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BioC 3.0: CHECK report for GeneAnswers on oaxaca

This page was generated on 2015-04-10 10:03:47 -0700 (Fri, 10 Apr 2015).

Package 344/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.8.0
Lei Huang and Gang Feng
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/GeneAnswers
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: GeneAnswers
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_2.8.0.tar.gz
StartedAt: 2015-04-09 23:46:01 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:57:19 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 677.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneAnswers.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘2.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’
  ‘Heatplus’ ‘RColorBrewer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GeneAnswers’ can be installed ... [16s/17s] OK
* checking installed package size ... NOTE
  installed size is 35.4Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.0Mb
    doc        1.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GeneAnswers/R/zzz.R’:
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

getHomoGeneIDs: no visible global function definition for ‘useMart’
getHomoGeneIDs: no visible global function definition for ‘getLDS’
getTotalGeneNumber: no visible global function definition for
  ‘count.mappedkeys’
getTotalGeneNumber: no visible global function definition for ‘toTable’
getTotalGeneNumber: no visible binding for global variable
  ‘reactomePATHNAME2ID’
* 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 ... [455s/488s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        59.117  2.372  61.585
GeneAnswers-class          35.025  1.600  38.355
buildNet                   27.474  1.291  29.084
GeneAnswers-package        27.050  1.312  28.613
geneAnswersBuilder         27.054  1.212  28.468
geneAnswersConcepts        26.862  0.713  27.729
geneAnswersHeatmap         26.768  0.745  27.747
geneAnswersHomoMapping     26.758  0.701  27.974
geneAnswersSort            26.667  0.679  27.362
getMultiLayerGraphIDs      26.173  0.975  27.274
getConnectedGraph          26.109  0.742  26.864
geneAnswersConceptRelation 25.871  0.717  26.868
geneAnswersConceptNet      25.677  0.750  27.693
geneAnswersChartPlots      24.405  0.883  25.872
getGOList                  13.827  1.222  42.175
* 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 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.

GeneAnswers.Rcheck/00install.out:

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

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.6420.0150.674
DOLite0.0370.0060.043
DOLiteTerm0.0040.0010.005
DmIALite0.0920.0050.099
GeneAnswers-class35.025 1.60038.355
GeneAnswers-package27.050 1.31228.613
HsIALite0.2890.0130.301
MmIALite0.0170.0070.024
RnIALite0.0090.0070.016
buildNet27.474 1.29129.084
caBIO.PATHGenes0.0000.0000.001
caBIO2entrez0.0000.0010.001
categoryNet000
chartPlots0.0420.0170.089
drawTable1.0410.0521.093
entrez2caBIO0.0010.0000.000
geneAnnotationHeatmap0.0030.0000.004
geneAnswersBuilder27.054 1.21228.468
geneAnswersChartPlots24.405 0.88325.872
geneAnswersConceptNet25.677 0.75027.693
geneAnswersConceptRelation25.871 0.71726.868
geneAnswersConcepts26.862 0.71327.729
geneAnswersHeatmap26.768 0.74527.747
geneAnswersHomoMapping26.758 0.70127.974
geneAnswersReadable59.117 2.37261.585
geneAnswersSort26.667 0.67927.362
geneConceptNet0.0000.0000.001
getCategoryList0.3480.0300.420
getCategoryTerms0.0710.0030.075
getConceptTable1.0010.0521.054
getConnectedGraph26.109 0.74226.864
getDOLiteTerms0.0050.0010.005
getGOList13.827 1.22242.175
getHomoGeneIDs0.3320.0150.348
getListGIF0.0010.0000.001
getMultiLayerGraphIDs26.173 0.97527.274
getNextGOIDs0.1250.0050.131
getPATHList0.0630.0050.068
getPATHTerms0.0370.0040.040
getREACTOMEPATHList0.0010.0000.000
getREACTOMEPATHTerms0.0010.0000.001
getSingleLayerGraphIDs0.0040.0010.004
getSymbols0.0480.0030.052
getTotalGeneNumber0.2070.0170.226
getcaBIOPATHList0.0010.0000.001
getcaBIOPATHTerms0.0010.0010.000
groupReport1.0560.0561.113
humanExpr0.0070.0010.008
humanGeneInput0.0040.0010.004
mouseExpr0.0060.0010.006
mouseGeneInput0.0050.0000.005
sampleGroupsData0.1300.0370.167
searchEntrez0.0000.0000.001
topCategory0.0010.0000.001
topCategoryGenes0.0010.0000.000
topDOLITE0.0010.0000.001
topDOLITEGenes0.0010.0000.000
topGO0.0000.0010.001
topGOGenes000
topPATH0.0010.0000.001
topPATHGenes0.0010.0000.000
topREACTOME.PATH0.0010.0000.001
topREACTOME.PATHGenes000
topcaBIO.PATH0.0000.0000.001