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BioC 3.4: CHECK report for CrispRVariants on moscato1

This page was generated on 2016-09-21 03:47:51 -0700 (Wed, 21 Sep 2016).

Package 271/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.1.4
Helen Lindsay
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CrispRVariants
Last Changed Rev: 118904 / Revision: 121152
Last Changed Date: 2016-06-23 07:11:22 -0700 (Thu, 23 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.1.4
Command: rm -rf CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && mkdir CrispRVariants.buildbin-libdir CrispRVariants.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.1.4.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out && D:\biocbld\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_1.1.4.tar.gz
StartedAt: 2016-09-20 06:34:38 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:39:52 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 314.1 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CrispRVariants.buildbin-libdir CrispRVariants_1.1.4.tar.gz >CrispRVariants.Rcheck\00install.out 2>&1 && cp CrispRVariants.Rcheck\00install.out CrispRVariants-install.out  && D:\biocbld\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_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/CrispRVariants.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.1.4'
* 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  6.1   0.07    6.16
* 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_1.1.4.zip
* DONE (CrispRVariants)

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

nameusersystemelapsed
CrisprRun-class0.500.030.53
CrisprSet-class3.370.023.39
abifToFastq0.220.000.25
barplotAlleleFreqs0.640.000.64
consensusSeqs0.20.00.2
dispatchDots0.010.000.02
findChimeras0.040.000.03
getChimeras0.030.000.03
indelCounts0.090.000.09
mergeCrisprSets3.530.023.54
mutationEfficiency0.030.000.03
narrowAlignments0.250.000.25
plotAlignments0.610.000.61
plotChimeras0.840.000.85
plotFreqHeatmap0.570.000.56
plotVariants4.690.064.77
readsToTarget3.830.003.83
variantCounts0.040.000.04

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

nameusersystemelapsed
CrisprRun-class0.610.020.63
CrisprSet-class4.430.014.44
abifToFastq0.250.000.27
barplotAlleleFreqs1.190.001.19
consensusSeqs0.250.000.25
dispatchDots000
findChimeras0.040.000.04
getChimeras0.040.000.03
indelCounts0.110.000.11
mergeCrisprSets4.500.034.54
mutationEfficiency0.030.000.03
narrowAlignments0.330.000.33
plotAlignments0.830.020.84
plotChimeras1.120.011.14
plotFreqHeatmap0.380.000.38
plotVariants6.100.076.16
readsToTarget4.150.004.15
variantCounts0.030.010.05