Package: ShortRead

Version: 1.16.4

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ShortRead_1.16.4.tar.gz

StartedAt: 2013-03-25 01:16:11 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:21:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 319.2 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ShortRead.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.16.4'
* 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 'ShortRead' can be installed ... OK
* checking installed package size ... OK
* 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 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'
coerce,AlignedRead-GappedReads: possible error in GappedReads(seqnames
  = chromosome(from), pos = position(from), cigar = cigar, strand =
  strand(from), qname = id(from), qseq = sread(from)): unused
  argument(s) (qname = id(from))
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'
narrow,GappedReads: no visible global function definition for
  'updateCigarAndStart'
qnarrow,GappedReads: no visible global function definition for
  'updateCigarAndStart'
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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 12.049  1.459  14.141
qa2             5.623  0.185   5.889
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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-2.11-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	0.444	0.020	0.487
BAMQA-class	0.002	0.000	0.002
BowtieQA-class	0.000	0.001	0.001
ExperimentPath-class	0.001	0.000	0.001
FastqQA-class	0.000	0.000	0.001
GappedReads-class	0.278	0.006	0.289
Intensity-class	0.513	0.030	0.558
MAQMapQA-class	0.001	0.000	0.001
QA-class	0.002	0.000	0.001
QualityScore-class	0.001	0.001	0.000
QualityScore	0.007	0.000	0.008
RochePath-class	0.000	0.001	0.000
RocheSet-class	0.001	0.000	0.001
RtaIntensity-class	0.082	0.001	0.083
RtaIntensity	0.036	0.001	0.037
SRFilter-class	0.000	0.001	0.000
SRFilterResult-class	0.065	0.001	0.067
SRSet-class	0.001	0.000	0.001
SRUtil-class	0.005	0.001	0.005
Sampler-class	0.916	0.015	0.938
ShortRead-class	0.090	0.002	0.097
ShortReadQ-class	0.589	0.027	0.627
Snapshot-class	12.049	1.459	14.141
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0.001	0.000	0.001
SolexaIntensity-class	0.158	0.028	0.199
SolexaPath-class	0.129	0.005	0.135
SolexaSet-class	0.117	0.004	0.130
SpTrellis-class	0.856	0.063	0.989
accessors	0.004	0.003	0.007
alphabetByCycle	0.026	0.006	0.032
clean	0.002	0.000	0.001
countLines	0.012	0.009	0.021
deprecated	0	0	0
dotQA-class	0.001	0.000	0.001
dustyScore	0.767	0.015	0.788
polyn	0.001	0.000	0.000
qa	0.767	0.027	0.798
qa2	5.623	0.185	5.889
readAligned	0.275	0.026	0.308
readBaseQuality	0.027	0.004	0.031
readFasta	0.104	0.009	0.132
readFastq	0.164	0.008	0.173
readIntensities	0.104	0.020	0.125
readPrb	0.094	0.009	0.104
readQseq	0.014	0.003	0.019
readXStringColumns	0.153	0.007	0.160
renew	0.097	0.006	0.108
report	0.006	0.003	0.010
spViewPerFeature	2.648	0.159	2.835
srFilter	0.572	0.019	0.594
srapply	0.006	0.001	0.008
srdistance	0.214	0.008	0.229
srduplicated	0.125	0.006	0.138
tables	0.160	0.009	0.172
trimTails	0.043	0.004	0.046