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BioC 3.4: CHECK report for CrispRVariants on tokay1

This page was generated on 2017-04-15 16:20:36 -0400 (Sat, 15 Apr 2017).

Package 279/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.2.0
Helen Lindsay
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CrispRVariants
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CrispRVariants
Version: 1.2.0
Command: rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.2.0.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CrispRVariants.buildbin-libdir --install="check:CrispRVariants-install.out" --force-multiarch --no-vignettes --timings CrispRVariants_1.2.0.tar.gz
StartedAt: 2017-04-14 21:45:55 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:51:24 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 329.6 seconds
RetCode: 0
Status:  OK  
CheckDir: CrispRVariants.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.2.0.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CrispRVariants.buildbin-libdir --install="check:CrispRVariants-install.out" --force-multiarch --no-vignettes --timings CrispRVariants_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/CrispRVariants.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.2.0'
* 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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotVariants    6.26   0.08    6.34
mergeCrisprSets 5.76   0.00    5.77
CrisprSet-class 5.43   0.01    5.45
* 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_1.2.0.zip
* DONE (CrispRVariants)

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

nameusersystemelapsed
CrisprRun-class0.450.000.46
CrisprSet-class3.030.063.09
abifToFastq0.170.000.17
barplotAlleleFreqs0.570.030.60
consensusSeqs0.150.000.15
dispatchDots000
findChimeras0.030.000.03
getChimeras0.040.000.03
indelCounts0.070.000.08
mergeCrisprSets3.190.063.25
mutationEfficiency0.030.000.03
narrowAlignments0.210.020.22
plotAlignments0.540.030.58
plotChimeras0.740.000.73
plotFreqHeatmap0.280.000.29
plotVariants3.860.063.92
readsToTarget3.250.003.25
variantCounts0.030.000.03

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

nameusersystemelapsed
CrisprRun-class0.600.000.59
CrisprSet-class5.430.015.45
abifToFastq0.360.001.00
barplotAlleleFreqs1.250.001.25
consensusSeqs0.320.000.31
dispatchDots000
findChimeras0.060.000.07
getChimeras0.030.000.03
indelCounts0.20.00.2
mergeCrisprSets5.760.005.77
mutationEfficiency0.040.000.03
narrowAlignments0.860.000.86
plotAlignments0.780.000.78
plotChimeras1.090.001.09
plotFreqHeatmap0.390.000.39
plotVariants6.260.086.34
readsToTarget4.290.004.29
variantCounts0.040.000.04