release v10.1: fedora\v33\immcantation\v1.2 at date 20230407: from...

release v10.1: fedora\v33\immcantation\v1.2 at date 20230407: from gmillot/immcantation_v1.1:gitlab_v10.0  with lubridate added

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 />

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 \

fedora/v33/immcantation/v1.2/Dockerfile

+#########################################################################
+##                                                                     ##
+##     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"]
+
+
+