BioC 3.2: CHECK report for casper on zin1

Package: casper

Version: 2.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.4.0.tar.gz

StartedAt: 2016-04-22 22:48:43 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:52:40 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 236.6 seconds

RetCode: 0

Status:  OK

CheckDir: casper.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/casper.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘2.4.0’
* 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 ... [33s/34s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.6Mb
* 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 ... OK
* 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 ... [18s/18s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/casper.Rcheck/00check.log’
for details.

* installing *source* package ‘casper’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c casper.cpp -o casper.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cstat.cpp -o cstat.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c dataframe.cpp -o dataframe.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c discretedf.cpp -o discretedf.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c dropVariant.cpp -o dropVariant.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c exon.cpp -o exon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fragment.cpp -o fragment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c functions.c -o functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c model.cpp -o model.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c model_cmp.cpp -o model_cmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c procBam.c -o procBam.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rcasper.cpp -o rcasper.o
rcasper.cpp: In function ‘SEXPREC* calcDenovoSingle(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
rcasper.cpp:1136:32: warning: ‘bestModel’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      for (int j=0; j< m->count(); j++) {
                                ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c seppel.cpp -o seppel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
simReadsfunc.c: In function ‘build_cigar’:
simReadsfunc.c:279:59: warning: unused variable ‘rlb’ [-Wunused-variable]
   int i, rst, rltmp, *ans, sum=1, wis, done=0, correct=0, rlb; 
                                                           ^
simReadsfunc.c:279:48: warning: unused variable ‘correct’ [-Wunused-variable]
   int i, rst, rltmp, *ans, sum=1, wis, done=0, correct=0, rlb; 
                                                ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c smartmodeldist.cpp -o smartmodeldist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c variant.cpp -o variant.o
g++ -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/casper.Rcheck/casper/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘transcripts’ in package ‘casper’
Creating a generic function for ‘lines’ from package ‘graphics’ 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	0.132	0.019	0.152
annotatedGenome-class	0.001	0.000	0.001
asymmetryCheck	0.02	0.00	0.02
calcDenovo	0	0	0
calcExp	2.537	0.079	2.621
denovoExpr	2.939	0.097	3.042
denovoGeneExpr-class	0.001	0.000	0.001
denovoGenomeExpr-class	0.001	0.000	0.001
distrsGSE37704	0.139	0.007	0.147
genePlot	0.381	0.001	0.382
getDistrs	0.395	0.003	0.399
getIsland	0.083	0.001	0.083
getNreads	0	0	0
getReads	0	0	0
getRoc	0.001	0.000	0.001
hg19DB	0.078	0.000	0.081
mergeBatches	0.107	0.001	0.107
mergeExp	0.001	0.000	0.001
modelPrior	0.458	0.000	0.476
modelPriorAS-class	0.000	0.000	0.001
pathCounts-class	0.001	0.000	0.000
pathCounts	0	0	0
plot-methods	0.000	0.000	0.001
plotExpr	0.000	0.000	0.001
plotPriorAS	0.001	0.000	0.000
probNonEquiv	0.114	0.000	0.114
procBam-class	0.001	0.000	0.001
procBam	0.001	0.000	0.000
procGenome	0.001	0.000	0.001
qqnormGenomeWide	0.048	0.004	0.051
quantileNorm	0.012	0.000	0.012
relexprByGene	0.001	0.000	0.001
rmShortInserts	0.001	0.000	0.000
simMAE	0	0	0
simMAEcheck	0.000	0.000	0.001
simMultSamples	0.001	0.000	0.001
simReads	0.392	0.020	0.411
simulatedSamples-class	0.001	0.000	0.001
splitGenomeByLength	0	0	0
transcripts	0.224	0.000	0.224
wrapDenovo	0.001	0.000	0.000
wrapKnown	0.000	0.000	0.001