Package: ShortRead

Version: 1.17.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ShortRead_1.17.10.tar.gz

StartedAt: 2013-03-25 04:41:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:47:36 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 346.2 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.17.10'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ShortRead' can be installed ... [36s/38s] 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 ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
.readQual: no visible global function definition for 'readFASTA'
flag,QAReadQuality: no visible binding for global variable 'Score'
flag,QAReadQuality: no visible binding for global variable 'Id'
flag,QAReadQuality: no visible binding for global variable 'Density'
report,QAFrequentSequence: no visible binding for global variable
  'TopCount'
report,QAFrequentSequence: no visible binding for global variable 'Id'
report,QANucleotideByCycle: no visible binding for global variable
  'Base'
report,QANucleotideUse: no visible binding for global variable
  'Nucleotide'
report,QAQualityUse: no visible binding for global variable 'Count'
report,QAQualityUse: no visible binding for global variable 'Id'
report,QAQualityUse: no visible binding for global variable 'Quality'
report,QAReadQuality: no visible binding for global variable 'Id'
report,QASequenceUse: no visible binding for global variable
  'Occurrences'
report,QASequenceUse: no visible binding for global variable 'Id'
report,QASequenceUse: no visible binding for global variable 'Reads'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 11.025  1.164  12.391
qa2             5.751  0.161   5.994
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ShortRead_unit_tests.R' [40s/40s]
 [41s/41s] 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 were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck/00check.log'
for details.

* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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 for gzeof in -lz... yes
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
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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -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 -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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -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 -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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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-2.12-bioc/meat/ShortRead.Rcheck/ShortRead/libs/i386
** 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 (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.634	0.039	0.675
BAMQA-class	0.007	0.005	0.013
BowtieQA-class	0.011	0.006	0.019
ExperimentPath-class	0.007	0.006	0.014
FastqQA-class	0.005	0.005	0.011
GappedReads-class	0.286	0.019	0.305
Intensity-class	0.318	0.034	0.353
MAQMapQA-class	0.006	0.005	0.012
QA-class	0.007	0.006	0.014
QualityScore-class	0.012	0.012	0.025
QualityScore	0.016	0.008	0.023
RochePath-class	0.009	0.008	0.016
RocheSet-class	0.006	0.005	0.011
RtaIntensity-class	0.098	0.006	0.103
RtaIntensity	0.043	0.006	0.049
SRFilter-class	0.006	0.006	0.012
SRFilterResult-class	0.084	0.011	0.095
SRSet-class	0.007	0.005	0.012
SRUtil-class	0.017	0.010	0.027
Sampler-class	0.893	0.035	0.931
ShortRead-class	0.108	0.013	0.121
ShortReadQ-class	0.343	0.037	0.384
Snapshot-class	11.025	1.164	12.391
SnapshotFunction-class	0.008	0.011	0.018
SolexaExportQA-class	0.007	0.008	0.016
SolexaIntensity-class	0.170	0.029	0.203
SolexaPath-class	0.159	0.019	0.178
SolexaSet-class	0.137	0.016	0.153
SpTrellis-class	0.840	0.062	0.911
accessors	0.021	0.019	0.040
alphabetByCycle	0.036	0.015	0.051
clean	0.008	0.010	0.018
countLines	0.017	0.015	0.034
deprecated	0.004	0.008	0.013
dotQA-class	0.003	0.004	0.007
dustyScore	0.310	0.014	0.325
polyn	0.007	0.005	0.012
qa	0.427	0.034	0.463
qa2	5.751	0.161	5.994
readAligned	0.320	0.037	0.357
readBaseQuality	0.033	0.010	0.043
readFasta	0.160	0.026	0.200
readFastq	0.253	0.034	0.286
readIntensities	0.164	0.037	0.211
readPrb	0.102	0.013	0.116
readQseq	0.027	0.012	0.041
readXStringColumns	0.250	0.039	0.291
renew	0.137	0.026	0.164
report	0.015	0.013	0.028
spViewPerFeature	3.122	0.191	3.337
srFilter	0.828	0.059	0.901
srapply	0.018	0.011	0.030
srdistance	0.310	0.022	0.334
srduplicated	0.178	0.019	0.198
tables	0.217	0.021	0.250
trimTails	0.086	0.031	0.117