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BioC 3.5: CHECK report for CrispRVariants on tokay2

This page was generated on 2017-10-18 14:25:28 -0400 (Wed, 18 Oct 2017).

Package 296/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.4.1
Helen Lindsay
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/CrispRVariants
Branch: RELEASE_3_5
Last Commit: c8256d1
Last Changed Date: 2017-10-04 12:57:05 -0400 (Wed, 04 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CrispRVariants
Version: 1.4.1
Command: rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.4.1.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CrispRVariants.buildbin-libdir --install="check:CrispRVariants-install.out" --force-multiarch --no-vignettes --timings CrispRVariants_1.4.1.tar.gz
StartedAt: 2017-10-17 23:05:08 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:11:26 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 377.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CrispRVariants.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.4.1.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CrispRVariants.buildbin-libdir --install="check:CrispRVariants-install.out" --force-multiarch --no-vignettes --timings CrispRVariants_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CrispRVariants.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CrispRVariants/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrispRVariants' version '1.4.1'
* 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 'CrispRVariants' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plotVariants 5.32   0.07    5.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plotVariants 6.82   0.06    6.89
* 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

CrispRVariants.Rcheck/00install.out:


install for i386

* installing *source* package 'CrispRVariants' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CrispRVariants' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrispRVariants' as CrispRVariants_1.4.1.zip
* DONE (CrispRVariants)

CrispRVariants.Rcheck/examples_i386/CrispRVariants-Ex.timings:

nameusersystemelapsed
CrisprRun-class0.970.000.97
CrisprSet-class3.530.013.55
abifToFastq0.170.000.17
barplotAlleleFreqs2.130.002.13
consensusSeqs0.620.000.62
dispatchDots000
findChimeras0.020.020.03
getChimeras0.000.030.03
indelCounts0.070.030.11
mergeCrisprSets3.100.023.11
mutationEfficiency0.030.000.03
narrowAlignments0.220.000.22
plotAlignments0.900.000.91
plotChimeras0.930.000.92
plotFreqHeatmap0.250.000.25
plotVariants5.320.075.41
readsToTarget2.880.022.89
variantCounts0.030.000.03

CrispRVariants.Rcheck/examples_x64/CrispRVariants-Ex.timings:

nameusersystemelapsed
CrisprRun-class1.280.001.28
CrisprSet-class4.300.024.31
abifToFastq0.180.001.70
barplotAlleleFreqs2.920.002.92
consensusSeqs0.360.000.36
dispatchDots0.020.000.02
findChimeras0.020.000.01
getChimeras0.010.020.04
indelCounts0.080.000.07
mergeCrisprSets4.450.004.46
mutationEfficiency0.050.000.04
narrowAlignments0.330.000.33
plotAlignments1.640.001.64
plotChimeras1.460.011.47
plotFreqHeatmap0.360.000.37
plotVariants6.820.066.89
readsToTarget3.690.023.70
variantCounts0.030.000.03