Multiple platform build/check report for BioC 3.11 - CHECK report for gep2pep on tokay2

Package: gep2pep

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gep2pep.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gep2pep_1.8.0.tar.gz

StartedAt: 2020-10-17 04:27:42 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:32:56 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 314.5 seconds

RetCode: 0

Status: OK

CheckDir: gep2pep.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gep2pep.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gep2pep_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gep2pep.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gep2pep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gep2pep' version '1.8.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
CondSEA         1.14   0.04    6.56
clearCache      0.92   0.18   37.47
getResults      0.91   0.13    8.47
checkRepository 0.39   0.02   13.08
getCollections  0.28   0.06    6.35
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/gep2pep_1.8.0.tar.gz && rm -rf gep2pep.buildbin-libdir && mkdir gep2pep.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gep2pep.buildbin-libdir gep2pep_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gep2pep_1.8.0.zip && rm gep2pep_1.8.0.tar.gz gep2pep_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  100k  100  100k    0     0  1524k      0 --:--:-- --:--:-- --:--:-- 1677k

install for i386

* installing *source* package 'gep2pep' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gep2pep'
    finding HTML links ... done
    CategorizedCollection-class             html  
    CategorizedCollection                   html  
    CondSEA                                 html  
    PathSEA                                 html  
    addSingleGeneSets                       html  
    as.CategorizedCollection                html  
    buildPEPs                               html  
    checkRepository                         html  
    clearCache                              html  
    createMergedRepository                  html  
    createRepository                        html  
    exportSEA                               html  
    gene2pathways                           html  
    gep2pep-package                         html  
    getCollections                          html  
    getDetails                              html  
    getResults                              html  
    importFromRawMode                       html  
    importMSigDB.xml                        html  
    loadCollection                          html  
    loadESmatrix                            html  
    loadPVmatrix                            html  
    loadSampleGEP                           html  
    loadSamplePWS                           html  
    makeCollectionIDs                       html  
    openRepository                          html  
    setId2setName                           html  
** 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

install for x64

* installing *source* package 'gep2pep' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gep2pep' as gep2pep_1.8.0.zip
* DONE (gep2pep)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gep2pep' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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 C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpAXykh3/WriteXLS/1.csv
. No such file or directory
ERROR: cannot open C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpAXykh3/WriteXLS/1.csv
. No such file or directory
Chunk 1 of 2, 519 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 539 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 691 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 12.3 Kb)
== testthat results  ===========================================================
[ OK: 154 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  17.82    1.34   26.17


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpOKX8zw/WriteXLS/1.csv
. No such file or directory
ERROR: cannot open C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpOKX8zw/WriteXLS/1.csv
. No such file or directory
Chunk 1 of 2, 519 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 539 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 691 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 12.3 Kb)
== testthat results  ===========================================================
[ OK: 154 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  17.25    1.29   22.42

name	user	system	elapsed
CategorizedCollection	0.12	0.00	0.13
CondSEA	1.14	0.04	6.56
PathSEA	0.89	0.07	1.33
addSingleGeneSets	0.86	0.03	1.12
as.CategorizedCollection	0.50	0.11	1.13
buildPEPs	0.83	0.09	2.06
checkRepository	0.39	0.02	13.08
clearCache	0.92	0.18	37.47
createMergedRepository	1.14	0.16	4.56
createRepository	0.27	0.09	2.12
exportSEA	0.88	0.11	2.34
gene2pathways	0.36	0.04	1.00
getCollections	0.28	0.06	6.35
getDetails	0.95	0.09	2.93
getResults	0.91	0.13	8.47
importFromRawMode	0.96	0.09	2.77
importMSigDB.xml	0.33	0.05	0.79
loadCollection	0.22	0.17	1.33
loadESmatrix	0.77	0.17	2.89
loadPVmatrix	0.83	0.11	2.77
loadSampleGEP	0	0	0
loadSamplePWS	0	0	0
makeCollectionIDs	0.08	0.00	0.08
openRepository	0.33	0.05	1.35
setId2setName	0.08	0.00	0.07

name	user	system	elapsed
CategorizedCollection	0.21	0.00	0.20
CondSEA	1.11	0.14	2.25
PathSEA	1.08	0.14	1.72
addSingleGeneSets	0.92	0.02	1.16
as.CategorizedCollection	0.42	0.08	1.30
buildPEPs	0.80	0.08	1.26
checkRepository	0.30	0.09	0.61
clearCache	0.92	0.16	1.81
createMergedRepository	0.95	0.21	2.38
createRepository	0.31	0.02	0.53
exportSEA	0.88	0.06	1.33
gene2pathways	0.28	0.02	0.50
getCollections	0.30	0.00	0.54
getDetails	0.86	0.00	1.27
getResults	0.79	0.08	1.27
importFromRawMode	0.77	0.06	2.12
importMSigDB.xml	0.23	0.06	0.95
loadCollection	0.21	0.06	0.52
loadESmatrix	0.64	0.02	1.19
loadPVmatrix	0.69	0.02	1.66
loadSampleGEP	0	0	0
loadSamplePWS	0	0	0
makeCollectionIDs	0.06	0.00	0.07
openRepository	0.30	0.02	0.56
setId2setName	0.08	0.00	0.08

CHECK report for gep2pep on tokay2

Summary

Command output

Installation output

Tests output

Example timings