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BioC 2.13: CHECK report for CAGEr on moscato1

This page was generated on 2014-04-05 09:51:14 -0700 (Sat, 05 Apr 2014).

Package 106/750HostnameOS / ArchBUILDCHECKBUILD BIN
CAGEr 1.4.1
Vanja Haberle
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CAGEr
Last Changed Rev: 83252 / Revision: 88450
Last Changed Date: 2013-11-13 06:43:25 -0800 (Wed, 13 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CAGEr
Version: 1.4.1
Command: rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.4.1.tar.gz >CAGEr-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.4.1.tar.gz && mv CAGEr.buildbin-libdir/* CAGEr.Rcheck/ && rmdir CAGEr.buildbin-libdir
StartedAt: 2014-04-05 02:43:33 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:50:23 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 410.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/CAGEr.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.4.1'
* 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
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'BSgenome.Mmusculus.UCSC.mm9'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
.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'
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' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'CAGEr.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [60s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           16.08   0.35   17.19
plotCorrelation             5.53   1.98    7.63
cumulativeCTSSdistribution  5.41   0.28    5.72
scoreShift                  5.15   0.02    5.17
** running examples for arch 'x64' ... [83s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           18.87   0.32   19.19
plotCorrelation             7.00   2.27    9.45
cumulativeCTSSdistribution  9.06   0.20    9.27
quantilePositions           8.58   0.01    8.59
scoreShift                  8.57   0.00    8.57
* 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 were 4 notes.
See
  'D:/biocbld/bbs-2.13-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
Warning: replacing previous import by 'data.table::last' when loading 'CAGEr'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'data.table::last' when loading 'CAGEr'

install for x64

* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'data.table::last' when loading 'CAGEr'
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.4.1.zip
* DONE (CAGEr)

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

nameusersystemelapsed
CAGEset-class0.190.000.18
CTSSclusteringMethod0.020.020.04
CTSScoordinates0.030.000.03
CTSSnormalizedTpm0.190.000.19
CTSStagCount0.030.000.03
aggregateTagClusters0.840.000.84
clusterCTSS2.090.052.13
consensusClusters0.010.010.03
consensusClustersTpm0.020.020.04
cumulativeCTSSdistribution5.410.285.72
exportCTSStoBedGraph2.540.002.56
exportToBed0.850.000.84
expressionClasses0.030.000.03
extractExpressionClass0.030.000.03
genomeName0.010.010.04
getCTSS0.880.251.12
getExpressionProfiles0.640.000.64
getShiftingPromoters0.030.000.03
importPublicData16.08 0.3517.19
inputFiles0.030.000.03
inputFilesType0.040.000.03
librarySizes0.010.000.02
mergeSamples0.060.000.06
normalizeTagCount0.070.000.07
plotCorrelation5.531.987.63
plotExpressionProfiles0.370.002.11
plotInterquantileWidth0.030.010.04
plotReverseCumulatives0.060.000.07
quantilePositions4.990.004.99
sampleLabels0.030.000.03
scoreShift5.150.025.17
setColors0.030.000.03
tagClusters0.030.000.03

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

nameusersystemelapsed
CAGEset-class0.280.000.28
CTSSclusteringMethod0.040.000.04
CTSScoordinates0.050.000.05
CTSSnormalizedTpm0.340.000.34
CTSStagCount0.060.000.06
aggregateTagClusters1.410.002.20
clusterCTSS3.280.173.45
consensusClusters0.030.000.03
consensusClustersTpm0.020.020.03
cumulativeCTSSdistribution9.060.209.27
exportCTSStoBedGraph2.840.003.05
exportToBed1.420.001.42
expressionClasses0.030.000.03
extractExpressionClass0.060.000.06
genomeName0.030.000.04
getCTSS1.480.191.67
getExpressionProfiles0.810.001.20
getShiftingPromoters0.050.010.06
importPublicData18.87 0.3219.19
inputFiles0.030.000.03
inputFilesType0.020.000.01
librarySizes0.030.000.04
mergeSamples0.060.000.06
normalizeTagCount0.070.000.07
plotCorrelation7.002.279.45
plotExpressionProfiles0.630.000.62
plotInterquantileWidth0.060.000.07
plotReverseCumulatives0.110.000.11
quantilePositions8.580.018.59
sampleLabels0.030.000.03
scoreShift8.570.008.57
setColors0.030.000.03
tagClusters0.020.000.01