Package: ShortRead

Version: 1.14.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.14.0.tar.gz

StartedAt: 2012-04-01 03:23:24 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:26:42 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 197.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ShortRead.Rcheck

Warnings: 1

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/ShortRead.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.14.0'
* 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  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   1.4Mb
* 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 ... WARNING
Undocumented code objects:
  'FastqSamplerList' 'FastqStreamerList' 'QA' 'QAAdapterContamination'
  'QACollate' 'QAData' 'QAFastqSource' 'QAFiltered' 'QAFlagged'
  'QAFrequentSequence' 'QANucleotideByCycle' 'QANucleotideUse'
  'QAQualityByCycle' 'QAQualityUse' 'QAReadQuality' 'QASequenceUse'
  'flag' 'qa2'
Undocumented S4 classes:
  '.QA2' 'FastqSamplerList' 'FastqStreamerList' 'QA'
  'QAAdapterContamination' 'QACollate' 'QAData' 'QAFastqSource'
  'QAFiltered' 'QAFlagged' 'QAFrequentSequence' 'QANucleotideByCycle'
  'QANucleotideUse' 'QAQualityByCycle' 'QAQualityUse' 'QAReadQuality'
  'QASequenceUse' 'QASource' 'QASummary'
Undocumented S4 methods:
  generic 'FastqSamplerList' and siglist 'ANY'
  generic 'FastqSamplerList' and siglist 'character'
  generic 'FastqStreamerList' and siglist 'ANY'
  generic 'FastqStreamerList' and siglist 'character'
  generic 'QACollate' and siglist 'QAFastqSource'
  generic 'QACollate' and siglist 'missing'
  generic 'flag' and siglist '.QA2'
  generic 'flag' and siglist 'QAReadQuality'
  generic 'flag' and siglist 'QASource'
  generic 'qa2' and siglist 'FastqSampler'
  generic 'qa2' and siglist 'QAAdapterContamination'
  generic 'qa2' and siglist 'QACollate'
  generic 'qa2' and siglist 'QAFastqSource'
  generic 'qa2' and siglist 'QAFrequentSequence'
  generic 'qa2' and siglist 'QANucleotideByCycle'
  generic 'qa2' and siglist 'QANucleotideUse'
  generic 'qa2' and siglist 'QAQualityByCycle'
  generic 'qa2' and siglist 'QAQualityUse'
  generic 'qa2' and siglist 'QAReadQuality'
  generic 'qa2' and siglist 'QASequenceUse'
  generic 'rbind' and siglist 'QASummary'
  generic 'report' and siglist 'QA'
  generic 'report' and siglist 'QAAdapterContamination'
  generic 'report' and siglist 'QAFiltered'
  generic 'report' and siglist 'QAFlagged'
  generic 'report' and siglist 'QAFrequentSequence'
  generic 'report' and siglist 'QANucleotideByCycle'
  generic 'report' and siglist 'QANucleotideUse'
  generic 'report' and siglist 'QAQualityByCycle'
  generic 'report' and siglist 'QAQualityUse'
  generic 'report' and siglist 'QAReadQuality'
  generic 'report' and siglist 'QASequenceUse'
  generic 'report' and siglist 'QASource'
  generic 'show' and siglist 'QAAdapterContamination'
  generic 'show' and siglist 'QACollate'
  generic 'show' and siglist 'QAFastqSource'
  generic 'show' and siglist 'QAFrequentSequence'
  generic 'show' and siglist 'QAReadQuality'
  generic 'show' and siglist 'QASummary'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-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... /bin/grep
checking for egrep... /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... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io.c -o io.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c pileup.c -o pileup.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/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=8 -fpic  -g -O2  -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)':
readBfaToc.cc:36:52: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
readBfaToc.cc:37:48: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
readBfaToc.cc:38:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/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=8 -fpic  -g -O2  -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c trim.c -o trim.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c util.c -o util.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c xsnap.c -o xsnap.o
g++ -shared -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 -fopenmp -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/ShortRead.Rcheck/ShortRead/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 (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.496	0.008	0.511
BAMQA-class	0.000	0.000	0.001
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.000	0.000	0.001
FastqQA-class	0	0	0
GappedReads-class	0.192	0.004	0.207
Intensity-class	0.204	0.008	0.225
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.000	0.000	0.001
QualityScore-class	0	0	0
QualityScore	0.004	0.000	0.005
RochePath-class	0.004	0.000	0.000
RocheSet-class	0.000	0.000	0.001
RtaIntensity-class	0.064	0.000	0.064
RtaIntensity	0.032	0.000	0.034
SRFilter-class	0	0	0
SRFilterResult-class	0.056	0.000	0.056
SRSet-class	0.000	0.000	0.001
SRUtil-class	0.004	0.000	0.004
Sampler-class	1.228	0.004	0.688
ShortRead-class	0.064	0.004	0.068
ShortReadQ-class	0.276	0.000	0.259
Snapshot-class	8.029	0.088	8.230
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0	0	0
SolexaIntensity-class	0.116	0.000	0.127
SolexaPath-class	0.100	0.000	0.106
SolexaSet-class	0.080	0.004	0.090
SpTrellis-class	0.632	0.000	0.634
accessors	0.000	0.004	0.008
alphabetByCycle	0.020	0.004	0.029
clean	0.000	0.000	0.001
countLines	0.008	0.008	0.062
deprecated	0	0	0
dustyScore	0.304	0.000	0.310
polyn	0.000	0.000	0.001
qa	0.564	0.000	0.573
readAligned	0.220	0.004	0.259
readBaseQuality	0.024	0.004	0.039
readFasta	0.072	0.000	0.088
readFastq	0.116	0.004	0.129
readIntensities	0.080	0.000	0.091
readPrb	0.044	0.004	0.056
readQseq	0.012	0.000	0.019
readXStringColumns	0.124	0.004	0.139
renew	0.064	0.000	0.071
report	0.008	0.000	0.012
spViewPerFeature	1.880	0.016	1.937
srFilter	0.312	0.000	0.328
srapply	0.004	0.000	0.005
srdistance	0.184	0.000	0.216
srduplicated	0.092	0.000	0.098
tables	0.116	0.000	0.121
trimTails	0.308	0.012	0.082