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BioC 2.14: CHECK report for CAGEr on moscato2

This page was generated on 2014-10-08 08:55:21 -0700 (Wed, 08 Oct 2014).

Package 115/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.6.1
Vanja Haberle
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CAGEr
Last Changed Rev: 90954 / Revision: 95116
Last Changed Date: 2014-06-03 04:02:31 -0700 (Tue, 03 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CAGEr
Version: 1.6.1
Command: rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.6.1.tar.gz >CAGEr-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.6.1.tar.gz
StartedAt: 2014-10-07 23:22:00 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:30:06 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 485.7 seconds
RetCode: 0
Status:  OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.6.1.tar.gz >CAGEr-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/CAGEr.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.6.1'
* 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 whether package 'CAGEr' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cluster.ctss.strand: no visible binding for global variable 'tpm'
.ctss2clusters : <anonymous>: no visible binding for global variable
  'chr'
.ctss2clusters.predef : <anonymous>: no visible binding for global
  variable 'chr'
.distclu: no visible binding for global variable 'tpm'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'removedG'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'pos'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'V1'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'V2'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'nr_tags'
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable 'num'
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable 'nr_tags'
.getCumsum : <anonymous>: no visible binding for global variable 'chr'
.getCumsumChr2: no visible binding for global variable 'chr'
.getTotalTagCount: no visible binding for global variable 'tpm'
.getTotalTagCount: no visible binding for global variable
  'consensus.cluster'
.make.consensus.clusters: no visible binding for global variable 'tpm'
.paraclu: no visible binding for global variable 'tpm'
.paraclu3 : <anonymous>: no visible binding for global variable 'chr'
.paraclu3: no visible binding for global variable 'chr'
.paraclu3: no visible binding for global variable 'max_d'
.paraclu3: no visible binding for global variable 'min_d'
.paraclu3: no visible binding for global variable 'tpm'
.plotReverseCumulative: no visible binding for global variable 'num'
.plotReverseCumulative: no visible binding for global variable
  'nr_tags'
.predefined.clusters: no visible binding for global variable 'tpm'
.remove.added.G : <anonymous>: no visible binding for global variable
  'chr'
.remove.added.G: no visible binding for global variable 'removedG'
.remove.added.G: no visible binding for global variable 'chr'
.remove.added.G: no visible binding for global variable 'pos'
.remove.added.G: no visible binding for global variable 'nr_tags'
.remove.added.G: no visible binding for global variable 'tag_count'
.summarize.clusters: no visible binding for global variable 'chr'
.summarize.clusters: no visible binding for global variable 'pos'
.summarize.clusters: no visible binding for global variable 'tpm'
.summarize.clusters: no visible binding for global variable 'cluster'
.summarize.clusters: no visible binding for global variable 'nr_ctss'
.summarize.clusters.predef: no visible binding for global variable
  'chr'
.summarize.clusters.predef: no visible binding for global variable
  'pos'
.summarize.clusters.predef: no visible binding for global variable
  'tpm'
.summarize.clusters.predef: no visible binding for global variable
  'cluster'
aggregateTagClusters,CAGEset: no visible binding for global variable
  'consensus.cluster'
aggregateTagClusters,CAGEset: no visible binding for global variable
  'chr'
aggregateTagClusters,CAGEset: no visible binding for global variable
  'tpm'
cumulativeCTSSdistribution,CAGEset: no visible binding for global
  variable 'tpm'
extractExpressionClass,CAGEset: no visible binding for global variable
  'expression_class'
getCTSS,CAGEset: no visible binding for global variable 'tag_count'
getCTSS,CAGEset: no visible binding for global variable 'chr'
getCTSS,CAGEset: no visible binding for global variable 'pos'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'groupX.tpm'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'groupY.tpm'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'shifting.score'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'fdr.KS'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ENCODEtissueCAGEfly'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ENCODEhumanCellLinesSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOMhumanSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOMmouseSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOM5humanSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOM5mouseSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ZebrafishSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ZebrafishCAGE'
scoreShift,CAGEset-character-character : <anonymous>: no visible
  binding for global variable 'consensus.cluster'
scoreShift,CAGEset-character-character: no visible binding for global
  variable 'tagcount'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [93s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           36.98   0.66   50.23
plotCorrelation             6.29   1.73    8.02
quantilePositions           6.16   0.03    6.19
scoreShift                  6.05   0.00    6.05
cumulativeCTSSdistribution  5.57   0.25    5.82
** running examples for arch 'x64' ... [103s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           41.81   1.09   54.23
plotCorrelation             7.16   2.13   10.18
cumulativeCTSSdistribution  7.05   0.19    7.24
scoreShift                  6.18   0.00    6.18
quantilePositions           5.65   0.03    5.69
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/CAGEr.Rcheck/00check.log'
for details.

CAGEr.Rcheck/00install.out:


install for i386

* installing *source* package 'CAGEr' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.6.1.zip
* DONE (CAGEr)

CAGEr.Rcheck/examples_i386/CAGEr-Ex.timings:

nameusersystemelapsed
CAGEset-class000
CTSSclusteringMethod0.020.010.03
CTSScoordinates0.040.000.05
CTSSnormalizedTpm0.030.020.04
CTSStagCount0.040.000.04
aggregateTagClusters1.060.011.09
clusterCTSS2.020.132.15
consensusClusters0.040.000.03
consensusClustersTpm0.030.000.03
cumulativeCTSSdistribution5.570.255.82
exportCTSStoBedGraph0.650.010.87
exportToBed0.770.000.77
expressionClasses0.030.000.03
extractExpressionClass0.040.000.05
genomeName0.030.000.03
getCTSS0.180.000.17
getExpressionProfiles0.600.000.61
getShiftingPromoters0.040.020.05
importPublicData36.98 0.6650.23
inputFiles0.030.000.03
inputFilesType0.040.000.03
librarySizes0.030.000.03
mergeSamples0.060.000.06
normalizeTagCount0.060.010.08
plotCorrelation6.291.738.02
plotExpressionProfiles0.390.020.42
plotInterquantileWidth0.060.000.06
plotReverseCumulatives0.080.000.08
quantilePositions6.160.036.19
sampleLabels0.050.000.05
scoreShift6.050.006.05
setColors0.030.000.04
tagClusters0.030.000.03

CAGEr.Rcheck/examples_x64/CAGEr-Ex.timings:

nameusersystemelapsed
CAGEset-class000
CTSSclusteringMethod0.020.000.01
CTSScoordinates0.030.000.03
CTSSnormalizedTpm0.040.000.03
CTSStagCount0.040.000.05
aggregateTagClusters1.280.021.31
clusterCTSS2.750.072.82
consensusClusters0.030.000.03
consensusClustersTpm0.030.000.03
cumulativeCTSSdistribution7.050.197.24
exportCTSStoBedGraph0.810.020.85
exportToBed0.910.000.90
expressionClasses0.030.010.03
extractExpressionClass0.030.000.03
genomeName0.030.000.03
getCTSS0.160.020.17
getExpressionProfiles0.480.000.48
getShiftingPromoters0.050.000.05
importPublicData41.81 1.0954.23
inputFiles0.030.000.03
inputFilesType0.010.000.01
librarySizes0.010.000.02
mergeSamples0.070.000.06
normalizeTagCount0.060.020.08
plotCorrelation 7.16 2.1310.18
plotExpressionProfiles0.590.020.63
plotInterquantileWidth0.080.000.07
plotReverseCumulatives0.120.000.13
quantilePositions5.650.035.69
sampleLabels0.030.000.03
scoreShift6.180.006.18
setColors0.030.000.03
tagClusters0.030.000.03