diff --git a/R/v4.1.2/extended/v3.3/Dockerfile b/R/v4.1.2/extended/v3.3/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..3eb17c94e98de5dcafb9791e38a4950aea1e2b89
--- /dev/null
+++ b/R/v4.1.2/extended/v3.3/Dockerfile
@@ -0,0 +1,158 @@
+#########################################################################
+## ##
+## 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_v3.2:gitlab_v9.8
+# 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="\
+ 'lemon' \
+"
+
+
+# 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/v3.3/building.log b/R/v4.1.2/extended/v3.3/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..344777213373731b8378c0845dd5294f6e57ff4e
--- /dev/null
+++ b/R/v4.1.2/extended/v3.3/building.log
@@ -0,0 +1,689 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Hit:1 http://security.ubuntu.com/ubuntu focal-security InRelease
+Hit:2 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal 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...
+0 upgraded, 0 newly installed, 0 to remove and 162 not upgraded.
+
+
+
+
+================
+
+apt install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 162 not upgraded.
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 1 / 1: lemon
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/rlang_1.1.0.tar.gz'
+Content type 'application/x-gzip' length 761991 bytes (744 KB)
+==================================================
+downloaded 744 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/vctrs_0.6.1.tar.gz'
+Content type 'application/x-gzip' length 964734 bytes (942 KB)
+==================================================
+downloaded 942 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/ggplot2_3.4.1.tar.gz'
+Content type 'application/x-gzip' length 3150856 bytes (3.0 MB)
+==================================================
+downloaded 3.0 MB
+
+trying URL 'https://cran.irsn.fr/src/contrib/lemon_0.4.6.tar.gz'
+Content type 'application/x-gzip' length 2843925 bytes (2.7 MB)
+==================================================
+downloaded 2.7 MB
+
+
+The downloaded source packages are in
+ ‘/tmp/RtmpWMFqmq/downloaded_packages’
+
+
+STANDARD INSTALLATION ATTEMPT FOR lemon
+
+
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/lemon_0.4.6.tar.gz'
+Content type 'application/x-gzip' length 2843925 bytes (2.7 MB)
+==================================================
+downloaded 2.7 MB
+
+foundpkgs: lemon, /tmp/RtmpWMFqmq/downloaded_packages/lemon_0.4.6.tar.gz
+files: /tmp/RtmpWMFqmq/downloaded_packages/lemon_0.4.6.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmpWMFqmq/downloaded_packages/lemon_0.4.6.tar.gz''
+
+The downloaded source packages are in
+ ‘/tmp/RtmpWMFqmq/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
+ade4 ade4 /usr/local/lib/R/site-library
+airr airr /usr/local/lib/R/site-library
+alakazam alakazam /usr/local/lib/R/site-library
+ape ape /usr/local/lib/R/site-library
+aplot aplot /usr/local/lib/R/site-library
+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
+bit bit /usr/local/lib/R/site-library
+bit64 bit64 /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
+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
+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
+fastmatch fastmatch /usr/local/lib/R/site-library
+fontawesome fontawesome /usr/local/lib/R/site-library
+foreach foreach /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
+GenomicAlignments GenomicAlignments /usr/local/lib/R/site-library
+GenomicRanges GenomicRanges /usr/local/lib/R/site-library
+gert gert /usr/local/lib/R/site-library
+ggfun ggfun /usr/local/lib/R/site-library
+ggplot2 ggplot2 /usr/local/lib/R/site-library
+ggplotify ggplotify /usr/local/lib/R/site-library
+ggrepel ggrepel /usr/local/lib/R/site-library
+ggtree ggtree /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
+gridGraphics gridGraphics /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
+hms hms /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
+igraph igraph /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
+iterators iterators /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
+lazyeval lazyeval /usr/local/lib/R/site-library
+lemon lemon /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
+markdown markdown /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
+patchwork patchwork /usr/local/lib/R/site-library
+pdftools pdftools /usr/local/lib/R/site-library
+phangorn phangorn /usr/local/lib/R/site-library
+pheatmap pheatmap /usr/local/lib/R/site-library
+phylotate phylotate /usr/local/lib/R/site-library
+pillar pillar /usr/local/lib/R/site-library
+pinp pinp /usr/local/lib/R/site-library
+pixmap pixmap /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
+progress progress /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
+quadprog quadprog /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
+readr readr /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
+scoper scoper /usr/local/lib/R/site-library
+segmented segmented /usr/local/lib/R/site-library
+seqinr seqinr /usr/local/lib/R/site-library
+sessioninfo sessioninfo /usr/local/lib/R/site-library
+shazam shazam /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
+sp sp /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
+svglite svglite /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
+tidyr tidyr /usr/local/lib/R/site-library
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+
+
+
+
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+
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+
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+
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diff --git a/R/v4.1.2/extended/v3.3/installed_r_packages.csv b/R/v4.1.2/extended/v3.3/installed_r_packages.csv
new file mode 100644
index 0000000000000000000000000000000000000000..2b2c7b0705970079649c0986df06730a41be5aee
--- /dev/null
+++ b/R/v4.1.2/extended/v3.3/installed_r_packages.csv
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+sys;/usr/local/lib/R/site-library;3.4;NA;NA;NA;NA;unix (>= 1.4), spelling, testthat;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+systemfonts;/usr/local/lib/R/site-library;1.0.4;NA;R (>= 3.2.0);NA;cpp11 (>= 0.2.1);testthat (>= 2.1.0), covr, knitr, rmarkdown, tools;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+testthat;/usr/local/lib/R/site-library;3.1.5;NA;R (>= 3.1);brio, callr (>= 3.5.1), cli (>= 3.4.0), desc, digest, ellipsis(>= 0.2.0), evaluate, jsonlite, lifecycle, magrittr, methods,pkgload, praise, processx, ps (>= 1.3.4), R6 (>= 2.2.0), rlang(>= 1.0.1), utils, waldo (>= 0.4.0), withr (>= 2.4.3);NA;covr, curl (>= 0.9.5), diffviewer (>= 0.1.0), knitr, mockery,rmarkdown, rstudioapi, shiny, usethis, vctrs (>= 0.1.0), xml2;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+tibble;/usr/local/lib/R/site-library;3.1.8;NA;R (>= 3.1.0);fansi (>= 0.4.0), lifecycle (>= 1.0.0), magrittr, methods,pillar (>= 1.7.0), pkgconfig, rlang (>= 1.0.2), utils, vctrs(>= 0.3.8);NA;bench, bit64, blob, brio, callr, cli, covr, crayon (>=1.3.4), DiagrammeR, dplyr, evaluate, formattable, ggplot2, hms,htmltools, knitr, lubridate, mockr, nycflights13, pkgbuild,pkgload, purrr, rmarkdown, stringi, testthat (>= 3.0.2), tidyr,withr;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+tidyr;/usr/local/lib/R/site-library;1.2.1;NA;R (>= 3.1);dplyr (>= 1.0.0), ellipsis (>= 0.1.0), glue, lifecycle,magrittr, purrr, rlang, tibble (>= 2.1.1), tidyselect (>=1.1.0), utils, vctrs (>= 0.3.7);cpp11 (>= 0.4.0);covr, data.table, jsonlite, knitr, readr, repurrrsive (>=1.0.0), rmarkdown, testthat (>= 3.0.0);NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+tidyselect;/usr/local/lib/R/site-library;1.2.0;NA;R (>= 3.4);cli (>= 3.3.0), glue (>= 1.3.0), lifecycle (>= 1.0.3), rlang(>= 1.0.4), vctrs (>= 0.4.1), withr;NA;covr, crayon, dplyr, knitr, magrittr, rmarkdown, stringr,testthat (>= 3.1.1), tibble (>= 2.1.3);NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+tidytree;/usr/local/lib/R/site-library;0.4.1;NA;R (>= 3.4.0);ape, dplyr, lazyeval, magrittr, methods, rlang, tibble, tidyr,tidyselect, yulab.utils (>= 0.0.4), pillar;NA;knitr, rmarkdown, prettydoc, testthat, utils;NA;Artistic-2.0;NA;NA;NA;NA;no;4.1.2
+tint;/usr/local/lib/R/site-library;0.1.3;NA;NA;htmltools, knitr, rmarkdown;NA;ggplot2;NA;GPL-3;NA;NA;NA;NA;no;4.1.2
+tinytex;/usr/local/lib/R/site-library;0.42;NA;NA;xfun (>= 0.29);NA;testit, rstudioapi;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+treeio;/usr/local/lib/R/site-library;1.18.1;NA;R (>= 3.6.0);ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,tidytree (>= 0.3.0), utils;NA;Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown,phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml;NA;Artistic-2.0;NA;NA;NA;NA;no;4.1.2
+tzdb;/usr/local/lib/R/site-library;0.3.0;NA;R (>= 3.4.0);NA;cpp11 (>= 0.4.2);covr, testthat (>= 3.0.0);NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+urlchecker;/usr/local/lib/R/site-library;1.0.1;NA;R (>= 3.3);cli, curl, tools, xml2;NA;covr;NA;GPL-3;NA;NA;NA;NA;no;4.1.2
+usethis;/usr/local/lib/R/site-library;2.1.6;NA;R (>= 3.4);cli (>= 3.0.1), clipr (>= 0.3.0), crayon, curl (>= 2.7), desc(>= 1.4.0), fs (>= 1.3.0), gert (>= 1.4.1), gh (>= 1.2.1), glue(>= 1.3.0), jsonlite, lifecycle (>= 1.0.0), purrr, rappdirs,rlang (>= 1.0.0), rprojroot (>= 1.2), rstudioapi, stats, utils,whisker, withr (>= 2.3.0), yaml;NA;covr, knitr, magick, mockr, pkgload, rmarkdown, roxygen2 (>=7.1.2), spelling (>= 1.2), styler (>= 1.2.0), testthat (>=3.1.0);NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+utf8;/usr/local/lib/R/site-library;1.2.2;NA;R (>= 2.10);NA;NA;cli, covr, knitr, rlang, rmarkdown, testthat (>= 3.0.0),withr;NA;Apache License (== 2.0) | file LICENSE;NA;NA;NA;NA;yes;4.1.2
+vctrs;/usr/local/lib/R/site-library;0.6.1;NA;R (>= 3.5.0);cli (>= 3.4.0), glue, lifecycle (>= 1.0.3), rlang (>= 1.1.0);NA;bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr,pillar (>= 1.4.4), pkgdown (>= 2.0.1), rmarkdown, testthat (>=3.0.0), tibble (>= 3.1.3), waldo (>= 0.2.0), withr, xml2,zeallot;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+viridisLite;/usr/local/lib/R/site-library;0.4.1;NA;R (>= 2.10);NA;NA;hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+vroom;/usr/local/lib/R/site-library;1.6.0;NA;R (>= 3.4);bit64, cli (>= 3.2.0), crayon, glue, hms, lifecycle, methods,rlang (>= 0.4.2), stats, tibble (>= 2.0.0), tidyselect, tzdb(>= 0.1.1), vctrs (>= 0.2.0), withr;cpp11 (>= 0.2.0), progress (>= 1.2.1), tzdb (>= 0.1.1);archive, bench (>= 1.1.0), covr, curl, dplyr, forcats, fs,ggplot2, knitr, patchwork, prettyunits, purrr, rmarkdown,rstudioapi, scales, spelling, testthat (>= 2.1.0), tidyr,utils, waldo, xml2;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+waldo;/usr/local/lib/R/site-library;0.4.0;NA;NA;cli, diffobj (>= 0.3.4), fansi, glue, methods, rematch2, rlang(>= 1.0.0), tibble;NA;covr, R6, testthat (>= 3.0.0), withr, xml2;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+whisker;/usr/local/lib/R/site-library;0.4;NA;NA;NA;NA;markdown;NA;GPL-3;NA;NA;NA;NA;no;4.1.2
+withr;/usr/local/lib/R/site-library;2.5.0;NA;R (>= 3.2.0);graphics, grDevices, stats;NA;callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown(>= 2.12), RSQLite, testthat (>= 3.0.0);NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+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
+xml2;/usr/local/lib/R/site-library;1.3.3;NA;R (>= 3.1.0);methods;NA;covr, curl, httr, knitr, magrittr, mockery, rmarkdown,testthat (>= 2.1.0);NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+xopen;/usr/local/lib/R/site-library;1.0.0;NA;R (>= 3.1);processx;NA;ps, testthat;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.1.2
+xtable;/usr/local/lib/R/site-library;1.8-4;NA;R (>= 2.10.0);stats, utils;NA;knitr, plm, zoo, survival;NA;GPL (>= 2);NA;NA;NA;NA;no;4.1.2
+XVector;/usr/local/lib/R/site-library;0.34.0;NA;R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=0.27.12), IRanges (>= 2.23.9);methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors,IRanges;S4Vectors, IRanges;Biostrings, drosophila2probe, RUnit;NA;Artistic-2.0;NA;NA;NA;NA;yes;4.1.2
+yaml;/usr/local/lib/R/site-library;2.3.5;NA;NA;NA;NA;RUnit;NA;BSD_3_clause + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+yulab.utils;/usr/local/lib/R/site-library;0.0.5;NA;NA;utils;NA;NA;NA;Artistic-2.0;NA;NA;NA;NA;no;4.1.2
+zip;/usr/local/lib/R/site-library;2.2.1;NA;NA;NA;NA;covr, processx, R6, testthat, withr;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.1.2
+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
+littler;/usr/lib/R/site-library;0.3.15;NA;NA;NA;NA;simplermarkdown, docopt, rcmdcheck, foghorn;NA;GPL (>= 2);NA;NA;unix;NA;yes;4.1.2
+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/v1.3/Dockerfile b/R/v4.1.2/ig_clustering/v1.3/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..96dcef2da8208c0f63339e42c52a914b6e39d637
--- /dev/null
+++ b/R/v4.1.2/ig_clustering/v1.3/Dockerfile
@@ -0,0 +1,158 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## R ig_clustering ##
+## ##
+## 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_ig_clustering_v1.2:gitlab_v9.8
+# 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="\
+ 'lemon' \
+"
+
+
+# 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/v1.3/building.log b/R/v4.1.2/ig_clustering/v1.3/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..ae9b201bf3ca79f36f1766fa77babd7bdd9b0ca5
--- /dev/null
+++ b/R/v4.1.2/ig_clustering/v1.3/building.log
@@ -0,0 +1,689 @@
+
+
+
+
+================
+
+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 162 not upgraded.
+
+
+
+
+================
+
+apt install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 162 not upgraded.
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 1 / 1: lemon
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/rlang_1.1.0.tar.gz'
+Content type 'application/x-gzip' length 761991 bytes (744 KB)
+==================================================
+downloaded 744 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/vctrs_0.6.1.tar.gz'
+Content type 'application/x-gzip' length 964734 bytes (942 KB)
+==================================================
+downloaded 942 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/ggplot2_3.4.1.tar.gz'
+Content type 'application/x-gzip' length 3150856 bytes (3.0 MB)
+==================================================
+downloaded 3.0 MB
+
+trying URL 'https://cran.irsn.fr/src/contrib/lemon_0.4.6.tar.gz'
+Content type 'application/x-gzip' length 2843925 bytes (2.7 MB)
+==================================================
+downloaded 2.7 MB
+
+
+The downloaded source packages are in
+ ‘/tmp/RtmphyDX7o/downloaded_packages’
+
+
+STANDARD INSTALLATION ATTEMPT FOR lemon
+
+
+system (cmd0): /usr/lib/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/lemon_0.4.6.tar.gz'
+Content type 'application/x-gzip' length 2843925 bytes (2.7 MB)
+==================================================
+downloaded 2.7 MB
+
+foundpkgs: lemon, /tmp/RtmphyDX7o/downloaded_packages/lemon_0.4.6.tar.gz
+files: /tmp/RtmphyDX7o/downloaded_packages/lemon_0.4.6.tar.gz
+1): succeeded '/usr/lib/R/bin/R CMD INSTALL -l '/usr/local/lib/R/site-library' '/tmp/RtmphyDX7o/downloaded_packages/lemon_0.4.6.tar.gz''
+
+The downloaded source packages are in
+ ‘/tmp/RtmphyDX7o/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
+ade4 ade4 /usr/local/lib/R/site-library
+airr airr /usr/local/lib/R/site-library
+alakazam alakazam /usr/local/lib/R/site-library
+ape ape /usr/local/lib/R/site-library
+aplot aplot /usr/local/lib/R/site-library
+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
+bit bit /usr/local/lib/R/site-library
+bit64 bit64 /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
+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
+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
+fastmatch fastmatch /usr/local/lib/R/site-library
+fontawesome fontawesome /usr/local/lib/R/site-library
+foreach foreach /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
+GenomicAlignments GenomicAlignments /usr/local/lib/R/site-library
+GenomicRanges GenomicRanges /usr/local/lib/R/site-library
+gert gert /usr/local/lib/R/site-library
+ggfun ggfun /usr/local/lib/R/site-library
+ggplot2 ggplot2 /usr/local/lib/R/site-library
+ggplotify ggplotify /usr/local/lib/R/site-library
+ggrepel ggrepel /usr/local/lib/R/site-library
+ggtree ggtree /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
+gridGraphics gridGraphics /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
+hms hms /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
+igraph igraph /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
+iterators iterators /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
+lazyeval lazyeval /usr/local/lib/R/site-library
+lemon lemon /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
+markdown markdown /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
+patchwork patchwork /usr/local/lib/R/site-library
+pdftools pdftools /usr/local/lib/R/site-library
+phangorn phangorn /usr/local/lib/R/site-library
+pheatmap pheatmap /usr/local/lib/R/site-library
+phylotate phylotate /usr/local/lib/R/site-library
+pillar pillar /usr/local/lib/R/site-library
+pinp pinp /usr/local/lib/R/site-library
+pixmap pixmap /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
+progress progress /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
+quadprog quadprog /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
+readr readr /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
+scoper scoper /usr/local/lib/R/site-library
+segmented segmented /usr/local/lib/R/site-library
+seqinr seqinr /usr/local/lib/R/site-library
+sessioninfo sessioninfo /usr/local/lib/R/site-library
+shazam shazam /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
+sp sp /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
+svglite svglite /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
+tidyr tidyr /usr/local/lib/R/site-library
+tidyselect tidyselect /usr/local/lib/R/site-library
+tidytree tidytree /usr/local/lib/R/site-library
+tint tint /usr/local/lib/R/site-library
+tinytex tinytex /usr/local/lib/R/site-library
+treeio treeio /usr/local/lib/R/site-library
+tzdb tzdb /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
+vroom vroom /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
+yulab.utils yulab.utils /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
+ade4 1.7-19 <NA>
+airr 1.4.1 <NA>
+alakazam 1.2.1 <NA>
+ape 5.6-2 <NA>
+aplot 0.1.8 <NA>
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+bit 4.0.4 <NA>
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+bitops 1.0-7 <NA>
+brew 1.0-8 <NA>
+brio 1.1.3 <NA>
+bslib 0.4.0 <NA>
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+Cairo 1.6-0 <NA>
+calibrate 1.7.7 <NA>
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+CGHbase 1.54.0 <NA>
+CGHcall 2.56.0 <NA>
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+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>
+curl 4.3.3 <NA>
+data.table 1.14.2 <NA>
+DelayedArray 0.20.0 <NA>
+desc 1.4.2 <NA>
+diffobj 0.3.5 <NA>
+digest 0.6.29 <NA>
+diptest 0.76-0 <NA>
+DNAcopy 1.68.0 <NA>
+docopt 0.7.1 <NA>
+doParallel 1.0.17 <NA>
+downlit 0.4.2 <NA>
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+ellipsis 0.3.2 <NA>
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+farver 2.1.1 <NA>
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+fs 1.5.2 <NA>
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+future.apply 1.9.1 <NA>
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+GenomeInfoDb 1.30.1 <NA>
+GenomeInfoDbData 1.2.7 <NA>
+GenomicAlignments 1.30.0 <NA>
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+ggplot2 3.4.1 <NA>
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+ggtree 3.2.1 <NA>
+gh 1.3.1 <NA>
+gitcreds 0.1.2 <NA>
+globals 0.16.1 <NA>
+glue 1.6.2 <NA>
+gridExtra 2.3 <NA>
+gridGraphics 0.5-1 <NA>
+gtable 0.3.1 <NA>
+gtools 3.9.3 <NA>
+HiCcompare 1.16.0 <NA>
+highr 0.9 <NA>
+hms 1.1.2 <NA>
+htmltools 0.5.3 <NA>
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+httpuv 1.6.6 <NA>
+httr 1.4.4 <NA>
+igraph 1.3.5 <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>
+iterators 1.0.14 <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>
+lazyeval 0.2.2 <NA>
+lemon 0.4.6 <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>
+markdown 1.1 <NA>
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+
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diff --git a/R/v4.1.2/ig_clustering/v1.3/installed_r_packages.csv b/R/v4.1.2/ig_clustering/v1.3/installed_r_packages.csv
new file mode 100644
index 0000000000000000000000000000000000000000..2b2c7b0705970079649c0986df06730a41be5aee
--- /dev/null
+++ b/R/v4.1.2/ig_clustering/v1.3/installed_r_packages.csv
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+XVector;/usr/local/lib/R/site-library;0.34.0;NA;R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=0.27.12), IRanges (>= 2.23.9);methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors,IRanges;S4Vectors, IRanges;Biostrings, drosophila2probe, RUnit;NA;Artistic-2.0;NA;NA;NA;NA;yes;4.1.2
+yaml;/usr/local/lib/R/site-library;2.3.5;NA;NA;NA;NA;RUnit;NA;BSD_3_clause + file LICENSE;NA;NA;NA;NA;yes;4.1.2
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+zip;/usr/local/lib/R/site-library;2.2.1;NA;NA;NA;NA;covr, processx, R6, testthat, withr;NA;MIT + 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
+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
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diff --git a/README.md b/README.md
index a0253055fb4b9553c54509a85919bddb24908cb4..f1bd777faec8cb916425ab67e79ca90b2c652b97 100644
--- a/README.md
+++ b/README.md
@@ -72,6 +72,13 @@ 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
+### 9.9
+
+Dockerfiles modified: <br />
+R/v4.1.2/extended/v3.3 at date 20230331: from gmillot/r_v4.1.2_extended_v3.2:gitlab_v9.8 with lemon added<br />
+R/v4.1.2/ig_clustering/v1.3 at date 20230331: from gmillot/r_v4.1.2_ig_clustering_v1.2:gitlab_v9.8 with lemon added<br />
+
+
### 9.8
Dockerfiles modified: <br />