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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:37 -0400 (Sat, 13 Apr 2019).
| Package 640/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gep2pep 1.2.0 Francesco Napolitano
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### 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
gep2pep.Rcheck/00install.out
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###
### 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
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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
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gep2pep.Rcheck/examples_i386/gep2pep-Ex.timings
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gep2pep.Rcheck/examples_x64/gep2pep-Ex.timings
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