggplot2_3.3.6.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/pheatmap_1.0.12.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/gtools_3.9.3.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/rhdf5_2.38.1.tar.gz, /tmp/RtmpeWDUMj/downloaded_packages/HiCcompare_1.16.0.tar.gz
+files: /tmp/RtmpeWDUMj/downloaded_packages/colorspace_2.0-3.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/farver_2.1.1.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/labeling_0.4.2.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/munsell_0.5.0.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/viridisLite_0.4.1.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/isoband_0.2.6.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/scales_1.2.1.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/RColorBrewer_1.1-3.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/Rhdf5lib_1.16.0.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/rhdf5filters_1.6.0.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/ggplot2_3.3.6.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/pheatmap_1.0.12.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/gtools_3.9.3.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/rhdf5_2.38.1.tar.gz, 
+	/tmp/RtmpeWDUMj/downloaded_packages/HiCcompare_1.16.0.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/colorspace_2.0-3.tar.gz''
+2): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/farver_2.1.1.tar.gz''
+3): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/labeling_0.4.2.tar.gz''
+4): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/viridisLite_0.4.1.tar.gz''
+5): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/isoband_0.2.6.tar.gz''
+6): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/RColorBrewer_1.1-3.tar.gz''
+7): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/Rhdf5lib_1.16.0.tar.gz''
+8): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/gtools_3.9.3.tar.gz''
+9): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/munsell_0.5.0.tar.gz''
+10): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/rhdf5filters_1.6.0.tar.gz''
+11): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/scales_1.2.1.tar.gz''
+12): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/rhdf5_2.38.1.tar.gz''
+13): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/ggplot2_3.3.6.tar.gz''
+14): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/pheatmap_1.0.12.tar.gz''
+15): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWDUMj/downloaded_packages/HiCcompare_1.16.0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpeWDUMj/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 16 / 24: lubridate
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/lubridate_1.8.0.tar.gz'
+Content type 'application/x-gzip' length 475704 bytes (464 KB)
+==================================================
+downloaded 464 KB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpgF8oGp/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR lubridate
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/lubridate_1.8.0.tar.gz'
+Content type 'application/x-gzip' length 475704 bytes (464 KB)
+==================================================
+downloaded 464 KB
+
+foundpkgs: lubridate, /tmp/RtmpgF8oGp/downloaded_packages/lubridate_1.8.0.tar.gz
+files: /tmp/RtmpgF8oGp/downloaded_packages/lubridate_1.8.0.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpgF8oGp/downloaded_packages/lubridate_1.8.0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpgF8oGp/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 17 / 24: parallel
+
+================
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR parallel
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
+  re-install: 'parallel'
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 18 / 24: reshape2
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/plyr_1.8.7.tar.gz'
+Content type 'application/x-gzip' length 401481 bytes (392 KB)
+==================================================
+downloaded 392 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/reshape2_1.4.4.tar.gz'
+Content type 'application/x-gzip' length 37307 bytes (36 KB)
+==================================================
+downloaded 36 KB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpQhaW9V/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR reshape2
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/reshape2_1.4.4.tar.gz'
+Content type 'application/x-gzip' length 37307 bytes (36 KB)
+==================================================
+downloaded 36 KB
+
+foundpkgs: reshape2, /tmp/RtmpQhaW9V/downloaded_packages/reshape2_1.4.4.tar.gz
+files: /tmp/RtmpQhaW9V/downloaded_packages/reshape2_1.4.4.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpQhaW9V/downloaded_packages/reshape2_1.4.4.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpQhaW9V/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 19 / 24: binb
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/binb_0.0.6.tar.gz'
+Content type 'application/x-gzip' length 2999419 bytes (2.9 MB)
+==================================================
+downloaded 2.9 MB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpBaXgFI/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR binb
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/binb_0.0.6.tar.gz'
+Content type 'application/x-gzip' length 2999419 bytes (2.9 MB)
+==================================================
+downloaded 2.9 MB
+
+foundpkgs: binb, /tmp/RtmpBaXgFI/downloaded_packages/binb_0.0.6.tar.gz
+files: /tmp/RtmpBaXgFI/downloaded_packages/binb_0.0.6.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpBaXgFI/downloaded_packages/binb_0.0.6.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpBaXgFI/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 20 / 24: linl
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/linl_0.0.4.tar.gz'
+Content type 'application/x-gzip' length 76937 bytes (75 KB)
+==================================================
+downloaded 75 KB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmp6XSm2s/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR linl
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/linl_0.0.4.tar.gz'
+Content type 'application/x-gzip' length 76937 bytes (75 KB)
+==================================================
+downloaded 75 KB
+
+foundpkgs: linl, /tmp/Rtmp6XSm2s/downloaded_packages/linl_0.0.4.tar.gz
+files: /tmp/Rtmp6XSm2s/downloaded_packages/linl_0.0.4.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp6XSm2s/downloaded_packages/linl_0.0.4.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmp6XSm2s/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 21 / 24: pinp
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/pinp_0.0.10.tar.gz'
+Content type 'application/x-gzip' length 214270 bytes (209 KB)
+==================================================
+downloaded 209 KB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmp6EsOo9/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR pinp
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/pinp_0.0.10.tar.gz'
+Content type 'application/x-gzip' length 214270 bytes (209 KB)
+==================================================
+downloaded 209 KB
+
+foundpkgs: pinp, /tmp/Rtmp6EsOo9/downloaded_packages/pinp_0.0.10.tar.gz
+files: /tmp/Rtmp6EsOo9/downloaded_packages/pinp_0.0.10.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp6EsOo9/downloaded_packages/pinp_0.0.10.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmp6EsOo9/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 22 / 24: tint
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/tint_0.1.3.tar.gz'
+Content type 'application/x-gzip' length 1937029 bytes (1.8 MB)
+==================================================
+downloaded 1.8 MB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmps6dRbL/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR tint
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/tint_0.1.3.tar.gz'
+Content type 'application/x-gzip' length 1937029 bytes (1.8 MB)
+==================================================
+downloaded 1.8 MB
+
+foundpkgs: tint, /tmp/Rtmps6dRbL/downloaded_packages/tint_0.1.3.tar.gz
+files: /tmp/Rtmps6dRbL/downloaded_packages/tint_0.1.3.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmps6dRbL/downloaded_packages/tint_0.1.3.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmps6dRbL/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 23 / 24: pdftools
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/qpdf_1.3.0.tar.gz'
+Content type 'application/x-gzip' length 322350 bytes (314 KB)
+==================================================
+downloaded 314 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/pdftools_3.3.1.tar.gz'
+Content type 'application/x-gzip' length 936190 bytes (914 KB)
+==================================================
+downloaded 914 KB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpmoeKVr/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR pdftools
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/pdftools_3.3.1.tar.gz'
+Content type 'application/x-gzip' length 936190 bytes (914 KB)
+==================================================
+downloaded 914 KB
+
+foundpkgs: pdftools, /tmp/RtmpmoeKVr/downloaded_packages/pdftools_3.3.1.tar.gz
+files: /tmp/RtmpmoeKVr/downloaded_packages/pdftools_3.3.1.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpmoeKVr/downloaded_packages/pdftools_3.3.1.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpmoeKVr/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 24 / 24: qqman
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/calibrate_1.7.7.tar.gz'
+Content type 'application/x-gzip' length 306782 bytes (299 KB)
+==================================================
+downloaded 299 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/qqman_0.1.8.tar.gz'
+Content type 'application/x-gzip' length 1341458 bytes (1.3 MB)
+==================================================
+downloaded 1.3 MB
+
+
+The downloaded source packages are in
+	‘/tmp/RtmpUitqHF/downloaded_packages’
+STANDARD INSTALLATION ATTEMPT FOR qqman
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/qqman_0.1.8.tar.gz'
+Content type 'application/x-gzip' length 1341458 bytes (1.3 MB)
+==================================================
+downloaded 1.3 MB
+
+foundpkgs: qqman, /tmp/RtmpUitqHF/downloaded_packages/qqman_0.1.8.tar.gz
+files: /tmp/RtmpUitqHF/downloaded_packages/qqman_0.1.8.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpUitqHF/downloaded_packages/qqman_0.1.8.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpUitqHF/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGES INSTALLED
+
+================
+
+
+
+
+SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER
+
+
+now dyn.load("/usr/lib/R/library/tools/libs/tools.so") ...
+                                  Package                       LibPath
+askpass                           askpass /usr/local/lib/R/site-library
+base64enc                       base64enc /usr/local/lib/R/site-library
+BH                                     BH /usr/local/lib/R/site-library
+binb                                 binb /usr/local/lib/R/site-library
+Biobase                           Biobase /usr/local/lib/R/site-library
+BiocGenerics                 BiocGenerics /usr/local/lib/R/site-library
+BiocManager                   BiocManager /usr/local/lib/R/site-library
+BiocParallel                 BiocParallel /usr/local/lib/R/site-library
+BiocVersion                   BiocVersion /usr/local/lib/R/site-library
+Biostrings                     Biostrings /usr/local/lib/R/site-library
+bitops                             bitops /usr/local/lib/R/site-library
+brew                                 brew /usr/local/lib/R/site-library
+brio                                 brio /usr/local/lib/R/site-library
+bslib                               bslib /usr/local/lib/R/site-library
+cachem                             cachem /usr/local/lib/R/site-library
+Cairo                               Cairo /usr/local/lib/R/site-library
+calibrate                       calibrate /usr/local/lib/R/site-library
+callr                               callr /usr/local/lib/R/site-library
+CGHbase                           CGHbase /usr/local/lib/R/site-library
+CGHcall                           CGHcall /usr/local/lib/R/site-library
+cli                                   cli /usr/local/lib/R/site-library
+clipr                               clipr /usr/local/lib/R/site-library
+colorspace                     colorspace /usr/local/lib/R/site-library
+commonmark                     commonmark /usr/local/lib/R/site-library
+cpp11                               cpp11 /usr/local/lib/R/site-library
+crayon                             crayon /usr/local/lib/R/site-library
+credentials                   credentials /usr/local/lib/R/site-library
+curl                                 curl /usr/local/lib/R/site-library
+data.table                     data.table /usr/local/lib/R/site-library
+DelayedArray                 DelayedArray /usr/local/lib/R/site-library
+desc                                 desc /usr/local/lib/R/site-library
+diffobj                           diffobj /usr/local/lib/R/site-library
+digest                             digest /usr/local/lib/R/site-library
+DNAcopy                           DNAcopy /usr/local/lib/R/site-library
+docopt                             docopt /usr/local/lib/R/site-library
+downlit                           downlit /usr/local/lib/R/site-library
+dplyr                               dplyr /usr/local/lib/R/site-library
+ellipsis                         ellipsis /usr/local/lib/R/site-library
+evaluate                         evaluate /usr/local/lib/R/site-library
+fansi                               fansi /usr/local/lib/R/site-library
+farver                             farver /usr/local/lib/R/site-library
+fastmap                           fastmap /usr/local/lib/R/site-library
+fontawesome                   fontawesome /usr/local/lib/R/site-library
+formatR                           formatR /usr/local/lib/R/site-library
+fs                                     fs /usr/local/lib/R/site-library
+futile.logger               futile.logger /usr/local/lib/R/site-library
+futile.options             futile.options /usr/local/lib/R/site-library
+future                             future /usr/local/lib/R/site-library
+future.apply                 future.apply /usr/local/lib/R/site-library
+generics                         generics /usr/local/lib/R/site-library
+GenomeInfoDb                 GenomeInfoDb /usr/local/lib/R/site-library
+GenomeInfoDbData         GenomeInfoDbData /usr/local/lib/R/site-library
+GenomicRanges               GenomicRanges /usr/local/lib/R/site-library
+gert                                 gert /usr/local/lib/R/site-library
+ggplot2                           ggplot2 /usr/local/lib/R/site-library
+gh                                     gh /usr/local/lib/R/site-library
+gitcreds                         gitcreds /usr/local/lib/R/site-library
+globals                           globals /usr/local/lib/R/site-library
+glue                                 glue /usr/local/lib/R/site-library
+gridExtra                       gridExtra /usr/local/lib/R/site-library
+gtable                             gtable /usr/local/lib/R/site-library
+gtools                             gtools /usr/local/lib/R/site-library
+HiCcompare                     HiCcompare /usr/local/lib/R/site-library
+highr                               highr /usr/local/lib/R/site-library
+htmltools                       htmltools /usr/local/lib/R/site-library
+htmlwidgets                   htmlwidgets /usr/local/lib/R/site-library
+httpuv                             httpuv /usr/local/lib/R/site-library
+httr                                 httr /usr/local/lib/R/site-library
+impute                             impute /usr/local/lib/R/site-library
+ini                                   ini /usr/local/lib/R/site-library
+InteractionSet             InteractionSet /usr/local/lib/R/site-library
+IRanges                           IRanges /usr/local/lib/R/site-library
+isoband                           isoband /usr/local/lib/R/site-library
+jquerylib                       jquerylib /usr/local/lib/R/site-library
+jsonlite                         jsonlite /usr/local/lib/R/site-library
+knitr                               knitr /usr/local/lib/R/site-library
+labeling                         labeling /usr/local/lib/R/site-library
+lambda.r                         lambda.r /usr/local/lib/R/site-library
+later                               later /usr/local/lib/R/site-library
+lifecycle                       lifecycle /usr/local/lib/R/site-library
+limma                               limma /usr/local/lib/R/site-library
+linl                                 linl /usr/local/lib/R/site-library
+listenv                           listenv /usr/local/lib/R/site-library
+lubridate                       lubridate /usr/local/lib/R/site-library
+magrittr                         magrittr /usr/local/lib/R/site-library
+marray                             marray /usr/local/lib/R/site-library
+MatrixGenerics             MatrixGenerics /usr/local/lib/R/site-library
+matrixStats                   matrixStats /usr/local/lib/R/site-library
+memoise                           memoise /usr/local/lib/R/site-library
+mgcv                                 mgcv /usr/local/lib/R/site-library
+mime                                 mime /usr/local/lib/R/site-library
+miniUI                             miniUI /usr/local/lib/R/site-library
+munsell                           munsell /usr/local/lib/R/site-library
+openssl                           openssl /usr/local/lib/R/site-library
+parallelly                     parallelly /usr/local/lib/R/site-library
+pdftools                         pdftools /usr/local/lib/R/site-library
+pheatmap                         pheatmap /usr/local/lib/R/site-library
+pillar                             pillar /usr/local/lib/R/site-library
+pinp                                 pinp /usr/local/lib/R/site-library
+pkgbuild                         pkgbuild /usr/local/lib/R/site-library
+pkgconfig                       pkgconfig /usr/local/lib/R/site-library
+pkgload                           pkgload /usr/local/lib/R/site-library
+plyr                                 plyr /usr/local/lib/R/site-library
+praise                             praise /usr/local/lib/R/site-library
+prettyunits                   prettyunits /usr/local/lib/R/site-library
+processx                         processx /usr/local/lib/R/site-library
+profvis                           profvis /usr/local/lib/R/site-library
+promises                         promises /usr/local/lib/R/site-library
+ps                                     ps /usr/local/lib/R/site-library
+purrr                               purrr /usr/local/lib/R/site-library
+QDNAseq                           QDNAseq /usr/local/lib/R/site-library
+qpdf                                 qpdf /usr/local/lib/R/site-library
+qqman                               qqman /usr/local/lib/R/site-library
+R.methodsS3                   R.methodsS3 /usr/local/lib/R/site-library
+R.oo                                 R.oo /usr/local/lib/R/site-library
+R.utils                           R.utils /usr/local/lib/R/site-library
+R6                                     R6 /usr/local/lib/R/site-library
+rappdirs                         rappdirs /usr/local/lib/R/site-library
+rcmdcheck                       rcmdcheck /usr/local/lib/R/site-library
+RColorBrewer                 RColorBrewer /usr/local/lib/R/site-library
+Rcpp                                 Rcpp /usr/local/lib/R/site-library
+RCurl                               RCurl /usr/local/lib/R/site-library
+rematch2                         rematch2 /usr/local/lib/R/site-library
+remotes                           remotes /usr/local/lib/R/site-library
+reshape2                         reshape2 /usr/local/lib/R/site-library
+rhdf5                               rhdf5 /usr/local/lib/R/site-library
+rhdf5filters                 rhdf5filters /usr/local/lib/R/site-library
+Rhdf5lib                         Rhdf5lib /usr/local/lib/R/site-library
+Rhtslib                           Rhtslib /usr/local/lib/R/site-library
+rlang                               rlang /usr/local/lib/R/site-library
+rmarkdown                       rmarkdown /usr/local/lib/R/site-library
+roxygen2                         roxygen2 /usr/local/lib/R/site-library
+rprojroot                       rprojroot /usr/local/lib/R/site-library
+Rsamtools                       Rsamtools /usr/local/lib/R/site-library
+rstudioapi                     rstudioapi /usr/local/lib/R/site-library
+rversions                       rversions /usr/local/lib/R/site-library
+S4Vectors                       S4Vectors /usr/local/lib/R/site-library
+sass                                 sass /usr/local/lib/R/site-library
+scales                             scales /usr/local/lib/R/site-library
+sessioninfo                   sessioninfo /usr/local/lib/R/site-library
+shiny                               shiny /usr/local/lib/R/site-library
+snow                                 snow /usr/local/lib/R/site-library
+snowfall                         snowfall /usr/local/lib/R/site-library
+sourcetools                   sourcetools /usr/local/lib/R/site-library
+stringi                           stringi /usr/local/lib/R/site-library
+stringr                           stringr /usr/local/lib/R/site-library
+SummarizedExperiment SummarizedExperiment /usr/local/lib/R/site-library
+sys                                   sys /usr/local/lib/R/site-library
+systemfonts                   systemfonts /usr/local/lib/R/site-library
+testthat                         testthat /usr/local/lib/R/site-library
+tibble                             tibble /usr/local/lib/R/site-library
+tidyselect                     tidyselect /usr/local/lib/R/site-library
+tint                                 tint /usr/local/lib/R/site-library
+tinytex                           tinytex /usr/local/lib/R/site-library
+urlchecker                     urlchecker /usr/local/lib/R/site-library
+usethis                           usethis /usr/local/lib/R/site-library
+utf8                                 utf8 /usr/local/lib/R/site-library
+vctrs                               vctrs /usr/local/lib/R/site-library
+viridisLite                   viridisLite /usr/local/lib/R/site-library
+waldo                               waldo /usr/local/lib/R/site-library
+whisker                           whisker /usr/local/lib/R/site-library
+withr                               withr /usr/local/lib/R/site-library
+xfun                                 xfun /usr/local/lib/R/site-library
+xml2                                 xml2 /usr/local/lib/R/site-library
+xopen                               xopen /usr/local/lib/R/site-library
+xtable                             xtable /usr/local/lib/R/site-library
+XVector                           XVector /usr/local/lib/R/site-library
+yaml                                 yaml /usr/local/lib/R/site-library
+zip                                   zip /usr/local/lib/R/site-library
+zlibbioc                         zlibbioc /usr/local/lib/R/site-library
+littler                           littler       /usr/lib/R/site-library
+base                                 base            /usr/lib/R/library
+boot                                 boot            /usr/lib/R/library
+class                               class            /usr/lib/R/library
+cluster                           cluster            /usr/lib/R/library
+codetools                       codetools            /usr/lib/R/library
+compiler                         compiler            /usr/lib/R/library
+datasets                         datasets            /usr/lib/R/library
+foreign                           foreign            /usr/lib/R/library
+graphics                         graphics            /usr/lib/R/library
+grDevices                       grDevices            /usr/lib/R/library
+grid                                 grid            /usr/lib/R/library
+KernSmooth                     KernSmooth            /usr/lib/R/library
+lattice                           lattice            /usr/lib/R/library
+MASS                                 MASS            /usr/lib/R/library
+Matrix                             Matrix            /usr/lib/R/library
+methods                           methods            /usr/lib/R/library
+mgcv.1                               mgcv            /usr/lib/R/library
+nlme                                 nlme            /usr/lib/R/library
+nnet                                 nnet            /usr/lib/R/library
+parallel                         parallel            /usr/lib/R/library
+rpart                               rpart            /usr/lib/R/library
+spatial                           spatial            /usr/lib/R/library
+splines                           splines            /usr/lib/R/library
+stats                               stats            /usr/lib/R/library
+stats4                             stats4            /usr/lib/R/library
+survival                         survival            /usr/lib/R/library
+tcltk                               tcltk            /usr/lib/R/library
+tools                               tools            /usr/lib/R/library
+utils                               utils            /usr/lib/R/library
+                      Version    Priority
+askpass                   1.1        <NA>
+base64enc               0.1-3        <NA>
+BH                   1.78.0-0        <NA>
+binb                    0.0.6        <NA>
+Biobase                2.54.0        <NA>
+BiocGenerics           0.40.0        <NA>
+BiocManager           1.30.18        <NA>
+BiocParallel           1.28.3        <NA>
+BiocVersion            3.14.0        <NA>
+Biostrings             2.62.0        <NA>
+bitops                  1.0-7        <NA>
+brew                    1.0-8        <NA>
+brio                    1.1.3        <NA>
+bslib                   0.4.0        <NA>
+cachem                  1.0.6        <NA>
+Cairo                   1.6-0        <NA>
+calibrate               1.7.7        <NA>
+callr                   3.7.2        <NA>
+CGHbase                1.54.0        <NA>
+CGHcall                2.56.0        <NA>
+cli                     3.4.1        <NA>
+clipr                   0.8.0        <NA>
+colorspace              2.0-3        <NA>
+commonmark              1.8.0        <NA>
+cpp11                   0.4.3        <NA>
+crayon                  1.5.2        <NA>
+credentials             1.3.2        <NA>
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+DelayedArray           0.20.0        <NA>
+desc                    1.4.2        <NA>
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+digest                 0.6.29        <NA>
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+docopt                  0.7.1        <NA>
+downlit                 0.4.2        <NA>
+dplyr                  1.0.10        <NA>
+ellipsis                0.3.2        <NA>
+evaluate                 0.17        <NA>
+fansi                   1.0.3        <NA>
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+fastmap                 1.1.0        <NA>
+fontawesome             0.3.0        <NA>
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+fs                      1.5.2        <NA>
+futile.logger           1.4.3        <NA>
+futile.options          1.0.1        <NA>
+future                 1.28.0        <NA>
+future.apply            1.9.1        <NA>
+generics                0.1.3        <NA>
+GenomeInfoDb           1.30.1        <NA>
+GenomeInfoDbData        1.2.7        <NA>
+GenomicRanges          1.46.1        <NA>
+gert                    1.9.1        <NA>
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+gh                      1.3.1        <NA>
+gitcreds                0.1.2        <NA>
+globals                0.16.1        <NA>
+glue                    1.6.2        <NA>
+gridExtra                 2.3        <NA>
+gtable                  0.3.1        <NA>
+gtools                  3.9.3        <NA>
+HiCcompare             1.16.0        <NA>
+highr                     0.9        <NA>
+htmltools               0.5.3        <NA>
+htmlwidgets             1.5.4        <NA>
+httpuv                  1.6.6        <NA>
+httr                    1.4.4        <NA>
+impute                 1.68.0        <NA>
+ini                     0.3.1        <NA>
+InteractionSet         1.22.0        <NA>
+IRanges                2.28.0        <NA>
+isoband                 0.2.6        <NA>
+jquerylib               0.1.4        <NA>
+jsonlite                1.8.2        <NA>
+knitr                    1.40        <NA>
+labeling                0.4.2        <NA>
+lambda.r                1.2.4        <NA>
+later                   1.3.0        <NA>
+lifecycle               1.0.3        <NA>
+limma                  3.50.3        <NA>
+linl                    0.0.4        <NA>
+listenv                 0.8.0        <NA>
+lubridate               1.8.0        <NA>
+magrittr                2.0.3        <NA>
+marray                 1.72.0        <NA>
+MatrixGenerics          1.6.0        <NA>
+matrixStats            0.62.0        <NA>
+memoise                 2.0.1        <NA>
+mgcv                   1.8-40 recommended
+mime                     0.12        <NA>
+miniUI                0.1.1.1        <NA>
+munsell                 0.5.0        <NA>
+openssl                 2.0.3        <NA>
+parallelly             1.32.1        <NA>
+pdftools                3.3.1        <NA>
+pheatmap               1.0.12        <NA>
+pillar                  1.8.1        <NA>
+pinp                   0.0.10        <NA>
+pkgbuild                1.3.1        <NA>
+pkgconfig               2.0.3        <NA>
+pkgload                 1.3.0        <NA>
+plyr                    1.8.7        <NA>
+praise                  1.0.0        <NA>
+prettyunits             1.1.1        <NA>
+processx                3.7.0        <NA>
+profvis                 0.3.7        <NA>
+promises              1.2.0.1        <NA>
+ps                      1.7.1        <NA>
+purrr                   0.3.5        <NA>
+QDNAseq                1.30.0        <NA>
+qpdf                    1.3.0        <NA>
+qqman                   0.1.8        <NA>
+R.methodsS3             1.8.2        <NA>
+R.oo                   1.25.0        <NA>
+R.utils                2.12.0        <NA>
+R6                      2.5.1        <NA>
+rappdirs                0.3.3        <NA>
+rcmdcheck               1.4.0        <NA>
+RColorBrewer            1.1-3        <NA>
+Rcpp                    1.0.9        <NA>
+RCurl                1.98-1.9        <NA>
+rematch2                2.1.2        <NA>
+remotes                 2.4.2        <NA>
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+rhdf5                  2.38.1        <NA>
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+Rhtslib                1.26.0        <NA>
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+rmarkdown                2.17        <NA>
+roxygen2                7.2.1        <NA>
+rprojroot               2.0.3        <NA>
+Rsamtools              2.10.0        <NA>
+rstudioapi               0.14        <NA>
+rversions               2.1.2        <NA>
+S4Vectors              0.32.4        <NA>
+sass                    0.4.2        <NA>
+scales                  1.2.1        <NA>
+sessioninfo             1.2.2        <NA>
+shiny                   1.7.2        <NA>
+snow                    0.4-4        <NA>
+snowfall             1.84-6.2        <NA>
+sourcetools             0.1.7        <NA>
+stringi                 1.7.8        <NA>
+stringr                 1.4.1        <NA>
+SummarizedExperiment   1.24.0        <NA>
+sys                       3.4        <NA>
+systemfonts             1.0.4        <NA>
+testthat                3.1.5        <NA>
+tibble                  3.1.8        <NA>
+tidyselect              1.2.0        <NA>
+tint                    0.1.3        <NA>
+tinytex                  0.42        <NA>
+urlchecker              1.0.1        <NA>
+usethis                 2.1.6        <NA>
+utf8                    1.2.2        <NA>
+vctrs                   0.4.2        <NA>
+viridisLite             0.4.1        <NA>
+waldo                   0.4.0        <NA>
+whisker                   0.4        <NA>
+withr                   2.5.0        <NA>
+xfun                     0.33        <NA>
+xml2                    1.3.3        <NA>
+xopen                   1.0.0        <NA>
+xtable                  1.8-4        <NA>
+XVector                0.34.0        <NA>
+yaml                    2.3.5        <NA>
+zip                     2.2.1        <NA>
+zlibbioc               1.40.0        <NA>
+littler                0.3.15        <NA>
+base                    4.1.2        base
+boot                   1.3-28 recommended
+class                  7.3-20 recommended
+cluster                 2.1.2 recommended
+codetools              0.2-18 recommended
+compiler                4.1.2        base
+datasets                4.1.2        base
+foreign                0.8-82 recommended
+graphics                4.1.2        base
+grDevices               4.1.2        base
+grid                    4.1.2        base
+KernSmooth            2.23-20 recommended
+lattice               0.20-45 recommended
+MASS                   7.3-55 recommended
+Matrix                  1.4-0 recommended
+methods                 4.1.2        base
+mgcv.1                 1.8-38 recommended
+nlme                  3.1-155 recommended
+nnet                   7.3-17 recommended
+parallel                4.1.2        base
+rpart                  4.1.16 recommended
+spatial                7.3-15 recommended
+splines                 4.1.2        base
+stats                   4.1.2        base
+stats4                  4.1.2        base
+survival               3.2-13 recommended
+tcltk                   4.1.2        base
+tools                   4.1.2        base
+utils                   4.1.2        base
+
+
+
+
+================
+
+R PACKAGES NOT INSTALLED
+
+================
+
+
+
+
+SEE ALSO THE not_installed_r_packages.txt TABLE IN THE ROOT OF THE CONTAINER
+
+
+      Name
+1 devtools
+
+
+
+
+================
+
+apt-get autoremove
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 110 not upgraded.
+
+
+
+
+================
+
+apt-get clean
+
+================
+
+
+
+
+
+
+
+
+================
+
+rm
+
+================
+
+
+
+
+
+
+
+
+================
+
+LINUX PACKAGES INSTALLED
+
+================
+
+
+
+
+procps:
+  Installed: 2:3.3.16-1ubuntu2.3
+  Candidate: 2:3.3.16-1ubuntu2.3
+  Version table:
+ *** 2:3.3.16-1ubuntu2.3 100
+        100 /var/lib/dpkg/status
+libfontconfig1-dev:
+  Installed: 2.13.1-2ubuntu3
+  Candidate: 2.13.1-2ubuntu3
+  Version table:
+ *** 2.13.1-2ubuntu3 100
+        100 /var/lib/dpkg/status
+ghostscript:
+  Installed: 9.50~dfsg-5ubuntu4.6
+  Candidate: 9.50~dfsg-5ubuntu4.6
+  Version table:
+ *** 9.50~dfsg-5ubuntu4.6 100
+        100 /var/lib/dpkg/status
+lmodern:
+  Installed: 2.004.5-6
+  Candidate: 2.004.5-6
+  Version table:
+ *** 2.004.5-6 100
+        100 /var/lib/dpkg/status
+pandoc:
+  Installed: 2.5-3build2
+  Candidate: 2.5-3build2
+  Version table:
+ *** 2.5-3build2 100
+        100 /var/lib/dpkg/status
+pandoc-citeproc:
+  Installed: 0.15.0.1-1build4
+  Candidate: 0.15.0.1-1build4
+  Version table:
+ *** 0.15.0.1-1build4 100
+        100 /var/lib/dpkg/status
+qpdf:
+  Installed: 9.1.1-1ubuntu0.1
+  Candidate: 9.1.1-1ubuntu0.1
+  Version table:
+ *** 9.1.1-1ubuntu0.1 100
+        100 /var/lib/dpkg/status
+texinfo:
+  Installed: 6.7.0.dfsg.2-5
+  Candidate: 6.7.0.dfsg.2-5
+  Version table:
+ *** 6.7.0.dfsg.2-5 100
+        100 /var/lib/dpkg/status
+texlive-fonts-extra:
+  Installed: 2019.202000218-1
+  Candidate: 2019.202000218-1
+  Version table:
+ *** 2019.202000218-1 100
+        100 /var/lib/dpkg/status
+texlive-fonts-recommended:
+  Installed: 2019.20200218-1
+  Candidate: 2019.20200218-1
+  Version table:
+ *** 2019.20200218-1 100
+        100 /var/lib/dpkg/status
+texlive-latex-extra:
+  Installed: 2019.202000218-1
+  Candidate: 2019.202000218-1
+  Version table:
+ *** 2019.202000218-1 100
+        100 /var/lib/dpkg/status
+texlive-latex-recommended:
+  Installed: 2019.20200218-1
+  Candidate: 2019.20200218-1
+  Version table:
+ *** 2019.20200218-1 100
+        100 /var/lib/dpkg/status
+texlive-luatex:
+  Installed: 2019.20200218-1
+  Candidate: 2019.20200218-1
+  Version table:
+ *** 2019.20200218-1 100
+        100 /var/lib/dpkg/status
+texlive-plain-generic:
+  Installed: 2019.202000218-1
+  Candidate: 2019.202000218-1
+  Version table:
+ *** 2019.202000218-1 100
+        100 /var/lib/dpkg/status
+texlive-science:
+  Installed: 2019.202000218-1
+  Candidate: 2019.202000218-1
+  Version table:
+ *** 2019.202000218-1 100
+        100 /var/lib/dpkg/status
+texlive-xetex:
+  Installed: 2019.20200218-1
+  Candidate: 2019.20200218-1
+  Version table:
+ *** 2019.20200218-1 100
+        100 /var/lib/dpkg/status
+libpoppler-cpp-dev:
+  Installed: 22.02.0-focal0
+  Candidate: 22.02.0-focal0
+  Version table:
+ *** 22.02.0-focal0 100
+        100 /var/lib/dpkg/status
+build-essential:
+  Installed: 12.8ubuntu1.1
+  Candidate: 12.8ubuntu1.1
+  Version table:
+ *** 12.8ubuntu1.1 100
+        100 /var/lib/dpkg/status
+libcurl4-gnutls-dev:
+  Installed: 7.68.0-1ubuntu2.13
+  Candidate: 7.68.0-1ubuntu2.13
+  Version table:
+ *** 7.68.0-1ubuntu2.13 100
+        100 /var/lib/dpkg/status
+libxml2-dev:
+  Installed: 2.9.10+dfsg-5ubuntu0.20.04.4
+  Candidate: 2.9.10+dfsg-5ubuntu0.20.04.4
+  Version table:
+ *** 2.9.10+dfsg-5ubuntu0.20.04.4 100
+        100 /var/lib/dpkg/status
+libssl-dev:
+  Installed: 1.1.1f-1ubuntu2.16
+  Candidate: 1.1.1f-1ubuntu2.16
+  Version table:
+ *** 1.1.1f-1ubuntu2.16 100
+        100 /var/lib/dpkg/status
+libgit2-dev:
+  Installed: 0.28.4+dfsg.1-2
+  Candidate: 0.28.4+dfsg.1-2
+  Version table:
+ *** 0.28.4+dfsg.1-2 100
+        100 /var/lib/dpkg/status
+libcairo2-dev:
+  Installed: 1.16.0-4ubuntu1
+  Candidate: 1.16.0-4ubuntu1
+  Version table:
+ *** 1.16.0-4ubuntu1 100
+        100 /var/lib/dpkg/status
+libxt-dev:
+  Installed: 1:1.1.5-1
+  Candidate: 1:1.1.5-1
+  Version table:
+ *** 1:1.1.5-1 100
+        100 /var/lib/dpkg/status
diff --git a/R/v4.1.2/extended/v3.0/installed_r_packages.csv b/R/v4.1.2/extended/v3.0/installed_r_packages.csv
new file mode 100644
index 0000000000000000000000000000000000000000..54007ec52551c9f0ee1a2ca7e5f15fa5d5fd0199
--- /dev/null
+++ b/R/v4.1.2/extended/v3.0/installed_r_packages.csv
@@ -0,0 +1,201 @@
+Package;LibPath;Version;Priority;Depends;Imports;LinkingTo;Suggests;Enhances;License;License_is_FOSS;License_restricts_use;OS_type;MD5sum;NeedsCompilation;Built
+askpass;/usr/local/lib/R/site-library;1.1;NA;NA;sys (>= 2.1);NA;testthat;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+base64enc;/usr/local/lib/R/site-library;0.1-3;NA;R (>= 2.9.0);NA;NA;NA;png;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+BH;/usr/local/lib/R/site-library;1.78.0-0;NA;NA;NA;NA;NA;NA;BSL-1.0;NA;NA;NA;NA;no;4.1.2
+binb;/usr/local/lib/R/site-library;0.0.6;NA;NA;rmarkdown, knitr;NA;NA;NA;GPL (>= 2);NA;NA;NA;NA;no;4.1.2
+Biobase;/usr/local/lib/R/site-library;2.54.0;NA;R (>= 2.10), BiocGenerics (>= 0.27.1), utils;methods;NA;tools, tkWidgets, ALL, RUnit, golubEsets;NA;Artistic-2.0;NA;NA;NA;NA;yes;4.1.2
+BiocGenerics;/usr/local/lib/R/site-library;0.40.0;NA;R (>= 4.0.0), methods, utils, graphics, stats;methods, utils, graphics, stats;NA;Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,flowClust, MSnbase, annotate, RUnit;NA;Artistic-2.0;NA;NA;NA;NA;no;4.1.2
+BiocManager;/usr/local/lib/R/site-library;1.30.18;NA;NA;utils;NA;BiocVersion, remotes, rmarkdown, testthat, withr, curl, knitr;NA;Artistic-2.0;NA;NA;NA;NA;no;4.1.2
+BiocParallel;/usr/local/lib/R/site-library;1.28.3;NA;methods, R (>= 3.5.0);stats, utils, futile.logger, parallel, snow;BH;BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,BiocStyle, knitr, batchtools, data.table;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+BiocVersion;/usr/local/lib/R/site-library;3.14.0;NA;R (>= 4.1.0);NA;NA;NA;NA;Artistic-2.0;NA;NA;NA;NA;no;4.1.2
+Biostrings;/usr/local/lib/R/site-library;2.62.0;NA;R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2),GenomeInfoDb;methods, utils, grDevices, graphics, stats, crayon;S4Vectors, IRanges, XVector;BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy(>= 1.41.3), affydata (>= 1.11.5), RUnit;Rmpi;Artistic-2.0;NA;NA;NA;NA;yes;4.1.2
+bitops;/usr/local/lib/R/site-library;1.0-7;NA;NA;NA;NA;NA;NA;GPL (>= 2);NA;NA;NA;NA;yes;4.1.2
+brew;/usr/local/lib/R/site-library;1.0-8;NA;NA;NA;NA;testthat (>= 3.0.0);NA;GPL-2;NA;NA;NA;NA;no;4.1.2
+brio;/usr/local/lib/R/site-library;1.1.3;NA;NA;NA;NA;covr, testthat (>= 2.1.0);NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+bslib;/usr/local/lib/R/site-library;0.4.0;NA;R (>= 2.10);grDevices, htmltools (>= 0.5.2), jsonlite, sass (>= 0.4.0),jquerylib (>= 0.1.3), rlang, cachem, memoise;NA;shiny (>= 1.6.0), rmarkdown (>= 2.7), thematic, knitr,testthat, withr, rappdirs, curl, magrittr;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+cachem;/usr/local/lib/R/site-library;1.0.6;NA;NA;rlang, fastmap;NA;testthat;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+Cairo;/usr/local/lib/R/site-library;1.6-0;NA;R (>= 2.4.0);grDevices, graphics;NA;png;FastRWeb;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+calibrate;/usr/local/lib/R/site-library;1.7.7;NA;R (>= 3.5.0), MASS;NA;NA;NA;NA;GPL-2;NA;NA;NA;NA;no;4.1.2
+callr;/usr/local/lib/R/site-library;3.7.2;NA;R (>= 3.4);processx (>= 3.6.1), R6, utils;NA;cli (>= 1.1.0), covr, mockery, ps, rprojroot, spelling,testthat (>= 3.0.0), withr (>= 2.3.0);NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+CGHbase;/usr/local/lib/R/site-library;1.54.0;NA;R (>= 2.10), methods, Biobase (>= 2.5.5), marray;NA;NA;NA;NA;GPL;NA;NA;NA;NA;no;4.1.2
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+base;/usr/lib/R/library;4.1.2;base;NA;NA;NA;methods;NA;Part of R 4.1.2;NA;NA;NA;NA;NA;4.1.2
+boot;/usr/lib/R/library;1.3-28;recommended;R (>= 3.0.0), graphics, stats;NA;NA;MASS, survival;NA;Unlimited;NA;NA;NA;NA;no;4.0.5
+class;/usr/lib/R/library;7.3-20;recommended;R (>= 3.0.0), stats, utils;MASS;NA;NA;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+cluster;/usr/lib/R/library;2.1.2;recommended;R (>= 3.4.0);graphics, grDevices, stats, utils;NA;MASS, Matrix;NA;GPL (>= 2);NA;NA;NA;NA;yes;4.0.5
+codetools;/usr/lib/R/library;0.2-18;recommended;R (>= 2.1);NA;NA;NA;NA;GPL;NA;NA;NA;NA;no;4.0.3
+compiler;/usr/lib/R/library;4.1.2;base;NA;NA;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;NA;4.1.2
+datasets;/usr/lib/R/library;4.1.2;base;NA;NA;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;NA;4.1.2
+foreign;/usr/lib/R/library;0.8-82;recommended;R (>= 4.0.0);methods, utils, stats;NA;NA;NA;GPL (>= 2);NA;NA;NA;NA;yes;4.1.2
+graphics;/usr/lib/R/library;4.1.2;base;NA;grDevices;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+grDevices;/usr/lib/R/library;4.1.2;base;NA;NA;NA;KernSmooth;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+grid;/usr/lib/R/library;4.1.2;base;NA;grDevices, utils;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+KernSmooth;/usr/lib/R/library;2.23-20;recommended;R (>= 2.5.0), stats;NA;NA;MASS, carData;NA;Unlimited;NA;NA;NA;NA;yes;4.0.5
+lattice;/usr/lib/R/library;0.20-45;recommended;R (>= 3.0.0);grid, grDevices, graphics, stats, utils;NA;KernSmooth, MASS, latticeExtra;chron;GPL (>= 2);NA;NA;NA;NA;yes;4.1.1
+MASS;/usr/lib/R/library;7.3-55;recommended;R (>= 3.3.0), grDevices, graphics, stats, utils;methods;NA;lattice, nlme, nnet, survival;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+Matrix;/usr/lib/R/library;1.4-0;recommended;R (>= 3.5.0);methods, graphics, grid, stats, utils, lattice;NA;expm, MASS;MatrixModels, graph, SparseM, sfsmisc, igraph, maptools, sp,spdep;GPL (>= 2) | file LICENCE;NA;NA;NA;NA;yes;4.1.2
+methods;/usr/lib/R/library;4.1.2;base;NA;utils, stats;NA;codetools;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+mgcv;/usr/lib/R/library;1.8-38;recommended;R (>= 3.6.0), nlme (>= 3.1-64);methods, stats, graphics, Matrix, splines, utils;NA;parallel, survival, MASS;NA;GPL (>= 2);NA;NA;NA;NA;yes;4.1.1
+nlme;/usr/lib/R/library;3.1-155;recommended;R (>= 3.4.0);graphics, stats, utils, lattice;NA;Hmisc, MASS;NA;GPL (>= 2) | file LICENCE;NA;NA;NA;NA;yes;4.1.2
+nnet;/usr/lib/R/library;7.3-17;recommended;R (>= 3.0.0), stats, utils;NA;NA;MASS;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+parallel;/usr/lib/R/library;4.1.2;base;NA;tools, compiler;NA;methods;snow, nws, Rmpi;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+rpart;/usr/lib/R/library;4.1.16;recommended;R (>= 2.15.0), graphics, stats, grDevices;NA;NA;survival;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+spatial;/usr/lib/R/library;7.3-15;recommended;R (>= 3.0.0), graphics, stats, utils;NA;NA;MASS;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+splines;/usr/lib/R/library;4.1.2;base;NA;graphics, stats;NA;Matrix, methods;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+stats;/usr/lib/R/library;4.1.2;base;NA;utils, grDevices, graphics;NA;MASS, Matrix, SuppDists, methods, stats4;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+stats4;/usr/lib/R/library;4.1.2;base;NA;graphics, methods, stats;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;NA;4.1.2
+survival;/usr/lib/R/library;3.2-13;recommended;R (>= 3.5.0);graphics, Matrix, methods, splines, stats, utils;NA;NA;NA;LGPL (>= 2);NA;NA;NA;NA;yes;4.1.1
+tcltk;/usr/lib/R/library;4.1.2;base;NA;utils;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+tools;/usr/lib/R/library;4.1.2;base;NA;NA;NA;codetools, methods, xml2, curl, commonmark;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
+utils;/usr/lib/R/library;4.1.2;base;NA;NA;NA;methods, xml2, commonmark;NA;Part of R 4.1.2;NA;NA;NA;NA;yes;4.1.2
diff --git a/R/v4.1.2/ig_clustering/v1.0/Dockerfile b/R/v4.1.2/ig_clustering/v1.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..bc6c568b287dcc4e68511a4107001f31e4837500
--- /dev/null
+++ b/R/v4.1.2/ig_clustering/v1.0/Dockerfile
@@ -0,0 +1,167 @@
+#########################################################################
+##                                                                     ##
+##     Dockerfile                                                      ##
+##     R extended                                                      ##
+##                                                                     ##
+##     Gael A. Millot                                                  ##
+##     Bioinformatics and Biostatistics Hub                            ##
+##     Computational Biology Department                                ##
+##     Institut Pasteur Paris                                          ##
+##                                                                     ##
+#########################################################################
+
+
+
+# to see the log of the building:
+# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
+# cat building.log
+
+# to export the log file of the image building from the container:
+# sudo docker images
+# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
+# exit
+# sudo docker container ls -a # to get all the active containers
+# sudo docker cp <containerNAMES>:/building.log </host/path/target>
+# sudo docker cp <containerNAMES>:/installed_r_packages.csv </host/path/target>
+
+# base image:
+FROM gmillot/r_v4.1.2_extended_v3.0:gitlab_v9.3
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. Here, the image is present locally, or distantly on the gmillot repo. Thus, gmillot/r-base:4.0.5 is correct.
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+ENV APT_GET_LINUX_LIB=""
+
+ENV APT_LINUX_LIB=""
+
+ENV CRANREPO="'https://cran.irsn.fr/'"
+
+ENV BIOCONDUCTOR_REPO="'https://cloud.r-project.org'"
+
+ENV RLIB="\
+  'Rccp' \
+  'Biostrings' \
+  'GenomicAlignments' \
+  'IRanges' \
+  'igraph' \
+  'alakazam' \
+  'shazam' \
+  'tiger' \
+  'scoper' \
+  'dowser' \
+"
+
+
+# fun.warning.capture from fun_get_message() of the cute package.
+# I used a first loop because I cannot use array in dockerfiles.
+# Inactivate sink(file = tempo, append = TRUE, type = 'message') for debbuging.
+RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n" > building.log \
+  && add-apt-repository -y ppa:cran/poppler \
+  && apt-get update \
+    | tee -a building.log ; echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> building.log \
+  && apt-get install -y $APT_GET_LINUX_LIB \
+    | tee -a building.log ; echo "\n\n\n\n================\n\napt install\n\n================\n\n\n\n" >> building.log \
+  && apt -y install $APT_LINUX_LIB \
+    | tee -a building.log \
+  && RLIB_LENGTH=0 \
+  && for i2 in $RLIB ; do RLIB_LENGTH=$((RLIB_LENGTH+1)) ; done \
+  && COUNT=0 \
+  && for i2 in $RLIB ; do \
+    COUNT=$((COUNT+1)) ; \
+    Rscript --vanilla -e " \
+      options(warn = 1, verbose = TRUE) ; \
+      tempo <- file('building.log', open = 'a+b') ; \
+      sink(file = tempo, append = TRUE, type = 'message') ; \
+      fun.warning.capture <- function(expr){ \
+        W <- NULL ; \
+        w.handler <- function(w){ \
+          W <<- w ; \
+          invokeRestart('muffleWarning') \
+        } ; \
+        output <- list( \
+          value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)),  \
+          warning = W \
+        ) ; \
+        return(if(is.null(output\$warning)){NULL}else{as.character(output\$warning)}) \
+      } ; \
+      message(paste0('\n\n\n\n================\n\nR PACKAGE INSTALLATION ', $COUNT, ' / ', $RLIB_LENGTH, ': ', $i2, '\n\n================\n\n\n\n')) ; \
+      if( ! ($i2 %in% c('ggplot2', 'SARTools'))){ \
+        tempo.warn <- fun.warning.capture(exp = install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO)) ; \
+        if(is.null(tempo.warn)){ \
+            tempo <- paste0('STANDARD INSTALLATION ATTEMPT FOR ', $i2) ; \
+            message(paste0('\n\n', tempo, '\n\n')) ; \
+            cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
+            install.packages(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repo = $CRANREPO) \
+        }else{ \
+            tempo <- paste0('BiocManager INSTALLATION ATTEMPT FOR ', $i2) ; \
+            message(paste0('\n\n', tempo, '\n\n')) ; \
+            cat(paste0('\n\n\n', tempo, '\n\n\n')) ; \
+            BiocManager::install(pkgs = $i2, lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, update = FALSE, site_repository = $BIOCONDUCTOR_REPO) \
+        } \
+      }else if($i2 == 'ggplot2'){ \
+        devtools::install_version(package = 'ggplot2', version = '3.3.3', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, repos = $CRANREPO) \
+      }else if($i2 == 'SARTools'){ \
+        devtools::install_github('PF2-pasteur-fr/SARTools', build_opts='--no-resave-data', lib = '/usr/local/lib/R/site-library', dependencies = NA, verbose = TRUE, upgrade = "always") \
+      } \
+    " ; \
+  done \
+  && Rscript --vanilla -e  " \
+    options(warn = 1, verbose = TRUE) ; \
+    args <- commandArgs(trailingOnly = TRUE) ; \
+    if(any(is.na(args))){ \
+        stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE args OBJECT HAS NA\n\n================\n\n'), call. = FALSE) \
+    } ; \
+    tempo.arg.names <- c( \
+        'RLIB' \
+    ) ; \
+    if(length(args) != length(tempo.arg.names)){ \
+        stop(paste0('\n\n================\n\nERROR IN plot_insertion.R\nTHE NUMBER OF ELEMENTS IN args (', length(args),') IS DIFFERENT FROM THE NUMBER OF ELEMENTS IN tempo.arg.names (', length(tempo.arg.names),')\nargs:', paste0(args, collapse = ','), '\ntempo.arg.names:', paste0(tempo.arg.names, collapse = ','), '\n\n================\n\n'), call. = FALSE) \
+    } ; \
+    for(i1 in 1:length(tempo.arg.names)){ \
+        assign(tempo.arg.names[i1], args[i1]) \
+    } ; \
+    RLIB <- strsplit(RLIB, split = ',')[[1]] ; \
+    RLIB <- RLIB[RLIB != ''] ; \
+    if(file.exists('installed_r_packages.csv')){ \
+      file.remove('installed_r_packages.csv') \
+    } ; \
+    if(file.exists('not_installed_r_packages.txt')){ \
+      file.remove('not_installed_r_packages.txt') \
+    } ; \
+    tempo <- file('building.log', open = 'a+b') ; \
+    sink(file = tempo, append = TRUE, type = 'message') ; \
+    message(paste0('\n\n\n\n================\n\nR PACKAGES INSTALLED\n\n================\n\n\n\n')) ; \
+    message('SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
+    capture.output(as.data.frame(installed.packages())[1:4], file = tempo, append = TRUE, type = 'output') ; \
+    df <- as.data.frame(installed.packages()) ; \
+    for (i2 in 1:length(df)){ \
+      df[, i2] <- gsub(x = df[, i2], replacement = '', pattern = '\n', fixed = TRUE) \
+    } ; \
+    write.table(x = df, file = 'installed_r_packages.csv', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
+    message(paste0('\n\n\n\n================\n\nR PACKAGES NOT INSTALLED\n\n================\n\n\n\n')) ; \
+    df2 <- as.data.frame(RLIB[ ! RLIB %in% df[ , 'Package']]) ; \
+    if(nrow(df2) == 0){ \
+      message('ALL THE PACKAGES HAVE BEEN INSTALLED\n\n') \
+    }else{ \
+      message('SEE ALSO THE not_installed_r_packages.txt TABLE IN THE ROOT OF THE CONTAINER\n\n') ; \
+      names(df2) <- 'Name' ; \
+      capture.output(df2, file = tempo, append = TRUE, type = 'output') ; \
+      write.table(x = df2, file = 'not_installed_r_packages.txt', row.names = FALSE, col.names = TRUE, append = FALSE, quote = FALSE, sep = ';') ; \
+    } \
+  " $(echo "$RLIB" | sed 's/ \{1,\}/,/g' | sed "s/'//g") \
+  && echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n\n\n" >> building.log \
+  && apt-get autoremove -y \
+    | tee -a building.log ; echo "\n\n\n\n================\n\napt-get clean\n\n================\n\n\n\n" >> building.log \
+  && apt-get clean \
+    | tee -a building.log ; echo "\n\n\n\n================\n\nrm\n\n================\n\n\n\n" >> building.log \
+  && rm -rf /var/lib/apt/lists/* \
+    | tee -a building.log \
+  && echo "\n\n\n\n================\n\nLINUX PACKAGES INSTALLED\n\n================\n\n\n\n" >> /building.log \
+  && apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB \
+    >> /building.log
+
+# dependencies=NA means c("Depends", "Imports", "LinkingTo"). Do no use TRUE -> install suggesting packages which inflates tremendously the image.
+
+ENTRYPOINT ["/usr/bin/R"]
diff --git a/R/v4.1.2/ig_clustering/v1.0/building.log b/R/v4.1.2/ig_clustering/v1.0/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..00d1a15d17cb0581d3b0e25619f18b331ef65442
--- /dev/null
+++ b/R/v4.1.2/ig_clustering/v1.0/building.log
@@ -0,0 +1,1141 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Hit:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease
+Hit:2 http://ppa.launchpad.net/cran/poppler/ubuntu focal InRelease
+Hit:3 http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal InRelease
+Hit:4 http://archive.ubuntu.com/ubuntu focal InRelease
+Hit:5 http://security.ubuntu.com/ubuntu focal-security InRelease
+Hit:6 http://archive.ubuntu.com/ubuntu focal-updates InRelease
+Hit:7 http://archive.ubuntu.com/ubuntu focal-backports InRelease
+Reading package lists...
+
+
+
+
+================
+
+apt-get install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 110 not upgraded.
+
+
+
+
+================
+
+apt install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 110 not upgraded.
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 1 / 10: Rccp
+
+================
+
+
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR Rccp
+
+
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'Rccp'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+Warning: package ‘Rccp’ is not available for Bioconductor version '3.14'
+
+A version of this package for your version of R might be available elsewhere,
+see the ideas at
+https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 2 / 10: Biostrings
+
+================
+
+
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR Biostrings
+
+
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
+  re-install: 'Biostrings'
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 3 / 10: GenomicAlignments
+
+================
+
+
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR GenomicAlignments
+
+
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'GenomicAlignments'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicAlignments_1.30.0.tar.gz'
+Content type 'application/octet-stream' length 2300932 bytes (2.2 MB)
+==================================================
+downloaded 2.2 MB
+
+foundpkgs: GenomicAlignments, /tmp/RtmpOOqoVu/downloaded_packages/GenomicAlignments_1.30.0.tar.gz
+files: /tmp/RtmpOOqoVu/downloaded_packages/GenomicAlignments_1.30.0.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpOOqoVu/downloaded_packages/GenomicAlignments_1.30.0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpOOqoVu/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 4 / 10: IRanges
+
+================
+
+
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR IRanges
+
+
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
+  re-install: 'IRanges'
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 5 / 10: igraph
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/igraph_1.3.5.tar.gz'
+Content type 'application/x-gzip' length 2499723 bytes (2.4 MB)
+==================================================
+downloaded 2.4 MB
+
+
+The downloaded source packages are in
+	‘/tmp/Rtmp1J9Uqf/downloaded_packages’
+
+
+STANDARD INSTALLATION ATTEMPT FOR igraph
+
+
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/igraph_1.3.5.tar.gz'
+Content type 'application/x-gzip' length 2499723 bytes (2.4 MB)
+==================================================
+downloaded 2.4 MB
+
+foundpkgs: igraph, /tmp/Rtmp1J9Uqf/downloaded_packages/igraph_1.3.5.tar.gz
+files: /tmp/Rtmp1J9Uqf/downloaded_packages/igraph_1.3.5.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp1J9Uqf/downloaded_packages/igraph_1.3.5.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmp1J9Uqf/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 6 / 10: alakazam
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/bit_4.0.4.tar.gz'
+Content type 'application/x-gzip' length 279723 bytes (273 KB)
+==================================================
+downloaded 273 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/bit64_4.0.5.tar.gz'
+Content type 'application/x-gzip' length 135091 bytes (131 KB)
+==================================================
+downloaded 131 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/pixmap_0.4-12.tar.gz'
+Content type 'application/x-gzip' length 34637 bytes (33 KB)
+==================================================
+downloaded 33 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/sp_1.5-0.tar.gz'
+Content type 'application/x-gzip' length 1033924 bytes (1009 KB)
+==================================================
+downloaded 1009 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/hms_1.1.2.tar.gz'
+Content type 'application/x-gzip' length 43270 bytes (42 KB)
+==================================================
+downloaded 42 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/vroom_1.6.0.tar.gz'
+Content type 'application/x-gzip' length 719194 bytes (702 KB)
+==================================================
+downloaded 702 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/tzdb_0.3.0.tar.gz'
+Content type 'application/x-gzip' length 567544 bytes (554 KB)
+==================================================
+downloaded 554 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/ade4_1.7-19.tar.gz'
+Content type 'application/x-gzip' length 3475868 bytes (3.3 MB)
+==================================================
+downloaded 3.3 MB
+
+trying URL 'https://cran.irsn.fr/src/contrib/segmented_1.6-0.tar.gz'
+Content type 'application/x-gzip' length 170262 bytes (166 KB)
+==================================================
+downloaded 166 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/airr_1.4.1.tar.gz'
+Content type 'application/x-gzip' length 363456 bytes (354 KB)
+==================================================
+downloaded 354 KB
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+Content type 'application/x-gzip' length 2075971 bytes (2.0 MB)
+==================================================
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+
+
+The downloaded source packages are in
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+
+
+STANDARD INSTALLATION ATTEMPT FOR alakazam
+
+
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/alakazam_1.2.1.tar.gz'
+Content type 'application/x-gzip' length 2075971 bytes (2.0 MB)
+==================================================
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+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/Rtmp4r7Ppb/downloaded_packages/alakazam_1.2.1.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/Rtmp4r7Ppb/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 7 / 10: shazam
+
+================
+
+
+
+
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+Content type 'application/x-gzip' length 300266 bytes (293 KB)
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+
+STANDARD INSTALLATION ATTEMPT FOR shazam
+
+
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/shazam_1.1.2.tar.gz'
+Content type 'application/x-gzip' length 1749942 bytes (1.7 MB)
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+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpeWLrOc/downloaded_packages/shazam_1.1.2.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpeWLrOc/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 8 / 10: tiger
+
+================
+
+
+
+
+
+
+BiocManager INSTALLATION ATTEMPT FOR tiger
+
+
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'tiger'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+Warning: package ‘tiger’ is not available for Bioconductor version '3.14'
+
+A version of this package for your version of R might be available elsewhere,
+see the ideas at
+https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 9 / 10: scoper
+
+================
+
+
+
+
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+Content type 'application/x-gzip' length 588548 bytes (574 KB)
+==================================================
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+
+The downloaded source packages are in
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+
+
+STANDARD INSTALLATION ATTEMPT FOR scoper
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+
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
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+Content type 'application/x-gzip' length 588548 bytes (574 KB)
+==================================================
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+files: /tmp/RtmpD5NQlS/downloaded_packages/scoper_1.2.1.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpD5NQlS/downloaded_packages/scoper_1.2.1.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpD5NQlS/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 10 / 10: dowser
+
+================
+
+
+
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+Content type 'application/x-gzip' length 81050 bytes (79 KB)
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+==================================================
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+The downloaded source packages are in
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+
+BiocManager INSTALLATION ATTEMPT FOR dowser
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+
+Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
+Installing package(s) 'dowser'
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+also installing the dependencies ‘gridGraphics’, ‘ggplotify’, ‘patchwork’, ‘aplot’, ‘ggfun’, ‘yulab.utils’, ‘tidytree’, ‘treeio’, ‘ggtree’
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+Content type 'application/x-gzip' length 69207 bytes (67 KB)
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+Content type 'application/x-gzip' length 3192018 bytes (3.0 MB)
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+	/tmp/RtmpTA6149/downloaded_packages/patchwork_1.1.2.tar.gz, 
+	/tmp/RtmpTA6149/downloaded_packages/aplot_0.1.8.tar.gz, 
+	/tmp/RtmpTA6149/downloaded_packages/ggfun_0.0.7.tar.gz, 
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+5): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpTA6149/downloaded_packages/ggplotify_0.1.0.tar.gz''
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+7): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpTA6149/downloaded_packages/aplot_0.1.8.tar.gz''
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+9): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpTA6149/downloaded_packages/ggtree_3.2.1.tar.gz''
+10): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpTA6149/downloaded_packages/dowser_1.1.0.tar.gz''
+
+The downloaded source packages are in
+	‘/tmp/RtmpTA6149/downloaded_packages’
+
+
+
+
+================
+
+R PACKAGES INSTALLED
+
+================
+
+
+
+
+SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER
+
+
+now dyn.load("/usr/lib/R/library/tools/libs/tools.so") ...
+                                  Package                       LibPath
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+airr                                 airr /usr/local/lib/R/site-library
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+brew                                 brew /usr/local/lib/R/site-library
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+CGHbase                           CGHbase /usr/local/lib/R/site-library
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+credentials                   credentials /usr/local/lib/R/site-library
+curl                                 curl /usr/local/lib/R/site-library
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+desc                                 desc /usr/local/lib/R/site-library
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+diptest                           diptest /usr/local/lib/R/site-library
+DNAcopy                           DNAcopy /usr/local/lib/R/site-library
+docopt                             docopt /usr/local/lib/R/site-library
+doParallel                     doParallel /usr/local/lib/R/site-library
+downlit                           downlit /usr/local/lib/R/site-library
+dowser                             dowser /usr/local/lib/R/site-library
+dplyr                               dplyr /usr/local/lib/R/site-library
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+generics                         generics /usr/local/lib/R/site-library
+GenomeInfoDb                 GenomeInfoDb /usr/local/lib/R/site-library
+GenomeInfoDbData         GenomeInfoDbData /usr/local/lib/R/site-library
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+GenomicRanges               GenomicRanges /usr/local/lib/R/site-library
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+ggplot2                           ggplot2 /usr/local/lib/R/site-library
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+gh                                     gh /usr/local/lib/R/site-library
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+jquerylib                       jquerylib /usr/local/lib/R/site-library
+jsonlite                         jsonlite /usr/local/lib/R/site-library
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+labeling                         labeling /usr/local/lib/R/site-library
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+later                               later /usr/local/lib/R/site-library
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+openssl                           openssl /usr/local/lib/R/site-library
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+class                  7.3-20 recommended
+cluster                 2.1.2 recommended
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+compiler                4.1.2        base
+datasets                4.1.2        base
+foreign                0.8-82 recommended
+graphics                4.1.2        base
+grDevices               4.1.2        base
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+lattice               0.20-45 recommended
+MASS                   7.3-55 recommended
+Matrix                  1.4-0 recommended
+methods                 4.1.2        base
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+nlme                  3.1-155 recommended
+nnet                   7.3-17 recommended
+parallel                4.1.2        base
+rpart                  4.1.16 recommended
+spatial                7.3-15 recommended
+splines                 4.1.2        base
+stats                   4.1.2        base
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+survival               3.2-13 recommended
+tcltk                   4.1.2        base
+tools                   4.1.2        base
+utils                   4.1.2        base
+
+
+
+
+================
+
+R PACKAGES NOT INSTALLED
+
+================
+
+
+
+
+SEE ALSO THE not_installed_r_packages.txt TABLE IN THE ROOT OF THE CONTAINER
+
+
+   Name
+1  Rccp
+2 tiger
+
+
+
+
+================
+
+apt-get autoremove
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 110 not upgraded.
+
+
+
+
+================
+
+apt-get clean
+
+================
+
+
+
+
+
+
+
+
+================
+
+rm
+
+================
+
+
+
+
+
+
+
+
+================
+
+LINUX PACKAGES INSTALLED
+
+================
+
+
+
+
+Package files:
+ 100 /var/lib/dpkg/status
+     release a=now
+Pinned packages:
diff --git a/R/v4.1.2/ig_clustering/v1.0/installed_r_packages.csv b/R/v4.1.2/ig_clustering/v1.0/installed_r_packages.csv
new file mode 100644
index 0000000000000000000000000000000000000000..bc1529a36188923649b59eed61026db51c86540d
--- /dev/null
+++ b/R/v4.1.2/ig_clustering/v1.0/installed_r_packages.csv
@@ -0,0 +1,241 @@
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+BiocParallel;/usr/local/lib/R/site-library;1.28.3;NA;methods, R (>= 3.5.0);stats, utils, futile.logger, parallel, snow;BH;BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,BiocStyle, knitr, batchtools, data.table;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
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+xfun;/usr/local/lib/R/site-library;0.33;NA;NA;stats, tools;NA;testit, parallel, codetools, rstudioapi, tinytex (>= 0.30),mime, markdown, knitr, htmltools, remotes, pak, rhub, renv,curl, jsonlite, magick, rmarkdown;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
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+zlibbioc;/usr/local/lib/R/site-library;1.40.0;NA;NA;NA;NA;NA;NA;Artistic-2.0 + file LICENSE;NA;NA;NA;NA;yes;4.1.2
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+base;/usr/lib/R/library;4.1.2;base;NA;NA;NA;methods;NA;Part of R 4.1.2;NA;NA;NA;NA;NA;4.1.2
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+class;/usr/lib/R/library;7.3-20;recommended;R (>= 3.0.0), stats, utils;MASS;NA;NA;NA;GPL-2 | GPL-3;NA;NA;NA;NA;yes;4.1.2
+cluster;/usr/lib/R/library;2.1.2;recommended;R (>= 3.4.0);graphics, grDevices, stats, utils;NA;MASS, Matrix;NA;GPL (>= 2);NA;NA;NA;NA;yes;4.0.5
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+compiler;/usr/lib/R/library;4.1.2;base;NA;NA;NA;NA;NA;Part of R 4.1.2;NA;NA;NA;NA;NA;4.1.2
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diff --git a/README.md b/README.md
index 39c9a9ec32db9f8fdd039a54388f2dcd49052bc0..8678850ab4fc1251684f7e2d6afaaeee3f76b630 100644
--- a/README.md
+++ b/README.md
@@ -71,7 +71,14 @@ Hub-CDB Institut Pasteur & DSI Institut Pasteur
 
 Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below
 
-### 9.1
+### 9.3
+
+Dockerfiles added: <br />
+R/v4.1.2/extended/v3.0 at date 20221108: from gmillot/r-base_v4.1.2:gitlab_v8.2 used as base for R/v4.1.2/ig_clustering
+R/v4.1.2/ig_clustering/v1.0 at date 20221108: from gmillot/r_v4.1.2_extended_v3.0:gitlab_v9.3 <br />
+
+
+### 9.2
 
 Dockerfiles added: <br />
 python/3.9.10/changeo_presto/v1.0 at date 20221007: from ubuntu:20.04 & python v3.9.10 <br />