Nuno Saraiva-Agostinho
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cTRAP |
| Branch: RELEASE_3_8 |
| Last Commit: e97c3f1 |
| Last Changed Date: 2018-12-03 11:02:57 -0400 (Mon, 03 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:51 -0400 (Sat, 13 Apr 2019).
| Package 354/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cTRAP 1.0.3 Nuno Saraiva-Agostinho
| 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: cTRAP |
| Version: 1.0.3 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cTRAP_1.0.3.tar.gz |
| StartedAt: 2019-04-13 01:35:48 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:40:02 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 254.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cTRAP.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:cTRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cTRAP_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cTRAP.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 'cTRAP/DESCRIPTION' ... OK
* this is package 'cTRAP' version '1.0.3'
* package encoding: UTF-8
* 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 'cTRAP' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotL1000comparison 7.26 0.35 7.57
downloadL1000data 4.92 0.26 6.81
downloadENCODEknockdownMetadata 2.19 0.27 10.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotL1000comparison 11.11 0.39 11.57
downloadL1000data 7.02 0.47 9.16
downloadENCODEknockdownMetadata 3.44 0.42 12.08
* 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
cTRAP.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/cTRAP_1.0.3.tar.gz && rm -rf cTRAP.buildbin-libdir && mkdir cTRAP.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cTRAP.buildbin-libdir cTRAP_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cTRAP_1.0.3.zip && rm cTRAP_1.0.3.tar.gz cTRAP_1.0.3.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
65 2532k 65 1664k 0 0 22.1M 0 --:--:-- --:--:-- --:--:-- 22.8M
100 2532k 100 2532k 0 0 30.5M 0 --:--:-- --:--:-- --:--:-- 31.7M
install for i386
* installing *source* package 'cTRAP' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cTRAP'
finding HTML links ... done
ENCODEmetadata html
ENCODEsamples html
GCT-class html
cTRAP html
checkColnames html
closeOpenHandles html
compareAgainstL1000 html
correlatePerCellLine html
counts html
diffExprStat html
downloadENCODEknockdownMetadata html
downloadENCODEsamples html
downloadIfNeeded html
downloadL1000data html
filterL1000metadata html
fix.datatypes html
getENCODEcontrols html
getL1000Conditions html
getL1000PerturbationTypes html
l1000metadata html
l1000perturbationsKnockdown html
l1000perturbationsSmallMolecules html
loadENCODEsample html
loadL1000perturbations html
performDifferentialExpression html
performGSAperCellLine html
plotGSEA html
plotL1000comparison html
prepareENCODEgeneExpression html
processIds html
readGctxIds html
readGctxMeta html
subsetToIds html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cTRAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cTRAP' as cTRAP_1.0.3.zip
* DONE (cTRAP)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cTRAP' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
cTRAP.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(cTRAP)
>
> test_check("cTRAP")
Comparing with cell line HepG2
Comparing with cell line HepG2
Performing GSA using perturbation signatures...
Comparing with cell line HEPG2
Comparing with cell line HEPG2
Performing GSA using perturbation signatures...
== testthat results ===========================================================
OK: 24 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.78 0.73 16.56
|
cTRAP.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(cTRAP)
>
> test_check("cTRAP")
Comparing with cell line HepG2
Comparing with cell line HepG2
Performing GSA using perturbation signatures...
Comparing with cell line HEPG2
Comparing with cell line HEPG2
Performing GSA using perturbation signatures...
== testthat results ===========================================================
OK: 23 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
20.31 0.96 21.28
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cTRAP.Rcheck/examples_i386/cTRAP-Ex.timings
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cTRAP.Rcheck/examples_x64/cTRAP-Ex.timings
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