casper 0.99.5
David Rossell
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/casper | | Last Changed Rev: 72523 / Revision: 72575 | | Last Changed Date: 2013-01-14 17:25:22 -0800 (Mon, 14 Jan 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/casper.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘0.99.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ... OK
* checking package 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 for unstated 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calcExp 9.54 0.152 9.7
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/casper.Rcheck/00check.log’
for details.
* installing *source* package ‘casper’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c casper.cpp -o casper.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cstat.cpp -o cstat.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dataframe.cpp -o dataframe.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c discretedf.cpp -o discretedf.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c exon.cpp -o exon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fragFunc.c -o fragFunc.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fragment.cpp -o fragment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c functions.c -o functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash.c -o hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c join_exons.c -o join_exons.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c makeIslands.c -o makeIslands.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c model.cpp -o model.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c model_cmp.cpp -o model_cmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pathCounts.c -o pathCounts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c procBam.c -o procBam.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rcasper.cpp -o rcasper.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c seppel.cpp -o seppel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c simReads.c -o simReads.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c simReadsfunc.c -o simReadsfunc.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c smartmodeldist.cpp -o smartmodeldist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c uniqQname.c -o uniqQname.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c variant.cpp -o variant.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c variant_cmp.cpp -o variant_cmp.o
g++ -shared -L/usr/local/lib64 -o casper.so casper.o cstat.o dataframe.o discretedf.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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-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 ‘plot’ from package ‘graphics’ in package ‘casper’
** help
*** installing help indices
** building package indices
** installing vignettes
‘casper.Rnw’
** testing if installed package can be loaded
* DONE (casper)