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BioC 3.0: CHECK report for SeqVarTools on perceval

This page was generated on 2015-04-10 09:58:31 -0700 (Fri, 10 Apr 2015).

Package 815/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqVarTools 1.4.0
Stephanie M. Gogarten , Xiuwen Zheng
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SeqVarTools
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: SeqVarTools
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqVarTools_1.4.0.tar.gz
StartedAt: 2015-04-10 06:17:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:25:55 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 480.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SeqVarTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqVarTools_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SeqVarTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SeqVarTools’ can be installed ... [38s/39s] 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 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 ... NOTE
setVariantID: no visible global function definition for ‘openfn.gds’
setVariantID: no visible global function definition for ‘index.gdsn’
setVariantID: no visible global function definition for ‘read.gdsn’
setVariantID: no visible global function definition for ‘closefn.gds’
setVariantID: no visible global function definition for ‘objdesp.gdsn’
setVariantID: no visible global function definition for ‘delete.gdsn’
setVariantID: no visible global function definition for ‘add.gdsn’
* 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 ... [26s/26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [67s/68s]
 [68s/68s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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
allele-methods0.0410.0040.059
alleleFrequency0.8520.0260.881
applyMethod1.4270.0551.483
duplicateDiscordance0.0210.0020.023
getGenotype0.0120.0030.014
getVariableLengthData0.0120.0030.015
heterozygosity0.3610.0460.407
hwe0.1520.0150.175
inbreedCoeff0.3220.0280.351
isSNV0.0090.0020.010
isVariant0.0120.0030.016
meanBySample0.0600.0040.065
mendelErr0.0500.0020.052
missingGenotypeRate0.0530.0070.061
pca1.8860.0201.907
pedigree0.0100.0020.012
setVariantID0.0190.0060.044
titv0.6390.0230.663