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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 827/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.25.0  (landing page)
Francesco Napolitano
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gep2pep
git_branch: devel
git_last_commit: 45570c7
git_last_commit_date: 2024-04-30 11:02:39 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for gep2pep on palomino4

To the developers/maintainers of the gep2pep package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gep2pep.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: gep2pep
Version: 1.25.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gep2pep.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gep2pep_1.25.0.tar.gz
StartedAt: 2024-06-10 03:17:24 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:23:40 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 376.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gep2pep.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gep2pep_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/gep2pep.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gep2pep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gep2pep' version '1.25.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'gep2pep' can be installed ... OK
* checking installed package size ... OK
* 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) as.CategorizedCollection.Rd:27: Lost braces; missing escapes or markup?
    27 |     in the collection to {CategorizedCollection}. If
       |                          ^
checkRd: (-1) gep2pep-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loadESmatrix.Rd:19: Lost braces
    19 |     reports the ES for the pathway \code{i}, condition{j}. If
       |                                                       ^
checkRd: (-1) loadPVmatrix.Rd:19: Lost braces
    19 |     reports the PV for the pathway \code{i}, condition{j}. If
       |                                                       ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
createMergedRepository 0.67   6.03    7.97
PathSEA                0.78   4.89    6.41
buildPEPs              1.06   3.79    5.45
clearCache             0.97   3.80    5.65
CondSEA                0.97   3.63    5.35
getDetails             0.75   3.70    5.18
loadPVmatrix           0.62   3.66    5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/gep2pep.Rcheck/00check.log'
for details.


Installation output

gep2pep.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL gep2pep
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'gep2pep' ...
** 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 (gep2pep)

Tests output

gep2pep.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gep2pep)
> 
> test_check("gep2pep")
ERROR: cannot open F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp4aGjHa/WriteXLS/1.csv
. No such file or directory
ERROR: cannot open F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp4aGjHa/WriteXLS/1.csv
. No such file or directory
Chunk 1 of 2, 520 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 691 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 16.3 Kb)
[ FAIL 0 | WARN 2272 | SKIP 1 | PASS 154 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_rawMode.R:216:1'

[ FAIL 0 | WARN 2272 | SKIP 1 | PASS 154 ]
> 
> proc.time()
   user  system elapsed 
  28.76   34.79   71.29 

Example timings

gep2pep.Rcheck/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.110.810.93
CondSEA0.973.635.35
PathSEA0.784.896.41
addSingleGeneSets0.662.253.44
as.CategorizedCollection0.453.904.91
buildPEPs1.063.795.45
checkRepository0.472.103.02
clearCache0.973.805.65
createMergedRepository0.676.037.97
createRepository0.242.252.89
exportSEA0.683.694.94
gene2pathways0.242.252.95
getCollections0.282.252.92
getDetails0.753.705.18
getResults0.683.684.99
importFromRawMode0.682.433.85
importMSigDB.xml0.242.362.94
loadCollection0.192.523.05
loadESmatrix0.643.564.89
loadPVmatrix0.623.665.16
loadSampleGEP0.000.010.01
loadSamplePWS000
makeCollectionIDs0.040.000.04
openRepository0.182.362.93
setId2setName0.060.000.06