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CHECK report for rnaSeqMap on tokay1

This page was generated on 2021-05-06 12:33:19 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the rnaSeqMap package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1556/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaSeqMap 2.48.0  (landing page)
Michal Okoniewski
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/rnaSeqMap
Branch: RELEASE_3_12
Last Commit: a8c515e
Last Changed Date: 2020-10-27 10:39:23 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: rnaSeqMap
Version: 2.48.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rnaSeqMap.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rnaSeqMap_2.48.0.tar.gz
StartedAt: 2021-05-06 06:22:23 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:27:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 278.6 seconds
RetCode: 0
Status:   OK   
CheckDir: rnaSeqMap.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rnaSeqMap.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rnaSeqMap_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/rnaSeqMap.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rnaSeqMap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rnaSeqMap' version '2.48.0'
* 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 whether package 'rnaSeqMap' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.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'
.simplePlot: no visible global function definition for 'lines'
.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'
bam2sig: no visible global function definition for 'read.table'
combineND: no visible global function definition for 'Rle'
distrCOVPlot: no visible global function definition for 'topo.colors'
distrCOVPlot: no visible global function definition for 'par'
distrCOVPlot: no visible global function definition for 'lines'
distrCOVPlot: no visible global function definition for 'legend'
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'
distrCOVPlot: no visible global function definition for 'rect'
distrCOVPlotg: no visible global function definition for 'topo.colors'
distrCOVPlotg: no visible global function definition for 'par'
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 'lines'
distrCOVPlotg: no visible global function definition for 'legend'
distrCOVPlotg: no visible global function definition for
  'gene.to.transcript'
distrCOVPlotg: no visible global function definition for
  'transcript.to.exon'
distrCOVPlotg: no visible global function definition for 'rect'
distrSIPlot: no visible global function definition for 'par'
distrSIPlot: no visible global function definition for 'lines'
distrSIPlot: no visible global function definition for 'legend'
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'
getBamData: no visible global function definition for 'read.table'
getCoverageFromRS: no visible global function definition for
  'phenoData'
getSIFromND: no visible global function definition for 'Rle'
ks_test: no visible global function definition for 'ks.test'
newSeqReads: no visible global function definition for 'read.table'
newSeqReadsFromGene: no visible global function definition for
  'gene.details'
parseGff3: no visible global function definition for 'read.table'
parseGff3: no visible global function definition for 'write.table'
plotCoverageHistogram: no visible global function definition for
  'lines'
plotExonCoverage: no visible global function definition for
  'topo.colors'
plotExonCoverage: no visible global function definition for
  'exon.details'
plotExonCoverage: no visible global function definition for 'par'
plotExonCoverage: no visible global function definition for 'lines'
plotExonCoverage: no visible global function definition for 'legend'
plotGeneCoverage: no visible global function definition for 'par'
plotGeneCoverage: no visible global function definition for
  'topo.colors'
plotGeneCoverage: no visible global function definition for
  'gene.details'
plotGeneCoverage: no visible global function definition for 'lines'
plotGeneCoverage: no visible global function definition for 'legend'
plotGeneExonCoverage: no visible global function definition for 'par'
plotGeneExonCoverage: no visible global function definition for
  'topo.colors'
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'
plotGeneExonCoverage: no visible global function definition for 'lines'
plotGeneExonCoverage: no visible global function definition for 'rect'
plotGeneExonCoverage: no visible global function definition for
  'legend'
plotRegionCoverage: no visible global function definition for
  'topo.colors'
plotRegionCoverage: no visible global function definition for 'par'
plotRegionCoverage: no visible global function definition for 'lines'
plotSI: no visible global function definition for 'lines'
plotSI: no visible global function definition for 'legend'
qq_derivative_plot: no visible global function definition for 'qqplot'
qq_plot: no visible global function definition for 'qqplot'
setSpecies: no visible global function definition for 'menu'
simplePlot: no visible global function definition for 'lines'
spaceInChromosome: no visible binding for global variable 'out'
sumND: no visible global function definition for 'Rle'
Undefined global functions or variables:
  Rle dbGetQuery exon.details gene.details gene.to.exon
  gene.to.transcript ks.test legend lines menu out par phenoData
  phenoData<- qqplot read.table rect topo.colors transcript.to.exon
  write.table
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "legend", "lines", "par", "rect")
  importFrom("stats", "ks.test", "qqplot")
  importFrom("utils", "menu", "read.table", "write.table")
to your NAMESPACE file.
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/rnaSeqMap/libs/i386/rnaSeqMap.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/rnaSeqMap/libs/x64/rnaSeqMap.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/rnaSeqMap.Rcheck/00check.log'
for details.

Installation output

rnaSeqMap.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/rnaSeqMap_2.48.0.tar.gz && rm -rf rnaSeqMap.buildbin-libdir && mkdir rnaSeqMap.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rnaSeqMap.buildbin-libdir rnaSeqMap_2.48.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL rnaSeqMap_2.48.0.zip && rm rnaSeqMap_2.48.0.tar.gz rnaSeqMap_2.48.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  708k  100  708k    0     0  29.2M      0 --:--:-- --:--:-- --:--:-- 30.0M

install for i386

* installing *source* package 'rnaSeqMap' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                               ^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                    ^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                  ^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
             ^~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o rnaSeqMap.dll tmp.def Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/rnaSeqMap.buildbin-libdir/00LOCK-rnaSeqMap/00new/rnaSeqMap/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rnaSeqMap'
    finding HTML links ... done
    NDplots                                 html  
    NucleotideDistr-class                   html  
    RleList2matrix                          html  
    SeqReds                                 html  
    addBamData                              html  
    addDataToReadset                        html  
    addExperimentsToReadset                 html  
    averageND                               html  
    bam2sig                                 html  
    buildDESeq                              html  
    buildDGEList                            html  
    findRegionsAsIR                         html  
    findRegionsAsND                         html  
    fiveCol2GRanges                         html  
    gRanges2CamelMeasures                   html  
    geneInChromosome                        html  
    generators                              html  
    getBamData                              html  
    getCoverageFromRS                       html  
    getData                                 html  
    getExpDescription                       html  
    getFCFromND                             html  
    getSIFromND                             html  
    getSumsExp                              html  
    measures                                html  
    normalizations                          html  
    normalizeBySum                          html  
    parseGff3                               html  
    plotGeneCoverage                        html  
    readsInRange                            html  
    regionBasedCoverage                     html  
    regionCoverage                          html  
    rs.list                                 html  
    setData                                 html  
    setSAXPYData                            html  
    setSpecies                              html  
    simplePlot                              html  
    spaceInChromosome                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'rnaSeqMap' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                               ^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                    ^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                  ^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
             ^~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o rnaSeqMap.dll tmp.def Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/rnaSeqMap.buildbin-libdir/rnaSeqMap/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rnaSeqMap' as rnaSeqMap_2.48.0.zip
* DONE (rnaSeqMap)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'rnaSeqMap' successfully unpacked and MD5 sums checked

Tests output

Example timings

rnaSeqMap.Rcheck/examples_i386/rnaSeqMap-Ex.timings

nameusersystemelapsed
addBamData000
addDataToReadset000
addExperimentsToReadset000
averageND000
bam2sig0.020.000.01
buildDESeq000
buildDGEList000
findRegionsAsIR000
findRegionsAsND000
gRanges2CamelMeasures000
geneInChromosome000
generators000
getBamData000
getCoverageFromRS000
getFCFromND000
getSIFromND000
getSumsExp000
measures000
normalizations000
normalizeBySum000
parseGff3000
plotGeneCoverage000
readsInRange000
regionBasedCoverage000
regionCoverage000
rs.list000
setSpecies000
spaceInChromosome000

rnaSeqMap.Rcheck/examples_x64/rnaSeqMap-Ex.timings

nameusersystemelapsed
addBamData000
addDataToReadset000
addExperimentsToReadset000
averageND000
bam2sig000
buildDESeq000
buildDGEList000
findRegionsAsIR000
findRegionsAsND000
gRanges2CamelMeasures000
geneInChromosome000
generators000
getBamData000
getCoverageFromRS000
getFCFromND000
getSIFromND000
getSumsExp000
measures000
normalizations000
normalizeBySum000
parseGff3000
plotGeneCoverage000
readsInRange000
regionBasedCoverage000
regionCoverage000
rs.list000
setSpecies000
spaceInChromosome000