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Published 20 hours ago • verified publisher icon Irrationone

Installation failed

Open Sa753 opened this issue 4 years ago • 2 comments

I am using Mac Catalina 10.15 and tried to install Cellassign using R and using anaconda and all failed.

I managed to install tensorflow using Pip install but not using R though. I am using R version 4.0.1

This is the error I am getting trying to install cell assign

Downloading GitHub repo Irrationone/cellassign@master ✓ checking for file ‘/private/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T/Rtmp5QUhTy/remotes2ecb32d2dd94/Irrationone-cellassign-be66325/DESCRIPTION’ (598ms) ─ preparing ‘cellassign’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘cellassign_0.99.21.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cellassign/docs/articles/constructing-markers-from-purified-data_files/figure-html/unnamed-chunk-17-1.png’

  • installing source package ‘cellassign’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in system2(command = python, args = paste0(""", config_script, : running command ''/Users/samarelorbany/.virtualenvs/r-reticulate/bin/python' "" 2>/dev/null' had status 1 Warning in system2(command = python, args = paste0(""", config_script, : running command ''/Users/samarelorbany/.virtualenvs/r-reticulate/bin/python' "" 2>/dev/null' had status 1 Error: package or namespace load failed for ‘cellassign’: .onLoad failed in loadNamespace() for 'cellassign', details: call: python_config(python_version, required_module, python_versions) error: Error 1 occurred running /Users/samarelorbany/.virtualenvs/r-reticulate/bin/python Error: loading failed Execution halted ERROR: loading failed
  • removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cellassign’ Error: Failed to install 'cellassign' from GitHub: (converted from warning) installation of package ‘/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T//Rtmp5QUhTy/file2ecb31d1399d/cellassign_0.99.21.tar.gz’ had non-zero exit status

**I tried bioconductor and got that error:

BiocManager::install('cellassign') Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Installing package(s) 'cellassign' Warning message: package ‘cellassign’ is not available (for R version 4.0.1)

**I also tried using basilisks but failed:

install_github("LTLA/basilisk") Downloading GitHub repo LTLA/basilisk@master ✓ checking for file ‘/private/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T/Rtmp5QUhTy/remotes2ecb13e707ba/LTLA-basilisk-eed185a/DESCRIPTION’ (408ms) ─ preparing ‘basilisk’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘basilisk_1.1.8.tar.gz’

  • installing source package ‘basilisk’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading Error: object ‘activateEnvironment’ is not exported by 'namespace:basilisk.utils' Execution halted ERROR: lazy loading failed for package ‘basilisk’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/basilisk’
  • restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/basilisk’ Error: Failed to install 'basilisk' from GitHub: (converted from warning) installation of package ‘/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T//Rtmp5QUhTy/file2ecb24ac4e8b/basilisk_1.1.8.tar.gz’ had non-zero exit status

install_github("kieranrcampbell/cellassign") Downloading GitHub repo kieranrcampbell/cellassign@master ✓ checking for file ‘/private/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T/Rtmp5QUhTy/remotes2ecb4960fad4/kieranrcampbell-cellassign-ea5329e/DESCRIPTION’ (418ms) ─ preparing ‘cellassign’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘cellassign_0.99.27.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cellassign/docs/articles/constructing-markers-from-purified-data_files/figure-html/unnamed-chunk-17-1.png’

  • installing source package ‘cellassign’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in system2(command = python, args = paste0(""", config_script, : running command ''/Users/samarelorbany/.virtualenvs/r-reticulate/bin/python' "" 2>/dev/null' had status 1 Warning in system2(command = python, args = paste0(""", config_script, : running command ''/Users/samarelorbany/.virtualenvs/r-reticulate/bin/python' "" 2>/dev/null' had status 1 Error: package or namespace load failed for ‘cellassign’: .onLoad failed in loadNamespace() for 'cellassign', details: call: python_config(python_version, required_module, python_versions) error: Error 1 occurred running /Users/samarelorbany/.virtualenvs/r-reticulate/bin/python Error: loading failed Execution halted ERROR: loading failed
  • removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cellassign’ Error: Failed to install 'cellassign' from GitHub: (converted from warning) installation of package ‘/var/folders/40/r15m2x5n3vj1vd599d25fp4h0000gn/T//Rtmp5QUhTy/file2ecb7df399ee/cellassign_0.99.27.tar.gz’ had non-zero exit status

reticulate::py_config() Error in python_config(python_version, required_module, python_versions) : Error 1 occurred running /Users/samarelorbany/.virtualenvs/r-reticulate/bin/python In addition: Warning message: In system2(command = python, args = paste0(""", config_script, : running command ''/Users/samarelorbany/.virtualenvs/r-reticulate/bin/python' "" 2>/dev/null' had status 1

could you please help?

Sa753 avatar Jul 09 '20 08:07 Sa753

I tried to install CellAssign for an entire day and haven't completed it. Maybe the authors could provide a Docker version?

Wang-Cankun avatar Jul 29 '20 01:07 Wang-Cankun

I haven't used it myself but there is one now: https://hub.docker.com/r/uvarc/cellassign

rajewski avatar May 06 '22 20:05 rajewski