Installation Issue Seemingly Arising from R

[danphillips28]

Hi! Nice tool.

I'm having some issues testing MAX on the demo data. I copy and pasted the code (from the copy-and-paste section of the github), however get some errors which causes no output to be produced. I first tested it on the HPC, after loading an R module. This is where the first error pops up:

Number of arguments:  5
List of arguments:  mut=/data/ocdm-lmnamut-rnasec/mutationMAX/test_mutation_list_MAX2.txt gtf=/data/ocdm-lmnamut-rnasec/mutationMAX/test_FLT3.gtf ref=/data/ocdm-lmnamut-rnasec/mutationMAX/test_transcripts_FLT3.fa workdir=/data/ocdm-lmnamut-rnasec/mutationMAX hg=hg19
Warning in install.packages("BiocManager") :
  'lib = "/apps/system/easybuild/software/R/4.3.2-gfbf-2023a/lib64/R/library"' is not writable
Error in install.packages("BiocManager") : unable to install packages
Execution halted
cat: Mutant3.fa: No such file or directory
rm: cannot remove 'Mutant3.fa': No such file or directory
rm: cannot remove 'Mutant2.fa': No such file or directory
rm: cannot remove 'tmp_gtf.sqlite': No such file or directory

 WT_Mut.fa is generated.

I then tested it on my local ubuntu device which has a local R installation and got the following error at a similar place:

Number of arguments:  5
List of arguments:  mut=/home/danhatechav/Documents/TestingMAX/test_mutation_list_MAX2.txt gtf=/home/danhatechav/Documents/TestingMAX/test_FLT3.gtf ref=/home/danhatechav/Documents/TestingMAX/test_transcripts_FLT3.fa workdir=/home/danhatechav/Documents/TestingMAX hg=hg19 
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19'
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz'
Content type 'application/gzip' length 710245413 bytes (677.3 MB)
============
downloaded 163.5 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 0 != reported length 0
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BSgenome.Hsapiens.UCSC.hg19’ failed
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, mgcv, nlme,
    nnet, rpart, spatial, survival
  path: /usr/local/lib/R/site-library
  packages:
    askpass, brew, brio, cachem, callr, cli, commonmark, cpp11, credentials,
    curl, desc, downlit, evaluate, fansi, fontawesome, fs, gert, gh, glue,
    httpuv, httr, httr2, jsonlite, knitr, later, lifecycle, openssl, pkgbuild,
    prettyunits, promises, ps, purrr, Rcpp, remotes, roxygen2, rprojroot,
    rstudioapi, sass, stringi, stringr, sys, systemfonts, tinytex, usethis,
    utf8, vctrs, withr, xml2, xopen, yaml, zip
Old packages: 'ape', 'BH', 'bookdown', 'broom.helpers', 'bslib', 'circlize',
  'ComplexHeatmap', 'cowplot', 'data.table', 'DBI', 'dbplyr', 'deldir',
  'digest', 'DT', 'filelock', 'GGally', 'ggforce', 'ggfun', 'ggnewscale',
  'ggplot2', 'ggraph', 'ggrepel', 'ggsci', 'ggstats', 'ggthemes',
  'graphlayouts', 'gtable', 'Hmisc', 'htmltools', 'htmlwidgets', 'igraph',
  'interp', 'labelled', 'lme4', 'locfit', 'matrixStats', 'munsell',
  'patchwork', 'pkgdown', 'pkgload', 'processx', 'progress', 'ragg',
  'RcppArmadillo', 'RcppEigen', 'RCurl', 'readr', 'reprex', 'rlang',
  'rmarkdown', 'RSQLite', 'RUnit', 'rvest', 'scatterpie', 'shadowtext',
  'shape', 'shiny', 'testthat', 'tidygraph', 'tidyr', 'tidyselect', 'tidytree',
  'timechange', 'tweenr', 'uuid', 'vcfR', 'viridis', 'vroom', 'xfun', 'XML',
  'yulab.utils'

Any help?

Thanks! Daniel

[nghiavtr]

Hi @danphillips28 ,

Thank you for using MAX.

The issues in both HPC and your local ubuntu are due to installation of other R packages.

MAX currently requires the following packages: GenomicFeatures, BSgenome.Hsapiens.UCSC.hg38 (or BSgenome.Hsapiens.UCSC.hg19), polyester, Biostrings, data.table, foreach and doParallel

Could you try install them separately before running MAX? If you install these packages in advance, MAX will not re-install it, so the issue will be disappeared.

I hope it would help.

Best, Nghia

[danphillips28]

Hi Nghia, Thanks for your reply. I decided to take the analysis off the HPC and try the docker run, which works (with the test data at least). I therefore think it´s fair to close this issue for now. Will open a new one if something pops up. Thanks again, Daniel