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BioC 3.4: CHECK report for SeqVarTools on zin1

This page was generated on 2016-09-21 03:38:30 -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: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SeqVarTools_1.11.4.tar.gz
StartedAt: 2016-09-20 12:30:03 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:33:45 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 222.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SeqVarTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SeqVarTools_1.11.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SeqVarTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/SeqVarTools.Rcheck/00check.log’
for details.


SeqVarTools.Rcheck/00install.out:

* 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
* DONE (SeqVarTools)

SeqVarTools.Rcheck/SeqVarTools-Ex.timings:

nameusersystemelapsed
SeqVarData-class0.0920.0040.097
allele-methods0.0160.0000.017
alleleFrequency0.1080.0000.108
alternateAlleleDetection0.0040.0000.001
applyMethod0.2200.0080.228
countSingletons0.0680.0000.065
duplicateDiscordance0.0600.0120.073
getGenotype0.0120.0000.014
getVariableLengthData0.0120.0000.009
heterozygosity0.1680.0040.173
hwe0.0840.0000.083
inbreedCoeff0.1640.0000.164
isSNV0.0000.0040.004
isVariant0.0040.0000.006
meanBySample0.0360.0040.037
mendelErr0.0280.0040.033
missingGenotypeRate0.020.000.02
pca0.9560.0040.962
pedigree0.0080.0000.005
refFrac0.0520.0000.053
regression0.0920.0000.091
setVariantID0.0040.0000.008
titv0.1920.0040.197