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BioC 3.5: CHECK report for genotypeeval on tokay2

This page was generated on 2017-08-16 13:24:46 -0400 (Wed, 16 Aug 2017).

Package 547/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genotypeeval 1.8.0
Jennifer Tom
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/genotypeeval
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genotypeeval
Version: 1.8.0
Command: rm -rf genotypeeval.buildbin-libdir genotypeeval.Rcheck && mkdir genotypeeval.buildbin-libdir genotypeeval.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genotypeeval.buildbin-libdir genotypeeval_1.8.0.tar.gz >genotypeeval.Rcheck\00install.out 2>&1 && cp genotypeeval.Rcheck\00install.out genotypeeval-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genotypeeval.buildbin-libdir --install="check:genotypeeval-install.out" --force-multiarch --no-vignettes --timings genotypeeval_1.8.0.tar.gz
StartedAt: 2017-08-16 00:03:35 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:13:39 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 604.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: genotypeeval.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genotypeeval.buildbin-libdir genotypeeval.Rcheck && mkdir genotypeeval.buildbin-libdir genotypeeval.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genotypeeval.buildbin-libdir genotypeeval_1.8.0.tar.gz >genotypeeval.Rcheck\00install.out 2>&1 && cp genotypeeval.Rcheck\00install.out genotypeeval-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genotypeeval.buildbin-libdir --install="check:genotypeeval-install.out" --force-multiarch --no-vignettes --timings genotypeeval_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/genotypeeval.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genotypeeval/DESCRIPTION' ... OK
* this is package 'genotypeeval' version '1.8.0'
* 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 'genotypeeval' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... WARNING
Undocumented code objects:
  'makeHistogram' 'pcaPlot' 'tsnePlot'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
getPlots 6.33   0.02    6.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
getPlots 6.01   0.01    6.34
* 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 PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/genotypeeval.Rcheck/00check.log'
for details.


genotypeeval.Rcheck/00install.out:


install for i386

* installing *source* package 'genotypeeval' ...
** R
** 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 'genotypeeval' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genotypeeval' as genotypeeval_1.8.0.zip
* DONE (genotypeeval)

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

nameusersystemelapsed
GoldDataFromGRanges0.110.000.11
GoldDataParam000
ReadGoldData0.920.020.93
ReadVCFData3.430.083.50
ReadVCFDataChunk4.070.084.16
VCFEvaluate2.80.02.8
VCFQAParam000
didSamplePass2.970.012.98
didSamplePassOverall3.390.003.39
getName2.940.002.94
getPlots6.330.026.41
getResults4.530.014.54
getVR1.850.001.84

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

nameusersystemelapsed
GoldDataFromGRanges0.140.000.14
GoldDataParam000
ReadGoldData1.250.031.28
ReadVCFData4.470.034.50
ReadVCFDataChunk4.470.034.50
VCFEvaluate3.070.003.08
VCFQAParam000
didSamplePass3.210.003.20
didSamplePassOverall2.790.002.80
getName2.630.002.62
getPlots6.010.016.34
getResults4.470.024.48
getVR1.860.001.86