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 3.2: CHECK report for gQTLBase on perceval

This page was generated on 2015-11-10 14:49:25 -0800 (Tue, 10 Nov 2015).

Package 459/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLBase 1.2.0
VJ Carey
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/gQTLBase
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gQTLBase
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLBase_1.2.0.tar.gz
StartedAt: 2015-11-10 05:38:08 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 05:43:32 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 323.6 seconds
RetCode: 0
Status:  OK 
CheckDir: gQTLBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLBase_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gQTLBase.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLBase/DESCRIPTION’ ... OK
* this is package ‘gQTLBase’ version ‘1.2.0’
* 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 ‘gQTLBase’ can be installed ... [19s/19s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extractByProbes: no visible binding for global variable ‘x’
.extractByRanges: no visible binding for global variable ‘x’
cb2range: no visible global function definition for ‘select’
cb2range: no visible global function definition for ‘IRanges’
dendroReduce.bj: no visible global function definition for ‘batchMap’
dendroReduce.fe: no visible binding for global variable ‘i’
DFstoreToFf: no visible binding for global variable ‘x’
ffapp2: no visible global function definition for ‘as.ff’
ffapp2: no visible global function definition for ‘appendLevels’
ffapp2: no visible global function definition for ‘as.which’
mergeGWhits: no visible global function definition for ‘genome’
storeApply: no visible binding for global variable ‘x’
storeApply2: no visible binding for global variable ‘x’
storeToFf: no visible binding for global variable ‘x’
* checking Rd files ... NOTE
prepare_Rd: ufeatByTiling.Rd:50-52: Dropping empty section \seealso
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [80s/83s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
storeApply      41.598  0.953  43.906
mergeCIstates   14.265  0.328  15.142
extractByProbes 10.559  0.276  11.117
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [456s/59s]
 [456s/59s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/gQTLBase.Rcheck/00check.log’
for details.


gQTLBase.Rcheck/00install.out:

* installing *source* package ‘gQTLBase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gQTLBase)

gQTLBase.Rcheck/gQTLBase-Ex.timings:

nameusersystemelapsed
ciseStore-class1.2270.0251.399
describeStore0.0010.0000.001
extractByProbes10.559 0.27611.117
mergeCIstates14.265 0.32815.142
storeApply41.598 0.95343.906
storeMapResults0.0010.0000.001
storeToFf1.4490.0521.572
ufeatByTiling0.0010.0000.001