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CHECK report for gep2pep on tokay1

This page was generated on 2019-04-13 11:28:37 -0400 (Sat, 13 Apr 2019).

Package 640/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.2.0
Francesco Napolitano
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/gep2pep
Branch: RELEASE_3_8
Last Commit: fb62d67
Last Changed Date: 2018-10-30 11:42:07 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gep2pep
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gep2pep.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gep2pep_1.2.0.tar.gz
StartedAt: 2019-04-13 02:37:09 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:45:57 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 528.4 seconds
RetCode: 0
Status:  OK  
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gep2pep.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gep2pep_1.2.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/gep2pep.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.0'
* 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 ... 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 or elapsed time > 5s
                       user system elapsed
importFromRawMode      0.73   0.04    6.54
clearCache             0.60   0.09    6.16
CondSEA                0.52   0.16   85.34
createMergedRepository 0.53   0.11    5.11
buildPEPs              0.39   0.08    5.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
createMergedRepository 0.81   0.24    5.57
importFromRawMode      0.92   0.13    7.00
clearCache             0.77   0.12    6.67
* 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


Installation output

gep2pep.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/gep2pep_1.2.0.tar.gz && rm -rf gep2pep.buildbin-libdir && mkdir gep2pep.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gep2pep.buildbin-libdir gep2pep_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL gep2pep_1.2.0.zip && rm gep2pep_1.2.0.tar.gz gep2pep_1.2.0.zip
###
##############################################################################
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  % 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 97889  100 97889    0     0  2801k      0 --:--:-- --:--:-- --:--:-- 3186k

install for i386

* installing *source* package 'gep2pep' ...
** 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  
    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
In R CMD INSTALL

install for x64

* installing *source* package 'gep2pep' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gep2pep' as gep2pep_1.2.0.zip
* DONE (gep2pep)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'gep2pep' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

gep2pep.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
Chunk 1 of 2, 511 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 658 bytes (current file size: 11.8 Kb)
Chunk 1 of 2, 530 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 684 bytes (current file size: 11.8 Kb)
Chunk 1 of 2, 541 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 678 bytes (current file size: 11.8 Kb)
== testthat results  ===========================================================
OK: 158 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.35    0.76   22.95 

gep2pep.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
Chunk 1 of 2, 511 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 658 bytes (current file size: 11.8 Kb)
Chunk 1 of 2, 530 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 684 bytes (current file size: 11.8 Kb)
Chunk 1 of 2, 541 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 678 bytes (current file size: 11.8 Kb)
== testthat results  ===========================================================
OK: 158 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.85    0.75   17.36 

Example timings

gep2pep.Rcheck/examples_i386/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.110.010.13
CondSEA 0.52 0.1685.34
PathSEA0.560.023.92
as.CategorizedCollection0.250.071.60
buildPEPs0.390.085.79
checkRepository0.140.050.97
clearCache0.600.096.16
createMergedRepository0.530.115.11
createRepository0.140.020.92
exportSEA0.550.061.69
gene2pathways0.200.061.50
getCollections0.140.081.14
getDetails0.620.062.40
getResults0.660.102.35
importFromRawMode0.730.046.54
importMSigDB.xml0.160.070.91
loadCollection0.130.041.17
loadESmatrix0.360.132.10
loadPVmatrix0.390.081.81
loadSampleGEP000
loadSamplePWS000
makeCollectionIDs0.070.000.08
openRepository0.100.060.78
setId2setName0.030.000.03

gep2pep.Rcheck/examples_x64/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.090.030.12
CondSEA0.610.111.88
PathSEA0.640.052.03
as.CategorizedCollection0.260.011.60
buildPEPs0.440.082.22
checkRepository0.150.020.78
clearCache0.770.126.67
createMergedRepository0.810.245.57
createRepository0.170.040.90
exportSEA0.740.062.38
gene2pathways0.220.051.11
getCollections0.210.061.17
getDetails0.750.112.42
getResults0.690.111.87
importFromRawMode0.920.137.00
importMSigDB.xml0.190.000.77
loadCollection0.170.050.83
loadESmatrix0.590.091.72
loadPVmatrix0.530.111.84
loadSampleGEP000
loadSamplePWS000
makeCollectionIDs0.050.000.05
openRepository0.190.011.14
setId2setName0.060.000.06