BioC 3.5: CHECK report for casper on malbec2

Package: casper

Version: 2.10.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.10.0.tar.gz

StartedAt: 2017-10-17 21:46:47 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:50:58 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 251.2 seconds

RetCode: 0

Status:  OK

CheckDir: casper.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/casper.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.10.0’
* 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 ‘casper’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mergeFramesViaRanges: no visible global function definition for
  ‘queryHits’
.mergeFramesViaRanges: no visible global function definition for
  ‘subjectHits’
assignExons2GeneF: no visible global function definition for
  ‘queryHits’
assignExons2GeneF: no visible global function definition for
  ‘subjectHits’
findNewExonsF: no visible global function definition for ‘queryHits’
generateNOexons: no visible global function definition for ‘queryHits’
generateNOexons: no visible global function definition for
  ‘subjectHits’
getDistrsFromBam: no visible global function definition for
  ‘subjectHits’
getDistrsFromBam: no visible global function definition for ‘queryHits’
getDistrsFrompBam: no visible global function definition for
  ‘subjectHits’
getDistrsFrompBam: no visible global function definition for
  ‘queryHits’
procPaths: no visible global function definition for ‘queryHits’
procPaths: no visible global function definition for ‘subjectHits’
Undefined global functions or variables:
  queryHits subjectHits
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
denovoExpr 4.908  1.660   6.572
calcExp    3.284  2.108   5.398
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/casper.Rcheck/00check.log’
for details.

* installing *source* package ‘casper’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c casper.cpp -o casper.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cstat.cpp -o cstat.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dataframe.cpp -o dataframe.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c discretedf.cpp -o discretedf.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dropVariant.cpp -o dropVariant.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c exon.cpp -o exon.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fragment.cpp -o fragment.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c functions.c -o functions.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c model.cpp -o model.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c model_cmp.cpp -o model_cmp.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c procBam.c -o procBam.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rcasper.cpp -o rcasper.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c seppel.cpp -o seppel.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c variant.cpp -o variant.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c variant_cmp.cpp -o variant_cmp.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/casper.Rcheck/casper/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘transcripts’ in package ‘casper’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (casper)

name	user	system	elapsed
K562.r1l1	0.160	0.016	0.173
annotatedGenome-class	0.004	0.000	0.001
asymmetryCheck	0.076	0.000	0.075
calcDenovo	0.000	0.000	0.001
calcExp	3.284	2.108	5.398
denovoExpr	4.908	1.660	6.572
denovoGeneExpr-class	0.000	0.000	0.001
denovoGenomeExpr-class	0.000	0.000	0.001
distrsGSE37704	0.188	0.000	0.185
genePlot	0.432	0.004	0.437
getDistrs	0.352	0.020	0.370
getIsland	0.080	0.000	0.079
getNreads	0.000	0.000	0.001
getReads	0.000	0.000	0.001
getRoc	0.004	0.000	0.001
hg19DB	0.076	0.000	0.078
mergeBatches	0.184	0.000	0.183
mergeExp	0	0	0
modelPrior	0.584	0.000	0.603
modelPriorAS-class	0.000	0.000	0.001
pathCounts-class	0.000	0.000	0.001
pathCounts	0.000	0.000	0.001
plot-methods	0.000	0.000	0.001
plotExpr	0	0	0
plotPriorAS	0	0	0
probNonEquiv	0.288	0.000	0.290
procBam-class	0.000	0.000	0.001
procBam	0	0	0
procGenome	0.000	0.000	0.001
qqnormGenomeWide	0.1	0.0	0.1
quantileNorm	0.032	0.000	0.031
relexprByGene	0	0	0
rmShortInserts	0	0	0
simMAE	0.004	0.000	0.001
simMAEcheck	0.000	0.000	0.001
simMultSamples	0.004	0.000	0.001
simReads	0.504	0.016	0.522
simulatedSamples-class	0.004	0.000	0.001
splitGenomeByLength	0	0	0
transcripts	0.196	0.000	0.195
wrapDenovo	0.000	0.000	0.001
wrapKnown	0	0	0