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BioC 3.4: CHECK report for genomation on zin1

This page was generated on 2016-09-21 03:39:29 -0700 (Wed, 21 Sep 2016).

Package 488/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomation 1.5.5
Altuna Akalin , Vedran Franke
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genomation
Last Changed Rev: 119336 / Revision: 121152
Last Changed Date: 2016-07-13 04:58:20 -0700 (Wed, 13 Jul 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genomation
Version: 1.5.5
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.5.5.tar.gz
StartedAt: 2016-09-20 06:59:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:03:20 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 203.5 seconds
RetCode: 0
Status:  OK 
CheckDir: genomation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.5.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.5.5’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
* 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
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
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’
Undefined global functions or variables:
  SampleName value
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’
 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-3.4-bioc/meat/genomation.Rcheck/00check.log’
for details.


genomation.Rcheck/00install.out:

* installing *source* package ‘genomation’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include"   -fpic  -g -O2 -c idxstats.cpp -o idxstats.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o genomation.so RcppExports.o idxstats.o -L/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck/genomation/libs
** 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-methods0.4800.0080.517
ScoreMatrix-methods3.7040.1083.813
ScoreMatrixBin-methods0.5240.0160.542
ScoreMatrixList-methods0.7280.0000.725
annotateWithFeature-methods0.0360.0000.034
annotateWithFeatureFlank-methods0.1760.0000.175
annotateWithGeneParts-methods0.3320.0040.336
binMatrix-methods0.1600.0040.164
convertBed2Exons-methods0.0720.0000.072
convertBed2Introns-methods0.0680.0000.068
findFeatureComb-methods0.2720.0040.275
getFeatsWithTargetsStats-methods0.3480.0000.347
getFlanks-methods0.1080.0000.110
getRandomEnrichment-methods0.0000.0000.003
getTargetAnnotationStats-methods0.3520.0040.356
gffToGRanges0.0760.0000.075
heatMatrix0.6480.0800.729
heatMeta0.420.000.42
intersectScoreMatrixList-methods0.2360.0040.249
multiHeatMatrix0.7600.0040.764
orderBy-methods0.7720.0040.775
patternMatrix-methods0.1040.0040.111
plotGeneAnnotation-methods0.6640.0080.671
plotMeta0.7920.0080.797
plotTargetAnnotation-methods0.3120.0080.320
readBed0.0520.0080.058
readBroadPeak0.0320.0040.035
readFeatureFlank-methods0.1080.0040.113
readGeneric0.0360.0040.039
readNarrowPeak0.0400.0040.041
readTranscriptFeatures-methods0.1680.0000.169
scaleScoreMatrix-methods0.1760.0000.173
scaleScoreMatrixList0.8000.0040.804