seqbias 1.4.0
Daniel Jones
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/seqbias | | Last Changed Rev: 64678 / Revision: 69725 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| 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-2.10-bioc/meat/seqbias.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.4.0’
* 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 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 ... OK
* 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 ... OK
* checking installed files from ‘inst/doc’ ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/seqbias.Rcheck/00check.log’
for details.
* installing *source* package ‘seqbias’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c miscmath.c -o miscmath.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c pos_table.c -o pos_table.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c samtools_extra.c -o samtools_extra.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c kmer_matrix.cpp -o kmer_matrix.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c logger.cpp -o logger.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c motif.cpp -o motif.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c seqbias.cpp -o seqbias.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c twobitseq.cpp -o twobitseq.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h:28:8: warning: unused parameter ‘type’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -fpic -g -O2 -Wall -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-2.10-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/seqbias.Rcheck/seqbias/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘overview.Rnw’
** testing if installed package can be loaded
* DONE (seqbias)