Package: ShortRead

Version: 1.17.10

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.17.10.tar.gz

StartedAt: 2013-03-25 04:36:49 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:45:33 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 523.7 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [42s/44s] 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [61s/63s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 18.161  0.316  19.081
qa2             8.589  0.064   8.871
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’ [108s/111s]
 [108s/112s] 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
  ‘/home/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... /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/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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  -Wall -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:35:59: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readBfaToc.cc:36:55: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readBfaToc.cc:37:51: 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/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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  -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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	0.700	0.016	0.716
BAMQA-class	0.016	0.000	0.017
BowtieQA-class	0.012	0.000	0.011
ExperimentPath-class	0.016	0.000	0.016
FastqQA-class	0.012	0.000	0.016
GappedReads-class	0.961	0.012	0.971
Intensity-class	0.408	0.012	0.426
MAQMapQA-class	0.028	0.000	0.026
QA-class	0.020	0.004	0.023
QualityScore-class	0.036	0.000	0.034
QualityScore	0.036	0.000	0.036
RochePath-class	0.024	0.000	0.024
RocheSet-class	0.016	0.000	0.015
RtaIntensity-class	0.156	0.000	0.156
RtaIntensity	0.08	0.00	0.08
SRFilter-class	0.012	0.000	0.012
SRFilterResult-class	0.132	0.000	0.130
SRSet-class	0.020	0.000	0.021
SRUtil-class	0.040	0.004	0.042
Sampler-class	2.900	0.020	3.233
ShortRead-class	0.148	0.012	0.180
ShortReadQ-class	0.480	0.068	0.608
Snapshot-class	18.161	0.316	19.081
SnapshotFunction-class	0.004	0.004	0.010
SolexaExportQA-class	0.008	0.000	0.008
SolexaIntensity-class	0.256	0.008	0.264
SolexaPath-class	0.248	0.000	0.247
SolexaSet-class	0.208	0.004	0.211
SpTrellis-class	1.168	0.020	1.191
accessors	0.036	0.000	0.037
alphabetByCycle	0.068	0.008	0.077
clean	0.012	0.000	0.010
countLines	0.016	0.012	0.031
deprecated	0.016	0.000	0.015
dotQA-class	0.008	0.000	0.009
dustyScore	1.112	0.008	1.122
polyn	0.020	0.000	0.022
qa	0.680	0.000	0.683
qa2	8.589	0.064	8.871
readAligned	0.376	0.024	0.402
readBaseQuality	0.044	0.008	0.052
readFasta	0.216	0.024	0.259
readFastq	0.264	0.012	0.277
readIntensities	0.192	0.016	0.206
readPrb	0.092	0.012	0.102
readQseq	0.036	0.000	0.034
readXStringColumns	0.252	0.024	0.277
renew	0.136	0.008	0.146
report	0.020	0.000	0.018
spViewPerFeature	2.908	0.044	2.988
srFilter	0.768	0.008	0.778
srapply	0.02	0.00	0.02
srdistance	0.232	0.004	0.238
srduplicated	0.208	0.016	0.226
tables	0.228	0.004	0.232
trimTails	0.084	0.000	0.083