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BioC 3.2: CHECK report for genomation on zin1

This page was generated on 2016-04-23 10:14:21 -0700 (Sat, 23 Apr 2016).

Package 416/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomation 1.2.2
Altuna Akalin , Vedran Franke
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/genomation
Last Changed Rev: 112480 / Revision: 116712
Last Changed Date: 2016-01-12 12:58:17 -0800 (Tue, 12 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genomation
Version: 1.2.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.2.2.tar.gz
StartedAt: 2016-04-23 01:01:35 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:04:54 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 198.6 seconds
RetCode: 0
Status:  OK 
CheckDir: genomation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/genomation.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.2.2’
* package encoding: latin1
* 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 ... NOTE
Found the following non-portable file paths:
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_120c592ae70227a80bd71d1131ccc4c2.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_120c592ae70227a80bd71d1131ccc4c2.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_120c592ae70227a80bd71d1131ccc4c2.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_03185a66520de729150cfb1852bb5006.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_03185a66520de729150cfb1852bb5006.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_03185a66520de729150cfb1852bb5006.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_86490e788fab0c8f043453bf99202c3f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_86490e788fab0c8f043453bf99202c3f.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_86490e788fab0c8f043453bf99202c3f.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_576afc3563af83ed74ec03c727f4232b.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_576afc3563af83ed74ec03c727f4232b.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_576afc3563af83ed74ec03c727f4232b.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_ac25db6b009507ff592afbe5ad95cfb8.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_ac25db6b009507ff592afbe5ad95cfb8.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_ac25db6b009507ff592afbe5ad95cfb8.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_756de4ecb8244a6a4b602d0075d5a4d7.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_756de4ecb8244a6a4b602d0075d5a4d7.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_756de4ecb8244a6a4b602d0075d5a4d7.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ctcfScoreMatrixList_f5b41013be63202fc6e4ca4190080810.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ctcfScoreMatrixList_f5b41013be63202fc6e4ca4190080810.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ctcfScoreMatrixList_f5b41013be63202fc6e4ca4190080810.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/eadAllPeaks_36192456734452b2100d08d310cad6c2.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/genomationDataInfo_2d3a9aa825913c08a2d268e342271e64.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationDataInfo_2d3a9aa825913c08a2d268e342271e64.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationDataInfo_2d3a9aa825913c08a2d268e342271e64.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationInfo_56448e256997dd20b678500e1bca7745.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationInfo_56448e256997dd20b678500e1bca7745.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationInfo_56448e256997dd20b678500e1bca7745.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/getFiles_annotation_cbbe016b6b24e785b0c354542e84fd74.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/getFiles_annotation_cbbe016b6b24e785b0c354542e84fd74.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/getFiles_annotation_cbbe016b6b24e785b0c354542e84fd74.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix1_873a36544c87e697c7bd9c73cc34f235.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix1_873a36544c87e697c7bd9c73cc34f235.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_d82f3a2e2e4ccfd78e50d40d2a12b093.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_d82f3a2e2e4ccfd78e50d40d2a12b093.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_d82f3a2e2e4ccfd78e50d40d2a12b093.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_c268e7a6897025a669bbb5afec2ebee7.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_c268e7a6897025a669bbb5afec2ebee7.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_c268e7a6897025a669bbb5afec2ebee7.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_425b687c1099c087210bd2603feaa0e2.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_425b687c1099c087210bd2603feaa0e2.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_425b687c1099c087210bd2603feaa0e2.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_ed86a2e320551d792bfdb29f9b2ea7f5.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_ed86a2e320551d792bfdb29f9b2ea7f5.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_ed86a2e320551d792bfdb29f9b2ea7f5.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_86bafba39ca9c9065bfe9c5829a59c89.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_86bafba39ca9c9065bfe9c5829a59c89.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_86bafba39ca9c9065bfe9c5829a59c89.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_cd62ea47fa5529e7161f0ae71660517f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_cd62ea47fa5529e7161f0ae71660517f.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_cd62ea47fa5529e7161f0ae71660517f.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_8fb1f19e8eb373f02424928d788134d6.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_8fb1f19e8eb373f02424928d788134d6.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_8fb1f19e8eb373f02424928d788134d6.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_e7a6174381584799782fe2f2c71127ec.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_e7a6174381584799782fe2f2c71127ec.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_e7a6174381584799782fe2f2c71127ec.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_004bdbea6b4b145d3c617cbe438b926f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_004bdbea6b4b145d3c617cbe438b926f.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_004bdbea6b4b145d3c617cbe438b926f.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_77020ba43747b40a8f546d325b3d23d7.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_77020ba43747b40a8f546d325b3d23d7.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_77020ba43747b40a8f546d325b3d23d7.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_da0574d00782abb0c797e859848f1a67.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_da0574d00782abb0c797e859848f1a67.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_da0574d00782abb0c797e859848f1a67.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_13360a2f103c552fbfd17d7c842ab0f4.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_13360a2f103c552fbfd17d7c842ab0f4.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_13360a2f103c552fbfd17d7c842ab0f4.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_6ec4137c859474a072bfcdf4b7710e9c.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_6ec4137c859474a072bfcdf4b7710e9c.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_6ec4137c859474a072bfcdf4b7710e9c.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_72c0c578355ed71e58e34d1544b3218f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_72c0c578355ed71e58e34d1544b3218f.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_72c0c578355ed71e58e34d1544b3218f.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGff1_f9948cd9fd6b2842c5da87209d48b29f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGff2_256845055c11ab38cca86adc58cf259f.RData
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  genomation/vignettes/GenomationManual-knitr_cache/html/readTranscriptFeatures_f8c7401a49cf740fadba4bb2cc7c3799.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readTranscriptFeatures_f8c7401a49cf740fadba4bb2cc7c3799.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/selectBamChipseq_c5ffdbd2a4bb43cdae77d5dccab7b2c4.RData
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  genomation/vignettes/GenomationManual-knitr_cache/html/selectBamChipseq_c5ffdbd2a4bb43cdae77d5dccab7b2c4.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/unnamed-chunk-1_6489b0da555c03e3633f9c2a0ea6d387.rdb
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  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_935005b22c58641fabbed76ebce7bc42.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_935005b22c58641fabbed76ebce7bc42.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_935005b22c58641fabbed76ebce7bc42.rdx

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genomation’ can be installed ... [16s/16s] 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
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘GenomicAlignments:::invertRleStrand’
  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
heatMeta: no visible binding for global variable ‘a’
ScoreMatrixBin,GRanges-GRanges : .local: no visible global function
  definition for ‘runValue’
plotGeneAnnotation,list: no visible binding for global variable
  ‘SampleName’
plotGeneAnnotation,list: no visible binding for global variable ‘value’
randomizeFeature,GRanges : <anonymous>: no visible global function
  definition for ‘Rle’
randomizeFeature,GRanges: no visible global function definition for
  ‘runValue’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘cache’
Please remove from your package.
* checking examples ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [24s/24s]
 [24s/24s] 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

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/genomation.Rcheck/00check.log’
for details.

genomation.Rcheck/00install.out:

* installing *source* package ‘genomation’ ...
** 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 (genomation)

genomation.Rcheck/genomation-Ex.timings:

nameusersystemelapsed
AnnotationByGeneParts-methods0.8320.0320.959
ScoreMatrix-methods3.5320.0203.570
ScoreMatrixBin-methods0.6240.0000.624
ScoreMatrixList-methods0.8110.0040.814
annotateWithFeature-methods0.0340.0000.034
annotateWithFeatureFlank-methods0.1980.0000.198
annotateWithGeneParts-methods0.450.000.45
binMatrix-methods0.2220.0000.221
convertBed2Exons-methods0.0810.0000.082
convertBed2Introns-methods0.0890.0000.088
findFeatureComb-methods0.3350.0000.335
getFeatsWithTargetsStats-methods0.4240.0040.427
getFlanks-methods0.1250.0000.126
getRandomEnrichment-methods0.0030.0000.003
getTargetAnnotationStats-methods0.4130.0040.416
gffToGRanges0.0720.0000.072
heatMatrix1.1970.0041.200
heatMeta0.8340.0040.837
intersectScoreMatrixList-methods0.3110.0000.311
multiHeatMatrix1.1120.0081.120
orderBy-methods0.8490.0000.848
patternMatrix-methods0.160.000.16
plotGeneAnnotation-methods0.8420.0080.849
plotMeta0.8950.0000.894
plotTargetAnnotation-methods0.4050.0000.406
readBed0.0600.0120.077
readBroadPeak0.0380.0080.046
readFeatureFlank-methods0.1420.0040.146
readGeneric0.0440.0040.048
readNarrowPeak0.0420.0040.046
readTranscriptFeatures-methods0.2260.0080.234
scaleScoreMatrix-methods0.2300.0040.238
scaleScoreMatrixList0.8590.0040.862