Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for SeqVarTools on moscato2

This page was generated on 2015-10-09 09:30:34 -0700 (Fri, 09 Oct 2015).

Package 895/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqVarTools 1.6.0
Stephanie M. Gogarten , Xiuwen Zheng
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/SeqVarTools
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: SeqVarTools
Version: 1.6.0
Command: rm -rf SeqVarTools.buildbin-libdir SeqVarTools.Rcheck && mkdir SeqVarTools.buildbin-libdir SeqVarTools.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqVarTools.buildbin-libdir SeqVarTools_1.6.0.tar.gz >SeqVarTools.Rcheck\00install.out 2>&1 && cp SeqVarTools.Rcheck\00install.out SeqVarTools-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SeqVarTools.buildbin-libdir --install="check:SeqVarTools-install.out" --force-multiarch --no-vignettes --timings SeqVarTools_1.6.0.tar.gz
StartedAt: 2015-10-09 06:09:47 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:16:01 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 374.3 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqVarTools.buildbin-libdir SeqVarTools_1.6.0.tar.gz >SeqVarTools.Rcheck\00install.out 2>&1 && cp SeqVarTools.Rcheck\00install.out SeqVarTools-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SeqVarTools.buildbin-libdir --install="check:SeqVarTools-install.out" --force-multiarch --no-vignettes --timings SeqVarTools_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/SeqVarTools.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.6.0'
* 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 '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
** 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 ... 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' ... [13s] OK
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [30s]
 [31s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [40s]
 [40s] 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
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'SeqVarTools' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'SeqVarTools' as SeqVarTools_1.6.0.zip
* DONE (SeqVarTools)

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

nameusersystemelapsed
allele-methods0.030.020.07
alleleFrequency0.510.010.53
applyMethod0.480.020.50
duplicateDiscordance0.030.000.03
getGenotype0.020.000.02
getVariableLengthData0.010.000.01
heterozygosity0.380.000.38
hwe0.150.000.15
inbreedCoeff0.330.000.33
isSNV0.020.000.02
isVariant0.010.000.01
meanBySample0.050.000.05
mendelErr0.050.000.05
missingGenotypeRate0.050.000.05
pca1.530.001.53
pedigree0.010.000.01
setVariantID0.020.010.03
titv0.390.000.39

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

nameusersystemelapsed
allele-methods0.030.000.03
alleleFrequency0.470.000.49
applyMethod0.320.020.34
duplicateDiscordance0.040.000.03
getGenotype000
getVariableLengthData000
heterozygosity0.250.000.25
hwe0.100.000.11
inbreedCoeff0.220.000.22
isSNV0.010.000.02
isVariant000
meanBySample0.050.000.04
mendelErr0.030.000.03
missingGenotypeRate0.010.000.01
pca1.020.011.03
pedigree0.010.000.02
setVariantID0.020.000.02
titv0.300.030.32