casper 2.3.1
David Rossell
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/casper | | Last Changed Rev: 107656 / Revision: 107696 | | Last Changed Date: 2015-08-21 08:15:39 -0700 (Fri, 21 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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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_2.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/casper.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 ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.3.1’
* 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 ... [35s/35s] 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 ... NOTE
rangesPlot,IRanges-ANY : .local: warning in genePlot(gene = gene, xlab
= "", ylab = "", xlim = xlim, ...): partial argument match of 'gene'
to 'generanges'
rangesPlot,procBam-ANY : .local: warning in genePlot(gene = gene, xlab
= "", ylab = "", xlim = xlim, ...): partial argument match of 'gene'
to 'generanges'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'readDistrsList,ANY'
generic 'procBam' and siglist 'ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getDistrs':
getDistrs
Code: function(DB, bam, pbam, islandid = NULL, verbose = FALSE,
nreads = 4 * 10^6, readLength, min.gt.freq = NULL,
tgroups = 5, mc.cores = 1)
Docs: function(DB, bam, pbam, islandid, verbose, nreads = 4 * 10^6,
readLength)
Argument names in code not in docs:
min.gt.freq tgroups mc.cores
Mismatches in argument default values:
Name: 'islandid' Code: NULL Docs:
Name: 'verbose' Code: FALSE Docs:
Codoc mismatches from documentation object 'procBam':
procBam
Code: function(bam, stranded = FALSE, seed = as.integer(1), verbose =
FALSE, rname = "null", keep.junx = FALSE, keep.flag =
FALSE, ispaired = TRUE, ...)
Docs: function(bam, stranded, seed, verbose = FALSE, rname, keep.junx
= FALSE, keep.flag = FALSE, ...)
Argument names in code not in docs:
ispaired
Mismatches in argument names:
Position: 8 Code: ispaired Docs: ...
Mismatches in argument default values:
Name: 'stranded' Code: FALSE Docs:
Name: 'seed' Code: as.integer(1) Docs:
Name: 'rname' Code: "null" Docs:
Codoc mismatches from documentation object 'simMAE':
simMAE
Code: function(nsim, islandid, nreads, readLength, fragLength, burnin
= 1000, pc, distr, readLength.pilot = readLength,
eset.pilot, usePilot = FALSE, retTxsError = FALSE,
genomeDB, mc.cores = 1, mc.cores.int = 1, verbose =
FALSE, writeBam = FALSE, bamFile = NULL)
Docs: function(nsim, islandid, nreads, readLength, fragLength, burnin
= 1000, pc, distr, readLength.pilot = readLength,
eset.pilot, usePilot = FALSE, retTxsError = FALSE,
genomeDB, mc.cores = 1, mc.cores.int = 1, verbose =
FALSE)
Argument names in code not in docs:
writeBam bamFile
* 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 ... [19s/19s] 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: 2 WARNINGs, 2 NOTEs
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)