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BioC 3.2: CHECK report for genomation on oaxaca

This page was generated on 2016-04-23 10:28:39 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.2.2.tar.gz
StartedAt: 2016-04-23 00:29:19 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:33:55 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 276.0 seconds
RetCode: 0
Status:  OK 
CheckDir: genomation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genomation.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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_0b78bf955ff81e46a30e3d27eee2d7de.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_0b78bf955ff81e46a30e3d27eee2d7de.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_0b78bf955ff81e46a30e3d27eee2d7de.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_0d9608df0858df029f215f40d002e9e3.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_0d9608df0858df029f215f40d002e9e3.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_0d9608df0858df029f215f40d002e9e3.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_72871beca9bad5e97868d55ee0a7de0c.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_72871beca9bad5e97868d55ee0a7de0c.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_72871beca9bad5e97868d55ee0a7de0c.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_c4d665f4c8647693f03d65c43fb2eef3.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_c4d665f4c8647693f03d65c43fb2eef3.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_c4d665f4c8647693f03d65c43fb2eef3.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_159faf6939f13f06850f08c87769d2fd.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_159faf6939f13f06850f08c87769d2fd.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_159faf6939f13f06850f08c87769d2fd.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_1a243bcfb963da304f2627297086f25d.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_1a243bcfb963da304f2627297086f25d.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_8ac860b773f535104d5e35694de0883e.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_8ac860b773f535104d5e35694de0883e.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_8ac860b773f535104d5e35694de0883e.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_32e92219a4d5638035310d346e9c1e14.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_32e92219a4d5638035310d346e9c1e14.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_32e92219a4d5638035310d346e9c1e14.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_1633a9251ff0b30bbcdde77247472a35.RData
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  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_1633a9251ff0b30bbcdde77247472a35.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_fddf2ea1e2d0d8bdcdde18dffe3a6c9f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_fddf2ea1e2d0d8bdcdde18dffe3a6c9f.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_fddf2ea1e2d0d8bdcdde18dffe3a6c9f.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_e972554c3c2fa0ec298a7010b8fc16cd.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_e972554c3c2fa0ec298a7010b8fc16cd.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_1254c76631ce60c0262b71feca02fc4a.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_1254c76631ce60c0262b71feca02fc4a.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_1254c76631ce60c0262b71feca02fc4a.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_1b3071a3494de05edad5ef6d78faade7.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_1b3071a3494de05edad5ef6d78faade7.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_1b3071a3494de05edad5ef6d78faade7.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_ddefe78f50cecb51db03bbef6a05c792.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_ddefe78f50cecb51db03bbef6a05c792.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_ddefe78f50cecb51db03bbef6a05c792.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_b65b1bf828c7f621c05350e2f3a1c18b.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_b65b1bf828c7f621c05350e2f3a1c18b.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_b65b1bf828c7f621c05350e2f3a1c18b.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_c7ec55c29a324cc15987871a0c98a212.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_c7ec55c29a324cc15987871a0c98a212.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_c7ec55c29a324cc15987871a0c98a212.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_3341e737dc0e63f86a872e113e96f35e.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_3341e737dc0e63f86a872e113e96f35e.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_11378360c8cf64f64949774868dccaf5.rdb
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  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_a7d67ed4fcc296eaff5d1468d0fae742.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_a7d67ed4fcc296eaff5d1468d0fae742.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_2c8810ba1da051d6296ea078969e2cea.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_2c8810ba1da051d6296ea078969e2cea.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_2c8810ba1da051d6296ea078969e2cea.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGff1_e6d9c4d435324b8230f849f2cd3b8ec9.RData
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  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_02a06ad0675cbecfe2e7fa9b09d5158b.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_02a06ad0675cbecfe2e7fa9b09d5158b.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 ... [21s/35s] 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 ... [30s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [30s/30s]
 [30s/30s] 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
  ‘/Users/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-methods1.0660.0792.315
ScoreMatrix-methods3.8920.1424.037
ScoreMatrixBin-methods0.7410.0070.750
ScoreMatrixList-methods1.0760.0211.145
annotateWithFeature-methods0.0530.0010.053
annotateWithFeatureFlank-methods0.2830.0020.285
annotateWithGeneParts-methods0.5610.0080.570
binMatrix-methods0.2980.0050.303
convertBed2Exons-methods0.0860.0010.087
convertBed2Introns-methods0.1130.0020.115
findFeatureComb-methods0.5000.0060.505
getFeatsWithTargetsStats-methods0.5680.0060.575
getFlanks-methods0.1810.0020.183
getRandomEnrichment-methods0.0030.0010.005
getTargetAnnotationStats-methods0.5390.0070.546
gffToGRanges0.1030.0010.105
heatMatrix1.2960.0641.362
heatMeta1.0360.0801.118
intersectScoreMatrixList-methods0.3960.0050.426
multiHeatMatrix1.2950.0501.346
orderBy-methods1.0520.0111.064
patternMatrix-methods0.1960.0030.199
plotGeneAnnotation-methods1.0670.0181.086
plotMeta1.1270.0501.179
plotTargetAnnotation-methods0.5090.0100.520
readBed0.0430.0080.051
readBroadPeak0.0370.0040.042
readFeatureFlank-methods0.1720.0050.177
readGeneric0.0370.0030.040
readNarrowPeak0.0360.0050.042
readTranscriptFeatures-methods0.2260.0060.232
scaleScoreMatrix-methods0.2540.0050.258
scaleScoreMatrixList1.1120.0071.120