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CHECK report for cTRAP on tokay1

This page was generated on 2019-04-13 11:29:51 -0400 (Sat, 13 Apr 2019).

Package 354/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.0.3
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)
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: 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

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: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


Installation output

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

Tests output

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 

Example timings

cTRAP.Rcheck/examples_i386/cTRAP-Ex.timings

nameusersystemelapsed
compareAgainstL10000.750.311.02
downloadENCODEknockdownMetadata 2.19 0.2710.95
downloadENCODEsamples000
downloadL1000data4.920.266.81
filterL1000metadata000
getL1000Conditions0.000.020.02
getL1000PerturbationTypes000
loadL1000perturbations000
performDifferentialExpression000
plotL1000comparison7.260.357.57
prepareENCODEgeneExpression0.000.010.01

cTRAP.Rcheck/examples_x64/cTRAP-Ex.timings

nameusersystemelapsed
compareAgainstL10001.050.251.38
downloadENCODEknockdownMetadata 3.44 0.4212.08
downloadENCODEsamples000
downloadL1000data7.020.479.16
filterL1000metadata0.020.000.02
getL1000Conditions000
getL1000PerturbationTypes000
loadL1000perturbations000
performDifferentialExpression0.010.000.02
plotL1000comparison11.11 0.3911.57
prepareENCODEgeneExpression000