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CHECK report for CAGEr on merida2

This page was generated on 2018-10-17 08:51:17 -0400 (Wed, 17 Oct 2018).

Package 179/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.22.3
Vanja Haberle , Charles Plessy
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: RELEASE_3_7
Last Commit: 5a42f82
Last Changed Date: 2018-06-25 03:38:36 -0400 (Mon, 25 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.22.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.22.3.tar.gz
StartedAt: 2018-10-16 20:13:37 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:22:05 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 508.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.22.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.22.3’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for '<<-'
  assignment to ‘idx’
clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for global
  variable ‘idx’
clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for '<<-'
  assignment to ‘idx’
clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for global
  variable ‘idx’
clusterCTSS,CAGEset: no visible binding for global variable ‘idx’
Undefined global functions or variables:
  idx
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
importPublicData           40.848  2.591  43.139
cumulativeCTSSdistribution 26.378  7.205  31.480
quantilePositions          28.744  0.854  29.634
aggregateTagClusters       13.438  4.341  11.493
clusterCTSS                10.064  0.405   8.746
distclu-functions           8.699  1.343   7.335
coverage-functions          5.018  0.616   5.674
scoreShift                  5.184  0.095   5.307
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck/00check.log’
for details.



Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CAGEr’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class4.3470.2994.681
CAGEr_Multicore0.0320.0060.038
CAGEset-class0.0040.0010.004
CTSS-class0.0420.0020.044
CTSSclusteringMethod0.0110.0010.012
CTSScoordinates0.0690.0000.071
CTSSnormalizedTpm1.5280.0911.275
CTSStagCount0.2800.0060.287
CTSStagCountTable0.0100.0000.011
CTSStoGenes0.5890.0040.597
CustomConsensusClusters1.0870.0101.099
GeneExpDESeq21.7010.0511.757
GeneExpSE0.0070.0000.008
QuantileWidthFunctions0.0020.0000.001
aggregateTagClusters13.438 4.34111.493
annotateCTSS1.5920.0181.618
byCtss0.0090.0000.010
clusterCTSS10.064 0.405 8.746
consensusClusterConvertors0.1560.0140.045
consensusClusters3.5440.4113.962
consensusClustersDESeq20.1310.0010.132
consensusClustersTpm0.0060.0000.007
coverage-functions5.0180.6165.674
cumulativeCTSSdistribution26.378 7.20531.480
distclu-functions8.6991.3437.335
exampleCAGEexp0.0120.0010.003
exampleCAGEset0.0880.0050.024
exportCTSStoBedGraph2.1030.0142.115
exportToBed4.2770.0504.341
expressionClasses0.0050.0000.006
extractExpressionClass0.0090.0000.010
genomeName0.0020.0000.002
getCTSS0.6660.1620.396
getExpressionProfiles0.8980.1090.514
getShiftingPromoters0.0050.0000.006
hanabi0.2500.0080.260
hanabiPlot0.3470.0250.375
import.CAGEscanMolecule0.0010.0000.000
import.CTSS0.0690.0020.071
import.bam0.0000.0000.001
import.bedCTSS0.0010.0000.001
import.bedScore0.0010.0000.001
import.bedmolecule0.0010.0000.001
importPublicData40.848 2.59143.139
inputFiles0.0080.0010.002
inputFilesType0.0080.0010.002
librarySizes0.0070.0020.002
mapStats0.4740.0360.292
mergeCAGEsets3.4490.0642.754
mergeSamples0.5230.0050.534
moleculesGR2CTSS0.1210.0000.122
normalizeTagCount0.6070.0140.464
parseCAGEscanBlocksToGrangeTSS0.0370.0020.039
plotAnnot2.7610.0102.797
plotCorrelation0.5850.0020.592
plotExpressionProfiles0.1530.0030.155
plotInterquantileWidth0.4430.0060.461
plotReverseCumulatives1.2540.0300.917
quantilePositions28.744 0.85429.634
ranges2annot0.1200.0000.121
ranges2genes0.0660.0000.068
ranges2names0.0650.0000.066
sampleLabels0.0010.0000.002
scoreShift5.1840.0955.307
seqNameTotalsSE0.0040.0000.005
setColors0.2970.0050.302
strandInvaders1.8142.7231.159
summariseChrExpr0.5710.0100.589
tagClusterConvertors0.2530.0030.256
tagClusters0.0560.0020.058