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Package 380/436HostnameOS / ArchBUILDCHECKBUILD BIN
seqbias 0.99.5
Daniel Jones
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias
Last Changed Rev: 52987 / Revision: 53255
Last Changed Date: 2011-02-18 12:32:21 -0800 (Fri, 18 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: seqbias
Version: 0.99.5
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings seqbias_0.99.5.tar.gz
StartedAt: 2011-02-24 19:50:03 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:52:13 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 130.0 seconds
RetCode: 0
Status:  OK  
CheckDir: seqbias.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/seqbias.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqbias/DESCRIPTION' ... OK
* this is package 'seqbias' version '0.99.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'seqbias' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

seqbias.Rcheck/00install.out:

* installing *source* package 'seqbias' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c kmers.cpp -o kmers.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c miscmath.cpp -o miscmath.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c common.cpp -o common.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c table.c -o table.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c superfasthash.c -o superfasthash.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c logger.c -o logger.o
logger.c: In function 'log_printf':
logger.c:92:5: warning: implicit declaration of function 'vasprintf'
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c seqbias.cpp -o seqbias.o
In file included from E:/biocbld/BBS-2˜1.8-B/R/include/R.h:44:0,
                 from seqbias.cpp:11:
E:/biocbld/BBS-2˜1.8-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/bam.c -o samtools/bam.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:166:2: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:166:2: warning: format '%s' expects type 'char *', but argument 3 has type 'int64_t'
samtools/bam_import.c:166:2: warning: too many arguments for format
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:179:13: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
samtools/bam_import.c: In function 'sam_read1':
samtools/bam_import.c:318:5: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:318:5: warning: too many arguments for format
samtools/bam_import.c:387:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387:10: warning: too many arguments for format
samtools/bam_import.c:401:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401:10: warning: too many arguments for format
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_core':
samtools/bam_index.c:205:6: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:205:6: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:205:6: warning: too many arguments for format
samtools/bam_index.c: In function 'bam_idxstats':
samtools/bam_index.c:524:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:524:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:524:4: warning: too many arguments for format
samtools/bam_index.c:528:2: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:528:2: warning: too many arguments for format
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/bgzf.c -o samtools/bgzf.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/faidx.c -o samtools/faidx.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:414:5: warning: unknown conversion type character 'l' in format
samtools/knetfile.c:414:5: warning: too many arguments for format
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/kstring.c -o samtools/kstring.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/razf.c -o samtools/razf.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/sam.c -o samtools/sam.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c samtools/sam_header.c -o samtools/sam_header.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall         -O2 -Wall  -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c gnulib/asprintf.c -o gnulib/asprintf.o
gnulib/asprintf.c: In function 'asprintf':
gnulib/asprintf.c:37:3: warning: implicit declaration of function 'vasprintf'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c gnulib/printf-args.c -o gnulib/printf-args.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c gnulib/printf-parse.c -o gnulib/printf-parse.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c gnulib/vasnprintf.c -o gnulib/vasnprintf.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall      -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Wall   -O3 -Wall  -std=gnu99 -c gnulib/vasprintf.c -o gnulib/vasprintf.o
g++ -shared -s -static-libgcc -o seqbias.dll tmp.def sequencing_bias.o kmers.o miscmath.o common.o table.o superfasthash.o logger.o seqbias.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/bam_index.o samtools/bam_pileup.o samtools/bgzf.o samtools/faidx.o samtools/knetfile.o samtools/kstring.o samtools/razf.o samtools/sam.o samtools/sam_header.o yaml-cpp/aliascontent.o yaml-cpp/conversion.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/map.o yaml-cpp/node.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/parserstate.o yaml-cpp/regex.o yaml-cpp/scalar.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/sequence.o yaml-cpp/simplekey.o yaml-cpp/stream.o yaml-cpp/tag.o gnulib/asprintf.o gnulib/printf-args.o gnulib/printf-parse.o gnulib/vasnprintf.o gnulib/vasprintf.o -lRzlib -lws2_32 -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/seqbias.Rcheck/seqbias/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (seqbias)

seqbias.Rcheck/seqbias-Ex.timings:

nameusersystemelapsed
count_reads0.080.000.09
kmer_freq0.610.010.67
random_intervals0.100.040.12
seqbias_fit1.190.011.22
seqbias_load1.450.331.78
seqbias_predict1.360.001.36
seqbias_save1.510.231.80