rworkflow/rcwl

Write CWL in R

rcwl's Issues

Fix the basilisk-related machinery

See the instructions in the vignette:

• You need a .BBSoptions file to indicate that 32-bit windows is not supported.
• basilisk should be loaded on first use, not as part of the package load.
• You need to turn off staged installs.

The first two points are causing a 32-bit version of Python to take precedence over the intended 64-bit version, resulting in failures on Riesling for basilisk and its clients. I have now prevented basilisk from using a 32-bit installer, so you'll end up with an explicit install-time failure for Rcwl on multi-arch builds for Windows.

Add LICENCE with GPL version

Thank you @hubentu ! Can you add a LICENSE.txt or similar with the text of the GPL version 2 or 3? That helps GitHub and humans understand better which license you mean.

Thanks!

Error installation / Error: package or namespace load failed for 'Rcwl

Here are my log:

> BiocManager::install("Rcwl")
Bioconductor version 3.10 (BiocManager 1.30.12), ?BiocManager::install for help
Bioconductor version '3.10' is out-of-date; the current release version '3.12' is available with R
  version '4.0'; see https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.10 (BiocManager 1.30.12), R 3.6.2 (2019-12-12)
Installing package(s) 'Rcwl'
installing the source package ‘Rcwl’

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Rcwl_1.2.1.tar.gz'
Content type 'application/x-gzip' length 681611 bytes (665 KB)
downloaded 665 KB

* installing *source* package 'Rcwl' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: le package 'yaml' a été compilé avec la version R 3.6.3 
2: le package 'S4Vectors' a été compilé avec la version R 3.6.3 
** help
*** installing help indices
  converting help for package 'Rcwl'
    finding HTML links ... fini
    InputArrayParam                         html  
    InputParam                              html  
    InputParamList                          html  
    OutputArrayParam                        html  
    OutputParam                             html  
    OutputParamList                         html  
    Rcwl                                    html  
    Step                                    html  
    cwlParam-methods                        html  
    cwlParam                                html  
    cwlShiny                                html  
    cwlStepParam                            html  
    plotCWL                                 html  
    plus-cwlStepParam-stepParam-method      html  
    readCWL                                 html  
    runCWL                                  html  
    runCWLBatch                             html  
    runs                                    html  
    short                                   html  
    stepInParam                             html  
    stepInParamList                         html  
    stepParam                               html  
    stepParamList                           html  
    steps                                   html  
    writeCWL                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: package 'yaml' was built under R version 3.6.3
Warning: package 'S4Vectors' was built under R version 3.6.3
Error: package or namespace load failed for 'Rcwl':
 .onLoad failed in loadNamespace() for 'Rcwl', details:
  call: system("which cwltool", intern = TRUE)
  error: 'which' not found
Erreur : le chargement a échoué
Exécution arrêtée
*** arch - x64
Warning: package 'yaml' was built under R version 3.6.3
Warning: package 'S4Vectors' was built under R version 3.6.3
Error: package or namespace load failed for 'Rcwl':
 .onLoad failed in loadNamespace() for 'Rcwl', details:
  call: system("which cwltool", intern = TRUE)
  error: 'which' not found
Erreur : le chargement a échoué
Exécution arrêtée
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/ylebras/Documents/R/win-library/3.6/Rcwl'

Add parsers for CWL documents

Hi, is there a plan to add such functionality?

vignette is crashing

> r1 <- runCWL(echo, outdir = tempdir())

Error in idx[1]:(idx[2] - 1) : NA/NaN argument
In addition: Warning message:
In system2(cwlRunner, args = paste0("--outdir ", outdir, " ", Args,  :
  running command ''cwltool' --outdir /var/folders/5_/14ld0y7s0vbg_z0g2c9l8v300000gr/T//RtmpTWaJcq  /var/folders/5_/14ld0y7s0vbg_z0g2c9l8v300000gr/T//RtmpTWaJcq/filec482f50e610.cwl /var/folders/5_/14ld0y7s0vbg_z0g2c9l8v300000gr/T//RtmpTWaJcq/filec482f50e610.yml 2>&1' had status 1