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BioC 3.1: CHECK report for rnaSeqMap on zin2

This page was generated on 2015-10-09 09:24:08 -0700 (Fri, 09 Oct 2015).

Package 834/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaSeqMap 2.26.0
Michal Okoniewski
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/rnaSeqMap
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  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: rnaSeqMap
Version: 2.26.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings rnaSeqMap_2.26.0.tar.gz
StartedAt: 2015-10-09 05:03:43 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:05:54 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 130.4 seconds
RetCode: 0
Status:  OK 
CheckDir: rnaSeqMap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings rnaSeqMap_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/rnaSeqMap.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaSeqMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rnaSeqMap’ version ‘2.26.0’
* 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 ‘rnaSeqMap’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.chr.convert’ ‘.countz’ ‘.munion’ ‘.tunion’ ‘.wytnij’ ‘getBamData’
  ‘newSeqReads’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
qq_derivative_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F):
  partial argument match of 'plot' to 'plot.it'
qq_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F): partial
  argument match of 'plot' to 'plot.it'
.exonCoverage: no visible global function definition for ‘exon.details’
.fillRleList: no visible global function definition for ‘Rle’
.geneCoverage: no visible global function definition for ‘gene.details’
.munion: no visible global function definition for ‘exon.details’
.munion: no visible global function definition for ‘gene.to.exon’
.rsCount: no visible global function definition for ‘gene.details’
.tunion: no visible global function definition for ‘exon.details’
.tunion: no visible global function definition for ‘transcript.to.exon’
addBamData: no visible global function definition for ‘phenoData’
addBamData: no visible global function definition for ‘phenoData<-’
averageND: no visible global function definition for ‘Rle’
bam2sig: no visible global function definition for ‘dbGetQuery’
combineND: no visible global function definition for ‘Rle’
distrCOVPlot: no visible global function definition for ‘gene.details’
distrCOVPlot: no visible global function definition for
  ‘gene.to.transcript’
distrCOVPlot: no visible global function definition for ‘exon.details’
distrCOVPlot: no visible global function definition for
  ‘transcript.to.exon’
distrCOVPlotg: no visible global function definition for ‘gene.details’
distrCOVPlotg: no visible global function definition for ‘exon.details’
distrCOVPlotg: no visible global function definition for ‘gene.to.exon’
distrCOVPlotg: no visible global function definition for
  ‘gene.to.transcript’
distrCOVPlotg: no visible global function definition for
  ‘transcript.to.exon’
generatorAdd: no visible global function definition for ‘Rle’
generatorAddSquare: no visible global function definition for ‘Rle’
generatorMultiply: no visible global function definition for ‘Rle’
generatorPeak: no visible global function definition for ‘Rle’
generatorSynth: no visible global function definition for ‘Rle’
getCoverageFromRS: no visible global function definition for
  ‘phenoData’
getSIFromND: no visible global function definition for ‘Rle’
newSeqReadsFromGene: no visible global function definition for
  ‘gene.details’
plotExonCoverage: no visible global function definition for
  ‘exon.details’
plotGeneCoverage: no visible global function definition for
  ‘gene.details’
plotGeneExonCoverage: no visible global function definition for
  ‘gene.details’
plotGeneExonCoverage: no visible global function definition for
  ‘exon.details’
plotGeneExonCoverage: no visible global function definition for
  ‘gene.to.exon’
spaceInChromosome: no visible binding for global variable ‘out’
sumND: no visible global function definition for ‘Rle’
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/rnaSeqMap.Rcheck/00check.log’
for details.


rnaSeqMap.Rcheck/00install.out:

* installing *source* package ‘rnaSeqMap’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gcoverage.c -o gcoverage.o
gcoverage.c: In function ‘gcoverage’:
gcoverage.c:7:31: warning: variable ‘nc’ set but not used [-Wunused-but-set-variable]
     int  start, i, j, na, nb, nc, nwyn;
                               ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ghistogram.c -o ghistogram.o
ghistogram.c: In function ‘ghistogram’:
ghistogram.c:9:10: warning: variable ‘xa’ set but not used [-Wunused-but-set-variable]
     int *xa, *xb, *xab;
          ^
ghistogram.c:8:20: warning: variable ‘nb’ set but not used [-Wunused-but-set-variable]
  int i, j, l , na, nb, nab, Is;
                    ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c regionmining.c -o regionmining.o
regionmining.c: In function ‘regionmining’:
regionmining.c:22:18: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
     int current, start, param, minsup,*xwyn; 
                  ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c splicingind.c -o splicingind.o
splicingind.c: In function ‘splicingind’:
splicingind.c:8:13: warning: variable ‘nb’ set but not used [-Wunused-but-set-variable]
  int j, na, nb, nab;
             ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/libs
** 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 (rnaSeqMap)

rnaSeqMap.Rcheck/rnaSeqMap-Ex.timings:

nameusersystemelapsed
addBamData0.0010.0000.000
addDataToReadset000
addExperimentsToReadset0.0010.0000.000
averageND0.0010.0000.000
bam2sig0.0000.0000.001
buildDESeq0.0010.0000.001
buildDGEList0.0010.0000.000
findRegionsAsIR0.0000.0000.001
findRegionsAsND0.0010.0000.000
gRanges2CamelMeasures0.0000.0000.001
geneInChromosome0.0010.0000.000
generators0.0000.0030.001
getBamData0.0000.0000.001
getCoverageFromRS0.0000.0010.000
getFCFromND0.0000.0000.001
getSIFromND0.0010.0000.000
getSumsExp0.0000.0000.001
measures0.0010.0000.000
normalizations0.0000.0000.001
normalizeBySum0.0010.0000.000
parseGff30.0000.0000.001
plotGeneCoverage0.0010.0000.000
readsInRange0.0000.0000.001
regionBasedCoverage0.0010.0000.000
regionCoverage0.0000.0000.001
rs.list0.0010.0000.000
setSpecies0.0000.0000.001
spaceInChromosome0.0010.0000.000