diff --git a/README.md b/README.md
index d78d7ca58564943684992536d4cb8048b30f5db9..4cb28f903bd69e75632126388a53db84e9f237de 100644
--- a/README.md
+++ b/README.md
@@ -72,6 +72,12 @@ 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
+### 10.1
+
+Dockerfiles modified: <br />
+fedora\v33\immcantation\v1.2 at date 20230407: from gmillot/immcantation_v1.1:gitlab_v10.0 with lubridate added<br />
+
+
### 10.0
Dockerfiles modified: <br />
diff --git a/fedora/v33/immcantation/v1.1/Dockerfile b/fedora/v33/immcantation/v1.1/Dockerfile
index 5cf64c782c48f538f743d4389de5acea1a49fe0a..48c304a1c5b5440864add34d98ad5c5535ba7895 100644
--- a/fedora/v33/immcantation/v1.1/Dockerfile
+++ b/fedora/v33/immcantation/v1.1/Dockerfile
@@ -46,7 +46,8 @@ ENV RLIB="\
# 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 RLIB_LENGTH=0 \
+RUN echo "" > building.log \
+ && RLIB_LENGTH=0 \
&& for i2 in $RLIB ; do RLIB_LENGTH=$((RLIB_LENGTH+1)) ; done \
&& COUNT=0 \
&& for i2 in $RLIB ; do \
diff --git a/fedora/v33/immcantation/v1.2/Dockerfile b/fedora/v33/immcantation/v1.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..b94800254a24d69fa693aae1c9214c08260cfb64
--- /dev/null
+++ b/fedora/v33/immcantation/v1.2/Dockerfile
@@ -0,0 +1,142 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## fedora base ##
+## ##
+## Gael A. Millot ##
+## Bioinformatics and Biostatistics Hub ##
+## 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>
+
+# see https://immcantation.readthedocs.io/en/stable/docker/intro.html
+FROM gmillot/immcantation_v1.1:gitlab_v10.0
+
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+
+ENV CRANREPO="'https://cran.irsn.fr/'"
+
+ENV BIOCONDUCTOR_REPO="'https://cloud.r-project.org'"
+
+ENV RLIB="\
+ 'lubridate' \
+"
+
+
+# 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 "" > 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, 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, 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, dependencies = NA, verbose = TRUE, update = FALSE, site_repository = $BIOCONDUCTOR_REPO) \
+ } \
+ }else if($i2 == 'ggplot2'){ \
+ devtools::install_version(package = 'ggplot2', version = '3.3.3', dependencies = NA, verbose = TRUE, repos = $CRANREPO) \
+ }else if($i2 == 'SARTools'){ \
+ devtools::install_github('PF2-pasteur-fr/SARTools', build_opts='--no-resave-data', dependencies = NA, verbose = TRUE, upgrade = "always") \
+ } \
+ " | tee -a building.log ; \
+ 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") | tee -a building.log
+
+# dependencies=NA means c("Depends", "Imports", "LinkingTo"). Do no use TRUE -> install suggesting packages which inflates tremendously the image.
+
+ENTRYPOINT ["/bin/bash"]
+
+
+
diff --git a/fedora/v33/immcantation/v1.2/building.log b/fedora/v33/immcantation/v1.2/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..a1437e95d4d29fac0836b5af2c04f274e3c65da3
--- /dev/null
+++ b/fedora/v33/immcantation/v1.2/building.log
@@ -0,0 +1,716 @@
+
+
+
+
+
+================
+
+R PACKAGE INSTALLATION 1 / 1: lubridate
+
+================
+
+
+
+
+trying URL 'https://cran.irsn.fr/src/contrib/timechange_0.2.0.tar.gz'
+Content type 'application/x-gzip' length 102806 bytes (100 KB)
+==================================================
+downloaded 100 KB
+
+trying URL 'https://cran.irsn.fr/src/contrib/lubridate_1.9.2.tar.gz'
+Content type 'application/x-gzip' length 427200 bytes (417 KB)
+==================================================
+downloaded 417 KB
+
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c common.cpp -o common.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cpp11.cpp -o cpp11.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c get.cpp -o get.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c parse.c -o parse.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c round.cpp -o round.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tzone.cpp -o tzone.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c update.cpp -o update.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_info.cc -o cctz/src/time_zone_info.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_libc.cc -o cctz/src/time_zone_libc.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_lookup.cc -o cctz/src/time_zone_lookup.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/time_zone_posix.cc -o cctz/src/time_zone_posix.o
+g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I./cctz/src/ -I'/usr/lib64/R/library/cpp11/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cctz/src/zone_info_source.cc -o cctz/src/zone_info_source.o
+ar rcs libcctz.a ./cctz/src/time_zone_fixed.o ./cctz/src/time_zone_if.o ./cctz/src/time_zone_impl.o ./cctz/src/time_zone_info.o ./cctz/src/time_zone_libc.o ./cctz/src/time_zone_lookup.o ./cctz/src/time_zone_posix.o ./cctz/src/zone_info_source.o
+g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o timechange.so common.o cpp11.o get.o parse.o round.o tzone.o update.o -L. -lcctz -L/usr/lib64/R/lib -lR
+ converting help for package 'timechange'
+ time-zones html
+ time_add html
+ time_get html
+ time_round html
+ time_update html
+ timechange-package html
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c datetime.c -o datetime.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c init.c -o init.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c period.c -o period.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tparse.c -o tparse.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils.c -o utils.o
+gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o lubridate.so datetime.o init.o period.o tparse.o utils.o -L/usr/lib64/R/lib -lR
+ converting help for package 'lubridate'
+ DateCoercion html
+ DateTimeUpdate html
+ Deprecated html
+ Duration-class html
+ Interval-class html
+ Period-class html
+ Timespan-class html
+ am html
+ as.duration html
+ as.interval html
+ as.period html
+ as_date html
+ cyclic_encoding html
+ date html
+ date_decimal html
+ date_utils html
+ day html
+ days_in_month html
+ decimal_date html
+ dst html
+ duration html
+ fit_to_timeline html
+ force_tz html
+ format_ISO8601 html
+ format_ISO8601_precision_check html
+ guess_formats html
+ hidden_aliases html
+ hms html
+ hour html
+ interval html
+ is.difftime html
+ is.instant html
+ is.timespan html
+ lakers html
+ leap_year html
+ local_time html
+ lubridate-package html
+ make_datetime html
+ make_difftime html
+ minute html
+ month html
+ mplus html
+ now html
+ origin html
+ parse_date_time html
+ period html
+ period_to_seconds html
+ posix_utils html
+ pretty_dates html
+ quarter html
+ reclass_date html
+ reclass_timespan html
+ reexports html
+ rollbackward html
+ round_date html
+ second html
+ stamp html
+ time_length html
+ timespan html
+ tz html
+ week html
+ with_tz html
+ within-interval html
+ year html
+ ymd html
+ ymd_hms html
+[0;1;31mSystem has not been booted with systemd as init system (PID 1). Can't operate.[0m
+[0;1;31mFailed to connect to bus: Host is down[0m
+Warning in system("timedatectl", intern = TRUE) :
+ running command 'timedatectl' had status 1
+[0;1;31mSystem has not been booted with systemd as init system (PID 1). Can't operate.[0m
+[0;1;31mFailed to connect to bus: Host is down[0m
+Warning in system("timedatectl", intern = TRUE) :
+ running command 'timedatectl' had status 1
+
+The downloaded source packages are in
+ '/tmp/RtmpeNvY8J/downloaded_packages'
+
+
+STANDARD INSTALLATION ATTEMPT FOR lubridate
+
+
+
+
+
+STANDARD INSTALLATION ATTEMPT FOR lubridate
+
+
+Installing package into '/usr/lib64/R/library'
+(as 'lib' is unspecified)
+system (cmd0): /usr/lib64/R/bin/R CMD INSTALL
+trying URL 'https://cran.irsn.fr/src/contrib/lubridate_1.9.2.tar.gz'
+Content type 'application/x-gzip' length 427200 bytes (417 KB)
+==================================================
+downloaded 417 KB
+
+foundpkgs: lubridate, /tmp/RtmpeNvY8J/downloaded_packages/lubridate_1.9.2.tar.gz
+files: /tmp/RtmpeNvY8J/downloaded_packages/lubridate_1.9.2.tar.gz
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c datetime.c -o datetime.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c init.c -o init.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c period.c -o period.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tparse.c -o tparse.o
+gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils.c -o utils.o
+gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o lubridate.so datetime.o init.o period.o tparse.o utils.o -L/usr/lib64/R/lib -lR
+ converting help for package 'lubridate'
+ DateCoercion html
+ DateTimeUpdate html
+ Deprecated html
+ Duration-class html
+ Interval-class html
+ Period-class html
+ Timespan-class html
+ am html
+ as.duration html
+ as.interval html
+ as.period html
+ as_date html
+ cyclic_encoding html
+ date html
+ date_decimal html
+ date_utils html
+ day html
+ days_in_month html
+ decimal_date html
+ dst html
+ duration html
+ fit_to_timeline html
+ force_tz html
+ format_ISO8601 html
+ format_ISO8601_precision_check html
+ guess_formats html
+ hidden_aliases html
+ hms html
+ hour html
+ interval html
+ is.difftime html
+ is.instant html
+ is.timespan html
+ lakers html
+ leap_year html
+ local_time html
+ lubridate-package html
+ make_datetime html
+ make_difftime html
+ minute html
+ month html
+ mplus html
+ now html
+ origin html
+ parse_date_time html
+ period html
+ period_to_seconds html
+ posix_utils html
+ pretty_dates html
+ quarter html
+ reclass_date html
+ reclass_timespan html
+ reexports html
+ rollbackward html
+ round_date html
+ second html
+ stamp html
+ time_length html
+ timespan html
+ tz html
+ week html
+ with_tz html
+ within-interval html
+ year html
+ ymd html
+ ymd_hms html
+[0;1;31mSystem has not been booted with systemd as init system (PID 1). Can't operate.[0m
+[0;1;31mFailed to connect to bus: Host is down[0m
+Warning in system("timedatectl", intern = TRUE) :
+ running command 'timedatectl' had status 1
+[0;1;31mSystem has not been booted with systemd as init system (PID 1). Can't operate.[0m
+[0;1;31mFailed to connect to bus: Host is down[0m
+Warning in system("timedatectl", intern = TRUE) :
+ running command 'timedatectl' had status 1
+1): succeeded '/usr/lib64/R/bin/R CMD INSTALL -l '/usr/lib64/R/library' '/tmp/RtmpeNvY8J/downloaded_packages/lubridate_1.9.2.tar.gz''
+
+The downloaded source packages are in
+ '/tmp/RtmpeNvY8J/downloaded_packages'
+Updating HTML index of packages in '.Library'
+Making 'packages.html' ... done
+[1] TRUE
+
+
+
+
+================
+
+R PACKAGES INSTALLED
+
+================
+
+
+
+
+SEE ALSO THE installed_r_packages.csv TABLE IN THE ROOT OF THE CONTAINER
+
+
+now dyn.load("/usr/lib64/R/library/tools/libs/tools.so") ...
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+zip zip /usr/lib64/R/library 2.2.0
+zlibbioc zlibbioc /usr/lib64/R/library 1.36.0
+ Priority
+BH <NA>
+Biobase <NA>
+BiocGenerics <NA>
+BiocManager <NA>
+BiocParallel <NA>
+BiocVersion <NA>
+Biostrings <NA>
+DelayedArray <NA>
+GenomeInfoDb <NA>
+GenomeInfoDbData <NA>
+GenomicAlignments <NA>
+GenomicRanges <NA>
+IRanges <NA>
+KernSmooth recommended
+MASS recommended
+Matrix recommended
+MatrixGenerics <NA>
+R6 <NA>
+RColorBrewer <NA>
+RCurl <NA>
+Rcpp <NA>
+Rhtslib <NA>
+Rsamtools <NA>
+S4Vectors <NA>
+SummarizedExperiment <NA>
+XVector <NA>
+ade4 <NA>
+airr <NA>
+alakazam <NA>
+ape <NA>
+aplot <NA>
+askpass <NA>
+base base
+base64enc <NA>
+beanplot <NA>
+bibtex <NA>
+bit <NA>
+bit64 <NA>
+bitops <NA>
+boot recommended
+brew <NA>
+brio <NA>
+caTools <NA>
+cachem <NA>
+callr <NA>
+captioner <NA>
+class recommended
+cli <NA>
+clipr <NA>
+cluster recommended
+codetools recommended
+colorspace <NA>
+commonmark <NA>
+compiler base
+cowplot <NA>
+cpp11 <NA>
+crayon <NA>
+credentials <NA>
+crosstalk <NA>
+curl <NA>
+data.table <NA>
+datasets base
+dendextend <NA>
+desc <NA>
+devtools <NA>
+diffobj <NA>
+digest <NA>
+diptest <NA>
+doParallel <NA>
+dowser <NA>
+dplyr <NA>
+ellipsis <NA>
+evaluate <NA>
+fansi <NA>
+farver <NA>
+fastmap <NA>
+fastmatch <NA>
+foreach <NA>
+foreign recommended
+formatR <NA>
+fs <NA>
+futile.logger <NA>
+futile.options <NA>
+generics <NA>
+gert <NA>
+getopt <NA>
+ggdendro <NA>
+ggfun <NA>
+ggplot2 <NA>
+ggplotify <NA>
+ggtree <NA>
+gh <NA>
+gitcreds <NA>
+glue <NA>
+gplots <NA>
+grDevices base
+graphics base
+grid base
+gridExtra <NA>
+gridGraphics <NA>
+gtable <NA>
+gtools <NA>
+hexbin <NA>
+highr <NA>
+hms <NA>
+htmltools <NA>
+htmlwidgets <NA>
+httr <NA>
+igraph <NA>
+ini <NA>
+isoband <NA>
+iterators <NA>
+jquerylib <NA>
+jsonlite <NA>
+kedd <NA>
+knitr <NA>
+labeling <NA>
+lambda.r <NA>
+later <NA>
+lattice recommended
+lazyeval <NA>
+lifecycle <NA>
+lubridate <NA>
+magrittr <NA>
+markdown <NA>
+matrixStats <NA>
+memoise <NA>
+methods base
+mgcv recommended
+mime <NA>
+munsell <NA>
+nlme recommended
+nnet recommended
+openssl <NA>
+optparse <NA>
+parallel base
+patchwork <NA>
+pdist <NA>
+phangorn <NA>
+phylotate <NA>
+pillar <NA>
+pixmap <NA>
+pkgbuild <NA>
+pkgconfig <NA>
+pkgload <NA>
+plotly <NA>
+plyr <NA>
+praise <NA>
+prestor <NA>
+prettyunits <NA>
+processx <NA>
+progress <NA>
+promises <NA>
+ps <NA>
+purrr <NA>
+quadprog <NA>
+rabhit <NA>
+rappdirs <NA>
+rcmdcheck <NA>
+rdi <NA>
+readr <NA>
+rematch2 <NA>
+remotes <NA>
+reshape2 <NA>
+rlang <NA>
+rmarkdown <NA>
+roxygen2 <NA>
+rpart recommended
+rprojroot <NA>
+rstudioapi <NA>
+rvcheck <NA>
+rversions <NA>
+scales <NA>
+scoper <NA>
+segmented <NA>
+seqinr <NA>
+sessioninfo <NA>
+shazam <NA>
+snow <NA>
+sp <NA>
+spatial recommended
+splines base
+splitstackshape <NA>
+stats base
+stats4 base
+stringi <NA>
+stringr <NA>
+survival recommended
+svglite <NA>
+sys <NA>
+systemfonts <NA>
+tcltk base
+testthat <NA>
+tibble <NA>
+tidyr <NA>
+tidyselect <NA>
+tidytree <NA>
+tigger <NA>
+timechange <NA>
+tinytex <NA>
+tools base
+treeio <NA>
+tzdb <NA>
+usethis <NA>
+utf8 <NA>
+utils base
+vctrs <NA>
+viridis <NA>
+viridisLite <NA>
+vroom <NA>
+waldo <NA>
+whisker <NA>
+withr <NA>
+xfun <NA>
+xml2 <NA>
+xopen <NA>
+yaml <NA>
+yulab.utils <NA>
+zip <NA>
+zlibbioc <NA>
+
+
+
+
+================
+
+R PACKAGES NOT INSTALLED
+
+================
+
+
+
+
+ALL THE PACKAGES HAVE BEEN INSTALLED
+
+
diff --git a/fedora/v33/immcantation/v1.2/installed_r_packages.csv b/fedora/v33/immcantation/v1.2/installed_r_packages.csv
new file mode 100644
index 0000000000000000000000000000000000000000..2737e62c9c86f140cc459d48864f12293838a249
--- /dev/null
+++ b/fedora/v33/immcantation/v1.2/installed_r_packages.csv
@@ -0,0 +1,221 @@
+Package;LibPath;Version;Priority;Depends;Imports;LinkingTo;Suggests;Enhances;License;License_is_FOSS;License_restricts_use;OS_type;MD5sum;NeedsCompilation;Built
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+BiocGenerics;/usr/lib64/R/library;0.36.1;NA;R (>= 4.0.0), methods, utils, graphics, stats, parallel;methods, utils, graphics, stats, parallel;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;4.0.5
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+BiocParallel;/usr/lib64/R/library;1.24.1;NA;methods;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;4.0.5
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+GenomeInfoDbData;/usr/lib64/R/library;1.2.4;NA;R (>= 3.5.0);NA;NA;NA;NA;Artistic-2.0;NA;NA;NA;NA;no;4.0.5
+GenomicAlignments;/usr/lib64/R/library;1.26.0;NA;R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1),GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.9.13),Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2);methods, utils, stats, BiocGenerics, S4Vectors, IRanges,GenomicRanges, Biostrings, Rsamtools, BiocParallel;S4Vectors, IRanges;ShortRead, rtracklayer, BSgenome, GenomicFeatures,RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Dmelanogaster.UCSC.dm3.ensGene,BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19,DESeq2, edgeR, RUnit, BiocStyle;NA;Artistic-2.0;NA;NA;NA;NA;yes;4.0.5
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+IRanges;/usr/lib64/R/library;2.24.1;NA;R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.36.0),S4Vectors (>= 0.27.12);stats4;S4Vectors;XVector, GenomicRanges, Rsamtools, GenomicAlignments,GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,RUnit, BiocStyle;NA;Artistic-2.0;NA;NA;NA;NA;yes;4.0.5
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+Matrix;/usr/lib64/R/library;1.3-2;recommended;R (>= 3.6.0);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;4.0.5
+MatrixGenerics;/usr/lib64/R/library;1.2.1;NA;matrixStats (> 0.57.0);methods;NA;sparseMatrixStats, DelayedMatrixStats, SummarizedExperiment,testthat (>= 2.1.0);NA;Artistic-2.0;NA;NA;NA;NA;no;4.0.5
+R6;/usr/lib64/R/library;2.5.1;NA;R (>= 3.0);NA;NA;testthat, pryr;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.0.5
+RColorBrewer;/usr/lib64/R/library;1.1-2;NA;R (>= 2.0.0);NA;NA;NA;NA;Apache License 2.0;NA;NA;NA;NA;no;4.0.5
+RCurl;/usr/lib64/R/library;1.98-1.5;NA;R (>= 3.4.0), methods;bitops;NA;XML;NA;BSD_3_clause + file LICENSE;NA;NA;NA;NA;yes;4.0.5
+Rcpp;/usr/lib64/R/library;1.0.7;NA;NA;methods, utils;NA;tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2);NA;GPL (>= 2);NA;NA;NA;NA;yes;4.0.5
+Rhtslib;/usr/lib64/R/library;1.22.0;NA;NA;zlibbioc;zlibbioc;BiocStyle, knitr;NA;LGPL (>= 2);NA;NA;NA;NA;yes;4.0.5
+Rsamtools;/usr/lib64/R/library;2.6.0;NA;methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8),Biostrings (>= 2.47.6);utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops,BiocParallel, stats;Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings;GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle;NA;Artistic-2.0 | file LICENSE;NA;NA;NA;NA;yes;4.0.5
+S4Vectors;/usr/lib64/R/library;0.28.1;NA;R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=0.36.0);NA;NA;IRanges, GenomicRanges, SummarizedExperiment, Matrix,DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle;NA;Artistic-2.0;NA;NA;NA;NA;yes;4.0.5
+SummarizedExperiment;/usr/lib64/R/library;1.20.0;NA;R (>= 3.2), methods, MatrixGenerics (>= 1.1.3), GenomicRanges(>= 1.41.5), Biobase;utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>=1.13.1), DelayedArray (>= 0.15.10);NA;HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db,GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite,rhdf5, airway, BiocStyle, knitr, rmarkdown, RUnit, testthat,digest;NA;Artistic-2.0;NA;NA;NA;NA;no;4.0.5
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+xopen;/usr/lib64/R/library;1.0.0;NA;R (>= 3.1);processx;NA;ps, testthat;NA;MIT + file LICENSE;NA;NA;NA;NA;no;4.0.5
+yaml;/usr/lib64/R/library;2.2.1;NA;NA;NA;NA;RUnit;NA;BSD_3_clause + file LICENSE;NA;NA;NA;NA;yes;4.0.5
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+zip;/usr/lib64/R/library;2.2.0;NA;NA;NA;NA;covr, processx, R6, testthat, withr;NA;MIT + file LICENSE;NA;NA;NA;NA;yes;4.0.5
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