seqbias 1.2.0
Daniel Jones
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/seqbias | | Last Changed Rev: 59920 / Revision: 64395 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/seqbias.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.2.0’
* 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 whether package ‘seqbias’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.9Mb
sub-directories of 1Mb or more:
libs 12.1Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘Rsamtools’
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/seqbias.Rcheck/seqbias/libs/seqbias.so’:
Found ‘__assert_fail’, possibly from ‘assert’ (C)
Found ‘printf’, possibly from ‘printf’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
‘Rsamtools’ ‘ggplot2’
* 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
* installing *source* package ‘seqbias’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c miscmath.c -o miscmath.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c pos_table.c -o pos_table.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c samtools_extra.c -o samtools_extra.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c kmer_matrix.cpp -o kmer_matrix.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c logger.cpp -o logger.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c motif.cpp -o motif.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c seqbias.cpp -o seqbias.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c twobitseq.cpp -o twobitseq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -shared -L/usr/local/lib64 -o seqbias.so common.o miscmath.o pos_table.o samtools_extra.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.9-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/seqbias.Rcheck/seqbias/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘overview.Rnw’
** testing if installed package can be loaded
* DONE (seqbias)