casper 2.6.0
David Rossell
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/casper | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/casper.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.6.0’
* 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 5.8Mb
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
.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/casper.Rcheck/00check.log’
for details.
* installing *source* package ‘casper’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c casper.cpp -o casper.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cstat.cpp -o cstat.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dataframe.cpp -o dataframe.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c discretedf.cpp -o discretedf.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dropVariant.cpp -o dropVariant.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fragFunc.c -o fragFunc.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-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-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c makeIslands.c -o makeIslands.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c model.cpp -o model.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c procBam.c -o procBam.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simReadsfunc.c -o simReadsfunc.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uniqQname.c -o uniqQname.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c variant.cpp -o variant.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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)