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BioC 3.0: CHECK report for GeneAnswers on perceval

This page was generated on 2015-04-10 09:54:43 -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: 2015-04-10 01:50:37 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:04:33 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 836.3 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-darwin10.8.0 (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 ... [20s/24s] OK
* checking installed package size ... NOTE
  installed size is 35.4Mb
  sub-directories of 1Mb or more:
    data       1.0Mb
    doc        1.6Mb
    External  32.4Mb
* 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’ ‘igraph’ ‘MASS’ ‘RColorBrewer’ ‘XML’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘biomaRt’ ‘GO.db’ ‘KEGG.db’ ‘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 ... [10m/10m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        74.503  4.459  79.118
GeneAnswers-class          48.201  3.436  77.921
GeneAnswers-package        34.439  2.297  36.784
getMultiLayerGraphIDs      34.196  1.706  35.960
buildNet                   32.527  2.268  34.836
geneAnswersSort            32.559  1.437  34.061
geneAnswersBuilder         31.838  2.030  34.052
geneAnswersConcepts        32.459  1.263  33.780
getConnectedGraph          32.146  1.341  33.511
geneAnswersConceptNet      31.952  1.261  33.270
geneAnswersChartPlots      31.395  1.540  32.996
geneAnswersHeatmap         31.672  1.173  32.945
geneAnswersHomoMapping     31.471  1.262  32.806
geneAnswersConceptRelation 30.959  1.198  32.188
getGOList                  18.209  2.013  22.218
* 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
DO0.7760.0280.834
DOLite0.0320.0100.041
DOLiteTerm0.0030.0010.005
DmIALite0.0800.0090.089
GeneAnswers-class48.201 3.43677.921
GeneAnswers-package34.439 2.29736.784
HsIALite0.2290.0110.240
MmIALite0.0140.0040.018
RnIALite0.0080.0030.011
buildNet32.527 2.26834.836
caBIO.PATHGenes0.0010.0010.000
caBIO2entrez0.0010.0000.000
categoryNet0.0010.0000.001
chartPlots0.0340.0180.214
drawTable1.0250.0441.070
entrez2caBIO0.0000.0000.001
geneAnnotationHeatmap0.0030.0000.003
geneAnswersBuilder31.838 2.03034.052
geneAnswersChartPlots31.395 1.54032.996
geneAnswersConceptNet31.952 1.26133.270
geneAnswersConceptRelation30.959 1.19832.188
geneAnswersConcepts32.459 1.26333.780
geneAnswersHeatmap31.672 1.17332.945
geneAnswersHomoMapping31.471 1.26232.806
geneAnswersReadable74.503 4.45979.118
geneAnswersSort32.559 1.43734.061
geneConceptNet0.0010.0000.001
getCategoryList0.3890.0440.465
getCategoryTerms0.1220.0050.127
getConceptTable1.1380.0431.181
getConnectedGraph32.146 1.34133.511
getDOLiteTerms0.0070.0010.008
getGOList18.209 2.01322.218
getHomoGeneIDs0.4040.0270.432
getListGIF0.0010.0000.001
getMultiLayerGraphIDs34.196 1.70635.960
getNextGOIDs0.1620.0050.166
getPATHList0.0910.0050.096
getPATHTerms0.0650.0020.068
getREACTOMEPATHList0.0010.0000.001
getREACTOMEPATHTerms0.0000.0000.001
getSingleLayerGraphIDs0.0030.0010.004
getSymbols0.0700.0040.074
getTotalGeneNumber0.2680.0210.289
getcaBIOPATHList0.0000.0010.001
getcaBIOPATHTerms0.0010.0000.000
groupReport1.0940.0571.152
humanExpr0.0080.0010.009
humanGeneInput0.0050.0010.005
mouseExpr0.0060.0010.006
mouseGeneInput0.0070.0020.009
sampleGroupsData0.1420.0450.187
searchEntrez0.0010.0000.001
topCategory0.0010.0000.001
topCategoryGenes0.0010.0000.000
topDOLITE0.0010.0000.001
topDOLITEGenes0.0010.0010.001
topGO0.0000.0000.001
topGOGenes0.0010.0000.001
topPATH0.0000.0000.001
topPATHGenes0.0010.0000.001
topREACTOME.PATH0.0010.0000.001
topREACTOME.PATHGenes0.0000.0000.001
topcaBIO.PATH0.0010.0000.001