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BioC 3.1: CHECK report for genomation on morelia

This page was generated on 2015-10-09 09:42:29 -0700 (Fri, 09 Oct 2015).

Package 391/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomation 1.0.0
Altuna Akalin , Vedran Franke
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/genomation
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: genomation
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.0.0.tar.gz
StartedAt: 2015-10-09 02:15:53 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:19:07 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 193.6 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/genomation.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genomation’ can be installed ... [15s/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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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
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 ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’ [22s/22s]
 [22s/22s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/genomation.Rcheck/00check.log’
for details.


genomation.Rcheck/00install.out:

* installing *source* package ‘genomation’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (genomation)

genomation.Rcheck/genomation-Ex.timings:

nameusersystemelapsed
AnnotationByGeneParts-methods0.8970.0260.923
ScoreMatrix-methods0.0010.0010.002
ScoreMatrixBin-methods0.0010.0000.001
ScoreMatrixList-methods0.0010.0000.001
annotateWithFeature-methods0.0450.0010.045
annotateWithFeatureFlank-methods0.3450.0210.365
annotateWithGeneParts-methods000
binMatrix-methods0.0010.0000.001
convertBed2Exons-methods0.1190.0210.140
convertBed2Introns-methods0.1190.0350.155
findFeatureComb-methods0.4990.0150.514
getFeatsWithTargetsStats-methods0.4590.0050.464
getFlanks-methods0.1940.0030.198
getRandomEnrichment-methods0.0010.0000.001
getTargetAnnotationStats-methods0.4840.0030.487
gffToGRanges0.0010.0000.001
heatMatrix0.0010.0000.001
heatMeta0.0010.0000.001
intersectScoreMatrixList-methods0.0010.0000.001
multiHeatMatrix0.0010.0000.001
orderBy-methods0.0010.0000.001
plotGeneAnnotation-methods0.0010.0010.001
plotMeta0.0010.0000.001
plotTargetAnnotation-methods0.6010.0130.614
readBed0.0010.0000.000
readBroadPeak0.0010.0000.001
readFeatureFlank-methods000
readGeneric0.0000.0010.000
readNarrowPeak0.0000.0000.001
readTranscriptFeatures-methods000
scaleScoreMatrix-methods000
scaleScoreMatrixList0.0010.0000.001