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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rnaSeqMap.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rnaSeqMap_2.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/rnaSeqMap.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.46.0’
* 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 ... 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
.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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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-3.11-bioc/meat/rnaSeqMap.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL rnaSeqMap
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘rnaSeqMap’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I"/home/biocbuild/bbs-3.11-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 -I"/home/biocbuild/bbs-3.11-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 -I"/home/biocbuild/bbs-3.11-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 -I"/home/biocbuild/bbs-3.11-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 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rnaSeqMap/00new/rnaSeqMap/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rnaSeqMap)