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This page was generated on 2024-12-19 15:01 -0500 (Thu, 19 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 387/430HostnameOS / ArchINSTALLBUILDCHECK
systemPipeRdata 2.11.0  (landing page)
Thomas Girke
Snapshot Date: 2024-12-19 07:30 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/systemPipeRdata
git_branch: devel
git_last_commit: f041ddb
git_last_commit_date: 2024-10-29 09:42:20 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for systemPipeRdata on nebbiolo1

To the developers/maintainers of the systemPipeRdata package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: systemPipeRdata
Version: 2.11.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:systemPipeRdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings systemPipeRdata_2.11.0.tar.gz
StartedAt: 2024-12-19 14:12:53 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 14:18:56 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 363.5 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeRdata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:systemPipeRdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings systemPipeRdata_2.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/systemPipeRdata.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘systemPipeRdata/DESCRIPTION’ ... OK
* this is package ‘systemPipeRdata’ version ‘2.11.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/extdata/param/.batchtools.conf.R
  inst/extdata/param/.batchtools.conf.R.sge
  inst/extdata/param/.batchtools.conf.R.torque
  inst/extdata/workflows/SPblast/.batchtools.conf.R
  inst/extdata/workflows/SPcheminfo/.batchtools.conf.R
  inst/extdata/workflows/SPscrna/.batchtools.conf.R
  inst/extdata/workflows/new/.batchtools.conf.R
  inst/rmarkdown/templates/systemPipeR_new/skeleton/.batchtools.conf.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeRdata’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 275.9Mb
  sub-directories of 1Mb or more:
    extdata  275.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.subsetAnno: no visible global function definition for ‘%within%’
.subsetAnno: no visible global function definition for ‘shift’
getSubsetReads: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  %within% anno shift
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/systemPipeRdata.Rcheck/00check.log’
for details.


Installation output

systemPipeRdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL systemPipeRdata
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘systemPipeRdata’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (systemPipeRdata)

Tests output


Example timings

systemPipeRdata.Rcheck/systemPipeRdata-Ex.timings

nameusersystemelapsed
availableWF0.0010.0000.001
genWorkenvir0.0020.0020.003
getSubsetReads0.0000.0000.001
pathList0.0030.0010.003