Package: ShortRead

Version: 1.12.4

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ShortRead_1.12.4.tar.gz

StartedAt: 2012-03-24 04:13:53 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 04:19:57 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 363.5 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.12.4'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'ShortRead' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   1.3Mb
* 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 ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
.plotNucleotideCount: no visible binding for global variable
  'Nucleotide'
.plotReadCount: no visible binding for global variable 'Census'
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'ShortRead_and_HilbertVis.pdf' from 1277Kb to 598Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ShortRead_unit_tests.R'
 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

* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 4
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -DHAVE_LIBZ=1 -fPIC  -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -DHAVE_LIBZ=1 -fPIC  -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c sampler.c -o sampler.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c trim.c -o trim.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck/ShortRead/libs/i386
** 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 (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.559	0.019	0.584
BAMQA-class	0.002	0.000	0.003
BowtieQA-class	0.001	0.000	0.001
ExperimentPath-class	0.001	0.000	0.002
FastqQA-class	0.001	0.000	0.001
GappedReads-class	0.317	0.007	0.348
Intensity-class	0.602	0.029	0.650
MAQMapQA-class	0.001	0.001	0.001
QA-class	0.001	0.000	0.001
QualityScore-class	0.000	0.001	0.001
QualityScore	0.009	0.001	0.010
RochePath-class	0.001	0.000	0.001
RocheSet-class	0.001	0.000	0.001
RtaIntensity-class	0.099	0.001	0.099
RtaIntensity	0.047	0.002	0.050
SRFilter-class	0	0	0
SRFilterResult-class	0.098	0.004	0.108
SRSet-class	0.001	0.000	0.001
SRUtil-class	0.006	0.000	0.007
Sampler-class	0.952	0.010	0.976
ShortRead-class	0.108	0.002	0.115
ShortReadQ-class	0.399	0.022	0.458
Snapshot-class	11.843	1.505	14.148
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0.000	0.000	0.001
SolexaIntensity-class	0.196	0.025	0.221
SolexaPath-class	0.158	0.012	0.174
SolexaSet-class	0.140	0.003	0.149
SpTrellis-class	1.151	0.072	1.236
accessors	0.006	0.001	0.008
alphabetByCycle	0.033	0.006	0.040
clean	0.002	0.000	0.002
countLines	0.016	0.010	0.026
deprecated	0.000	0.000	0.001
dustyScore	0.415	0.006	0.422
polyn	0.001	0.000	0.001
qa	0.883	0.018	0.913
readAligned	0.345	0.015	0.362
readBaseQuality	0.040	0.003	0.045
readFasta	0.124	0.007	0.143
readFastq	0.212	0.007	0.219
readIntensities	0.148	0.024	0.181
readPrb	0.083	0.004	0.087
readQseq	0.019	0.002	0.021
readXStringColumns	0.215	0.010	0.226
renew	0.106	0.005	0.111
report	0.005	0.002	0.006
spViewPerFeature	2.837	0.141	3.022
srFilter	0.536	0.026	0.631
srapply	0.009	0.001	0.011
srdistance	0.276	0.009	0.288
srduplicated	0.165	0.006	0.181
tables	0.180	0.008	0.192
trimTails	0.064	0.003	0.068