@sjcrh/proteinpaint-server 2.35.0 → 2.35.1

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Files changed (4) hide show
  1. package/package.json +1 -1
  2. package/server.js +1 -1
  3. package/utils/edge.R +14 -14
  4. package/utils/fastclust.R +28 -21
package/utils/edge.R CHANGED
@@ -4,20 +4,20 @@
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  # Checking if all R packages are installed or not, if not installing each one of them
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- jsonlite_path <- system.file(package='jsonlite')
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- if (nchar(jsonlite_path) == 0) {
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- install.packages("jsonlite", repos='https://cran.case.edu/')
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- }
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-
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- edgeR_path <- system.file(package='edgeR')
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- if (nchar(edgeR_path) == 0) {
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- BiocManager::install("edgeR")
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- }
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-
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- readr_path <- system.file(package='readr')
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- if (nchar(readr_path) == 0) {
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- install.packages("readr", repos='https://cran.case.edu/')
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- }
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+ #jsonlite_path <- system.file(package='jsonlite')
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+ #if (nchar(jsonlite_path) == 0) {
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+ # install.packages("jsonlite", repos='https://cran.case.edu/')
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+ #}
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+ #
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+ #edgeR_path <- system.file(package='edgeR')
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+ #if (nchar(edgeR_path) == 0) {
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+ # BiocManager::install("edgeR")
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+ #}
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+ #
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+ #readr_path <- system.file(package='readr')
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+ #if (nchar(readr_path) == 0) {
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+ # install.packages("readr", repos='https://cran.case.edu/')
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+ #}
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  library(jsonlite)
package/utils/fastclust.R CHANGED
@@ -3,27 +3,34 @@
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  # Image is in Rplots.pdf
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- # Checking if all R packages are installed or not, if not installing each one of them
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-
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- ggplot2_path <- system.file(package='ggplot2')
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- if (nchar(ggplot2_path) == 0) {
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- install.packages("ggplot2", repos='https://cran.case.edu/')
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- }
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-
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- jsonlite_path <- system.file(package='jsonlite')
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- if (nchar(jsonlite_path) == 0) {
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- install.packages("jsonlite", repos='https://cran.case.edu/')
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- }
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-
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- dendextend_path <- system.file(package='dendextend')
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- if (nchar(dendextend_path) == 0) {
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- install.packages("dendextend", repos='https://cran.case.edu/')
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- }
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-
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- reshape_path <- system.file(package='reshape')
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- if (nchar(reshape_path) == 0) {
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- install.packages("reshape", repos='https://cran.case.edu/')
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- }
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+ ############################
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+ # !!! NOTE !!! #
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+ ############################
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+ # must not auto-install missing package in any R script!
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+ # declare required packages in dockerfile
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+ # at 2023/12, a problem emerged for pp container running in gdc qa-pink
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+ # since the docker images lacks the packages, but the auto-install was prevented due to container safety (no internet query)
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+ # this script will not run, leading to hard to decipher crashing
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+
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+ #ggplot2_path <- system.file(package='ggplot2')
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+ #if (nchar(ggplot2_path) == 0) {
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+ # install.packages("ggplot2", repos='https://cran.case.edu/')
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+ #}
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+ #
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+ #jsonlite_path <- system.file(package='jsonlite')
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+ #if (nchar(jsonlite_path) == 0) {
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+ # install.packages("jsonlite", repos='https://cran.case.edu/')
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+ #}
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+ #
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+ #dendextend_path <- system.file(package='dendextend')
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+ #if (nchar(dendextend_path) == 0) {
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+ # install.packages("dendextend", repos='https://cran.case.edu/')
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+ #}
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+ #
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+ #reshape_path <- system.file(package='reshape')
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+ #if (nchar(reshape_path) == 0) {
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+ # install.packages("reshape", repos='https://cran.case.edu/')
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+ #}
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  #flashClust_path <- system.file(package='flashClust')
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  #if (nchar(flashClust_path) == 0) {