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 3.0: CHECK report for gCMAP on oaxaca

This page was generated on 2015-04-10 10:06:22 -0700 (Fri, 10 Apr 2015).

Package 337/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCMAP 1.10.2
Thomas Sandmann
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/gCMAP
Last Changed Rev: 99815 / Revision: 102249
Last Changed Date: 2015-02-25 15:04:52 -0800 (Wed, 25 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: gCMAP
Version: 1.10.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.10.2.tar.gz
StartedAt: 2015-04-09 23:40:27 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:46:22 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 355.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gCMAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gCMAP_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/gCMAP.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 ‘gCMAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCMAP’ version ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘bigmemoryExtras’
* 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 ‘gCMAP’ can be installed ... [36s/37s] 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
'library' or 'require' calls in package code:
  ‘DESeq’ ‘GO.db’ ‘KEGG.db’ ‘bigmemoryExtras’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘BiocGenerics’ ‘Category’ ‘annotate’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GSEABase’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘GSEABase:::.showGeneSet’
  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
.DESeq_nbinom: no visible global function definition for ‘conditions<-’
.DESeq_nbinom: no visible global function definition for ‘pData’
.DESeq_nbinom: no visible global function definition for ‘conditions’
.annotatedDataFrameFromMatrix: no visible global function definition
  for ‘annotatedDataFrameFrom’
.assayDataDimnames: no visible global function definition for
  ‘storageMode’
.gsealmPerm: no visible global function definition for ‘pData’
.gsealmPerm: no visible global function definition for ‘pData<-’
.harmonizeDimnames: no visible global function definition for
  ‘featureNames’
.harmonizeDimnames: no visible global function definition for
  ‘featureData’
.harmonizeDimnames: no visible global function definition for
  ‘sampleNames’
.harmonizeDimnames: no visible global function definition for
  ‘phenoData’
.harmonizeDimnames: no visible global function definition for
  ‘assayData’
.harmonizeDimnames: no visible global function definition for
  ‘featureNames<-’
.harmonizeDimnames: no visible global function definition for
  ‘assayData<-’
.harmonizeDimnames: no visible global function definition for
  ‘sampleNames<-’
.jg: no visible global function definition for ‘sampleNames’
.lookupAnno: no visible global function definition for ‘lookUp’
.map2indices: no visible global function definition for ‘ids2indices’
.map2indices: no visible global function definition for
  ‘symbols2indices’
.moderated_logFC: no visible global function definition for
  ‘sampleNames’
.moderated_logFC: no visible global function definition for ‘pData’
.probeAnno: no visible global function definition for ‘annotation’
.probeAnno: no visible global function definition for ‘featureNames’
.process_arrays: no visible global function definition for
  ‘assayDataNew’
.process_counts: no visible global function definition for
  ‘assayDataNew’
.vst_transform: no visible binding for global variable ‘counts’
CMAPCollection: no visible global function definition for
  ‘annotatedDataFrameFrom’
KEGG2cmap: no visible binding for global variable ‘KEGGPATHID2EXTID’
KEGG2cmap: no visible binding for global variable ‘KEGGPATHID2NAME’
KEGG2cmap: no visible global function definition for ‘incidence’
addFeatureData: no visible global function definition for ‘toTable’
addFeatureData: no visible global function definition for ‘annotation’
addFeatureData: no visible global function definition for
  ‘featureData<-’
annotate_eset_list: no visible binding for global variable ‘varLabels’
annotate_eset_list : <anonymous>: no visible global function definition
  for ‘pData’
center_eSet: no visible global function definition for
  ‘assayDataElementNames’
center_eSet: no visible global function definition for
  ‘assayDataElement’
center_eSet: no visible global function definition for
  ‘assayDataElement<-’
center_eSet: no visible global function definition for ‘pData’
center_eSet: no visible global function definition for ‘pData<-’
center_eSet: no visible global function definition for ‘varMetadata’
center_eSet: no visible global function definition for ‘varMetadata<-’
eSetOnDisk: no visible global function definition for ‘assayData’
eSetOnDisk: no visible global function definition for ‘storageMode<-’
eSetOnDisk: no visible global function definition for ‘assayData<-’
eSetOnDisk: no visible global function definition for
  ‘assayDataElementNames’
eSetOnDisk: no visible global function definition for
  ‘assayDataElement’
eSetOnDisk: no visible global function definition for ‘BigMatrix’
eSetProbeToGene: no visible global function definition for ‘pData<-’
eSetProbeToGene: no visible global function definition for ‘pData’
eSetProbeToGene: no visible global function definition for
  ‘featureData<-’
eSetProbeToGene: no visible global function definition for
  ‘annotation<-’
eSetProbeToGene: no visible global function definition for
  ‘assayDataElementNames’
eSetProbeToGene: no visible global function definition for
  ‘assayDataElement<-’
eSetProbeToGene: no visible global function definition for
  ‘assayDataElement’
eSetProbeToGene: no visible global function definition for
  ‘sampleNames’
eSetProbeToGene: no visible global function definition for
  ‘featureNames’
eset_instances: no visible global function definition for ‘sampleNames’
eset_instances : <anonymous>: no visible global function definition for
  ‘sampleNames’
eset_instances : <anonymous>: no visible global function definition for
  ‘pData’
eset_instances : <anonymous>: no visible global function definition for
  ‘pData<-’
generate_gCMAP_NChannelSet: no visible binding for global variable
  ‘featureNames’
generate_gCMAP_NChannelSet : <anonymous>: no visible global function
  definition for ‘varLabels’
generate_gCMAP_NChannelSet : <anonymous>: no visible global function
  definition for ‘newCountDataSet’
generate_gCMAP_NChannelSet : <anonymous>: no visible global function
  definition for ‘counts’
generate_gCMAP_NChannelSet : <anonymous>: no visible global function
  definition for ‘pData’
go2cmap: no visible binding for global variable ‘annotation’
go2cmap: no visible global function definition for ‘Term’
go2cmap: no visible global function definition for ‘incidence’
go2cmap: no visible global function definition for ‘experimentData’
go2cmap: no visible global function definition for ‘experimentData<-’
mapNmerge: no visible global function definition for ‘featureNames<-’
mapNmerge: no visible global function definition for ‘featureNames’
mapNmerge: no visible global function definition for ‘annotation<-’
mapNmerge: no visible global function definition for ‘annotation’
mapNmerge: no visible global function definition for ‘lookUp’
mapNmerge: no visible global function definition for
  ‘assayDataElementNames’
mapNmerge : <anonymous>: no visible global function definition for
  ‘assayDataElement’
mapNmerge : <anonymous>: no visible global function definition for
  ‘sampleNames’
mapNmerge: no visible global function definition for ‘storageMode<-’
mapNmerge: no visible global function definition for
  ‘AnnotatedDataFrame’
mapNmerge: no visible global function definition for ‘pData’
mapNmerge: no visible global function definition for ‘protocolData’
mapNmerge: no visible global function definition for ‘experimentData’
memorize: no visible global function definition for
  ‘assayDataElementNames’
memorize: no visible global function definition for ‘varMetadata’
memorize: no visible global function definition for ‘varMetadata<-’
memorize: no visible global function definition for ‘featureData’
memorize: no visible global function definition for ‘experimentData’
memorize: no visible global function definition for ‘annotation’
memorize: no visible global function definition for ‘protocolData’
mergeCMAPs: no visible global function definition for ‘annotation’
mergeCMAPs: no visible global function definition for
  ‘assayDataElementNames’
mergeCMAPs: no visible global function definition for ‘sampleNames’
mergeCMAPs: no visible global function definition for ‘varLabels’
mergeCMAPs: no visible global function definition for ‘featureNames’
mergeCMAPs: no visible global function definition for ‘annotation<-’
mergeCMAPs: no visible global function definition for
  ‘assayDataElement’
mergeCMAPs: no visible global function definition for
  ‘assayDataElement<-’
mergeCMAPs: no visible global function definition for ‘pData<-’
mergeCMAPs: no visible global function definition for ‘pData’
mergeCMAPs: no visible global function definition for ‘featureData<-’
mergeCMAPs: no visible global function definition for
  ‘AnnotatedDataFrame’
mergeCMAPs: no visible global function definition for ‘sampleNames<-’
pairwise_DESeq: no visible global function definition for ‘varLabels’
pairwise_DESeq: no visible global function definition for ‘pData’
pairwise_DESeq: no visible global function definition for ‘sampleNames’
pairwise_DESeq: no visible global function definition for
  ‘featureNames’
pairwise_compare: no visible global function definition for ‘varLabels’
pairwise_compare: no visible global function definition for ‘pData’
pairwise_compare: no visible global function definition for
  ‘sampleNames’
pairwise_compare: no visible global function definition for ‘exprs’
pairwise_compare: no visible global function definition for
  ‘featureNames’
pairwise_compare_limma: no visible global function definition for
  ‘varLabels’
pairwise_compare_limma: no visible global function definition for
  ‘pData’
pairwise_compare_limma: no visible global function definition for
  ‘sampleNames’
pairwise_compare_limma: no visible global function definition for
  ‘exprs’
pairwise_compare_limma: no visible global function definition for
  ‘featureNames’
pairwise_compare_limma: no visible global function definition for
  ‘eBayes’
pairwise_compare_limma: no visible global function definition for
  ‘lmFit’
pairwise_compare_limma: no visible global function definition for
  ‘topTable’
pickChannels: no visible global function definition for
  ‘assayDataElementNames’
pickChannels: no visible global function definition for ‘varMetadata’
pickChannels: no visible global function definition for ‘varMetadata<-’
pickChannels: no visible global function definition for ‘featureData’
pickChannels: no visible global function definition for
  ‘experimentData’
pickChannels: no visible global function definition for ‘annotation’
pickChannels: no visible global function definition for ‘protocolData’
splitPerturbations: no visible global function definition for ‘pData’
splitPerturbations : <anonymous>: no visible global function definition
  for ‘pData’
splitPerturbations : <anonymous>: no visible global function definition
  for ‘pData<-’
CMAPCollection,Matrix: no visible global function definition for
  ‘annotatedDataFrameFrom’
CMAPCollection,Matrix: no visible global function definition for
  ‘assayDataNew’
CMAPCollection,environment: no visible global function definition for
  ‘annotatedDataFrameFrom’
CMAPCollection,matrix: no visible global function definition for
  ‘annotatedDataFrameFrom’
CMAPCollection,matrix: no visible global function definition for
  ‘assayDataNew’
CMAPCollection,missing: no visible global function definition for
  ‘annotatedDataFrameFrom’
CMAPCollection,missing: no visible global function definition for
  ‘assayDataNew’
annotatedDataFrameFrom,Matrix: no visible global function definition
  for ‘annotatedDataFrameFrom’
camera_score,matrix-CMAPCollection: no visible global function
  definition for ‘ExpressionSet’
camera_score,matrix-GeneSet: no visible global function definition for
  ‘ExpressionSet’
camera_score,matrix-GeneSetCollection: no visible global function
  definition for ‘ExpressionSet’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘annotation’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘getAnnMap’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘annotation<-’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘featureNames’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘GeneSet’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘sampleNames’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘AnnoOrEntrezIdentifier’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘experimentData’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘abstract’
coerce,CMAPCollection-GeneSet: no visible global function definition
  for ‘pubMedIds’
coerce,CMAPCollection-GeneSetCollection: no visible global function
  definition for ‘annotation’
coerce,CMAPCollection-GeneSetCollection: no visible global function
  definition for ‘getAnnMap’
coerce,CMAPCollection-GeneSetCollection: no visible global function
  definition for ‘annotation<-’
coerce,CMAPCollection-GeneSetCollection: no visible global function
  definition for ‘sampleNames’
coerce,CMAPCollection-GeneSetCollection : <anonymous>: no visible
  global function definition for ‘featureNames’
coerce,CMAPCollection-GeneSetCollection : <anonymous>: no visible
  global function definition for ‘AnnoOrEntrezIdentifier’
coerce,CMAPCollection-GeneSetCollection : <anonymous>: no visible
  global function definition for ‘annotation’
coerce,CMAPCollection-GeneSetCollection : <anonymous>: no visible
  global function definition for ‘experimentData’
coerce,CMAPCollection-GeneSetCollection : <anonymous>: no visible
  global function definition for ‘abstract’
coerce,CMAPCollection-GeneSetCollection : <anonymous>: no visible
  global function definition for ‘pubMedIds’
coerce,CMAPCollection-GeneSetCollection: no visible global function
  definition for ‘GeneSetCollection’
coerce,CMAPResults-data.frame: no visible global function definition
  for ‘pData’
coerce,GeneSet-CMAPCollection: no visible global function definition
  for ‘setName’
coerce,GeneSet-CMAPCollection: no visible global function definition
  for ‘setName<-’
coerce,GeneSet-CMAPCollection: no visible global function definition
  for ‘GeneSetCollection’
coerce,GeneSet-CMAPCollection: no visible global function definition
  for ‘incidence’
coerce,GeneSet-CMAPCollection: no visible binding for global variable
  ‘geneIdType’
coerce,GeneSet-CMAPCollection: no visible global function definition
  for ‘annotation<-’
coerce,GeneSet-CMAPCollection: no visible global function definition
  for ‘annotation’
coerce,GeneSetCollection-CMAPCollection: no visible global function
  definition for ‘incidence’
coerce,GeneSetCollection-CMAPCollection: no visible binding for global
  variable ‘geneIdType’
coerce,GeneSetCollection-CMAPCollection: no visible global function
  definition for ‘annotation<-’
coerce,GeneSetCollection-CMAPCollection: no visible global function
  definition for ‘annotation’
coerce,GeneSetCollection-CMAPCollection: no visible binding for global
  variable ‘description’
coerce,GeneSetCollection-CMAPCollection: no visible global function
  definition for ‘pData’
coerce,GeneSetCollection-CMAPCollection: no visible global function
  definition for ‘pData<-’
coerce,MgsaMcmcResults-CMAPResults: no visible global function
  definition for ‘varMetadata’
coerce,MgsaMcmcResults-CMAPResults: no visible global function
  definition for ‘varMetadata<-’
coerce,list-CMAPCollection: no visible global function definition for
  ‘incidence’
connectivity_score,matrix-CMAPCollection: no visible global function
  definition for ‘ExpressionSet’
connectivity_score,matrix-GeneSetCollection: no visible global function
  definition for ‘ExpressionSet’
connectivity_score,matrix-SignedGeneSet: no visible global function
  definition for ‘ExpressionSet’
downIds,CMAPCollection : <anonymous>: no visible global function
  definition for ‘featureNames’
downIds,CMAPCollection: no visible global function definition for
  ‘sampleNames’
geneIds,CMAPCollection : <anonymous>: no visible global function
  definition for ‘featureNames’
geneIds,CMAPCollection: no visible global function definition for
  ‘sampleNames’
geneSign,SignedGeneSet: no visible global function definition for
  ‘geneColor’
geneSign<-,SignedGeneSet-character: no visible global function
  definition for ‘geneColor<-’
geneSign<-,SignedGeneSet-factor: no visible global function definition
  for ‘geneColor<-’
gsealm_jg_score,CMAPCollection-matrix: no visible global function
  definition for ‘ExpressionSet’
gsealm_jg_score,CMAPCollection-numeric: no visible global function
  definition for ‘ExpressionSet’
gsealm_jg_score,GeneSet-matrix: no visible global function definition
  for ‘ExpressionSet’
gsealm_jg_score,GeneSetCollection-matrix: no visible global function
  definition for ‘ExpressionSet’
incidence,GeneSetCollection : <anonymous>: no visible global function
  definition for ‘geneIds’
incidence,GeneSetCollection: no visible binding for global variable
  ‘geneIds’
incidence,GeneSetCollection: no visible binding for global variable
  ‘setName’
incidence,SignedGeneSet: no visible binding for global variable
  ‘geneIds’
incidence,SignedGeneSet: no visible binding for global variable
  ‘setName’
labels<-,CMAPResults: no visible global function definition for
  ‘varMetadata<-’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-GeneIdentifierType: no
  visible global function definition for ‘geneIds’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-GeneIdentifierType :
  <anonymous>: no visible global function definition for ‘GeneSet’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-GeneIdentifierType: no
  visible binding for global variable ‘mapIdentifiers’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-GeneIdentifierType: no
  visible binding for global variable ‘geneIds’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-GeneIdentifierType: no
  visible global function definition for ‘setName’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-GeneIdentifierType: no
  visible global function definition for ‘geneIdType’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-missing: no visible
  global function definition for ‘annotation’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-missing: no visible
  global function definition for ‘geneIdType’
mapIdentifiers,SignedGeneSet-GeneIdentifierType-missing: no visible
  global function definition for ‘mapIdentifiers’
members,CMAPCollection: no visible global function definition for
  ‘assayData’
mergeCollections,CMAPCollection-CMAPCollection: no visible global
  function definition for ‘featureNames’
mergeCollections,CMAPCollection-CMAPCollection: no visible global
  function definition for ‘pData’
mgsa_score,GeneSetCollection-CMAPCollection-character : <anonymous>: no
  visible global function definition for ‘geneIds’
mgsa_score,GeneSetCollection-CMAPCollection-character: no visible
  binding for global variable ‘setName’
mgsa_score,GeneSetCollection-NChannelSet-character : <anonymous>: no
  visible global function definition for ‘geneIds’
mgsa_score,GeneSetCollection-NChannelSet-character: no visible binding
  for global variable ‘setName’
mroast_score,matrix-CMAPCollection: no visible global function
  definition for ‘ExpressionSet’
mroast_score,matrix-GeneSet: no visible global function definition for
  ‘ExpressionSet’
mroast_score,matrix-GeneSetCollection: no visible global function
  definition for ‘ExpressionSet’
romer_score,matrix-CMAPCollection: no visible global function
  definition for ‘ExpressionSet’
romer_score,matrix-GeneSet: no visible global function definition for
  ‘ExpressionSet’
romer_score,matrix-GeneSetCollection: no visible global function
  definition for ‘ExpressionSet’
setSizes,CMAPCollection: no visible global function definition for
  ‘sampleNames’
show,CMAPResults: no visible global function definition for ‘varLabels’
show,SignedGeneSet: no visible global function definition for
  ‘selectSome’
signed,CMAPCollection: no visible global function definition for
  ‘pData’
signed,CMAPCollection: no visible global function definition for
  ‘sampleNames’
signed<-,CMAPCollection: no visible global function definition for
  ‘pData’
signed<-,CMAPCollection: no visible global function definition for
  ‘pData<-’
trend<-,CMAPResults: no visible global function definition for
  ‘updateObject’
upIds,CMAPCollection : <anonymous>: no visible global function
  definition for ‘featureNames’
upIds,CMAPCollection: no visible global function definition for
  ‘sampleNames’
wilcox_score,CMAPCollection-matrix: no visible global function
  definition for ‘ExpressionSet’
wilcox_score,CMAPCollection-numeric: no visible global function
  definition for ‘ExpressionSet’
wilcox_score,GeneSet-matrix: no visible global function definition for
  ‘ExpressionSet’
wilcox_score,GeneSet-numeric: no visible global function definition for
  ‘ExpressionSet’
wilcox_score,GeneSetCollection-matrix: no visible global function
  definition for ‘ExpressionSet’
wilcox_score,GeneSetCollection-numeric: no visible global function
  definition for ‘ExpressionSet’
zscores,CMAPResults: no visible global function definition for
  ‘varLabels’
* 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 ... [60s/59s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  13.282  0.418  18.346
romer_score-methods  8.460  0.610   9.119
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [43s/39s]
 [43s/40s] 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 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/gCMAP.Rcheck/00check.log’
for details.

gCMAP.Rcheck/00install.out:

* installing *source* package ‘gCMAP’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gCMAP)

gCMAP.Rcheck/gCMAP-Ex.timings:

nameusersystemelapsed
CMAPCollection-class1.0590.2831.033
CMAPResults-class3.2970.1013.402
KEGG2cmap0.0010.0000.001
SignedGeneSet-class0.0740.0010.075
annotate_eset_list0.1290.0070.160
camera_score-methods0.5650.0791.005
center_eSet0.0360.0010.037
connectivity_score-methods1.9901.1972.083
eSetOnDisk0.0100.0020.012
eset_instances0.3640.0770.442
featureScores-methods0.5180.3860.554
fisher_score-methods1.2170.5090.671
gCMAPData-dataset0.1680.0800.521
geneIndex-methods0.6380.2530.473
generate_gCMAP_NChannelSet0.2320.0260.259
gsealm_jg_score-methods1.3660.6160.870
gsealm_score-methods3.6700.1404.057
induceCMAPCollection-methods0.5870.2410.457
mapNmerge0.0010.0000.001
memorize0.0110.0010.012
mergeCMAPs0.1250.0190.143
mgsa_score-methods13.282 0.41818.346
minSetSize-methods0.7110.3610.532
mroast_score-methods1.1980.3491.135
romer_score-methods8.4600.6109.119
signedRankSumTest0.0030.0000.003
splitPerturbations0.0970.0050.105
wilcox_score-methods1.2960.6520.829