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BioC 3.4: CHECK report for SeqVarTools on moscato1

This page was generated on 2016-09-21 03:45:02 -0700 (Wed, 21 Sep 2016).

Package 1103/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqVarTools 1.11.4
Stephanie M. Gogarten , Xiuwen Zheng , Adrienne Stilp
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SeqVarTools
Last Changed Rev: 120026 / Revision: 121152
Last Changed Date: 2016-08-10 12:31:30 -0700 (Wed, 10 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqVarTools
Version: 1.11.4
Command: rm -rf SeqVarTools.buildbin-libdir SeqVarTools.Rcheck && mkdir SeqVarTools.buildbin-libdir SeqVarTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqVarTools.buildbin-libdir SeqVarTools_1.11.4.tar.gz >SeqVarTools.Rcheck\00install.out 2>&1 && cp SeqVarTools.Rcheck\00install.out SeqVarTools-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SeqVarTools.buildbin-libdir --install="check:SeqVarTools-install.out" --force-multiarch --no-vignettes --timings SeqVarTools_1.11.4.tar.gz
StartedAt: 2016-09-20 16:27:42 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:34:46 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 423.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SeqVarTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SeqVarTools.buildbin-libdir SeqVarTools.Rcheck && mkdir SeqVarTools.buildbin-libdir SeqVarTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqVarTools.buildbin-libdir SeqVarTools_1.11.4.tar.gz >SeqVarTools.Rcheck\00install.out 2>&1 && cp SeqVarTools.Rcheck\00install.out SeqVarTools-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SeqVarTools.buildbin-libdir --install="check:SeqVarTools-install.out" --force-multiarch --no-vignettes --timings SeqVarTools_1.11.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/SeqVarTools.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 'SeqVarTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqVarTools' version '1.11.4'
* 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 'SeqVarTools' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'SeqArray:::.altAllele' 'SeqArray:::.refAllele'
  See the note in ?`:::` about the use of this operator.
* 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/SeqVarTools.Rcheck/00check.log'
for details.


SeqVarTools.Rcheck/00install.out:


install for i386

* installing *source* package 'SeqVarTools' ...
** 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 'SeqVarTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqVarTools' as SeqVarTools_1.11.4.zip
* DONE (SeqVarTools)

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

nameusersystemelapsed
SeqVarData-class0.110.000.30
allele-methods0.030.000.03
alleleFrequency0.130.000.14
alternateAlleleDetection000
applyMethod0.250.020.27
countSingletons0.080.000.07
duplicateDiscordance0.070.010.10
getGenotype0.000.030.03
getVariableLengthData0.020.000.01
heterozygosity0.220.020.24
hwe0.120.000.12
inbreedCoeff0.210.000.21
isSNV000
isVariant0.010.000.01
meanBySample0.050.000.05
mendelErr0.050.000.05
missingGenotypeRate0.030.000.03
pca0.980.011.00
pedigree0.020.000.01
refFrac0.060.000.06
regression0.110.000.11
setVariantID0.010.000.00
titv0.530.030.56

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

nameusersystemelapsed
SeqVarData-class0.130.000.31
allele-methods0.020.000.01
alleleFrequency0.160.000.19
alternateAlleleDetection000
applyMethod0.280.020.30
countSingletons0.070.000.07
duplicateDiscordance0.090.000.09
getGenotype0.020.000.02
getVariableLengthData0.000.010.03
heterozygosity0.230.000.23
hwe0.110.000.11
inbreedCoeff0.240.000.24
isSNV000
isVariant000
meanBySample0.050.000.05
mendelErr0.050.020.09
missingGenotypeRate0.010.000.02
pca1.120.001.13
pedigree000
refFrac0.060.000.06
regression0.130.000.12
setVariantID0.010.000.02
titv0.240.000.23