Package: ShortRead

Version: 1.17.9

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.17.9.tar.gz

StartedAt: 2013-01-16 06:18:26 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:24:10 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 344.1 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.17.9’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 11.632  0.168  11.941
qa2             5.853  0.040   5.400
* 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 3 notes.
See
  ‘/loc/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... /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... 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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/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  -c readBfaToc.cc -o readBfaToc.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/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  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c xsnap.c -o xsnap.o
g++ -shared -L/usr/local/lib64 -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/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/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	0.468	0.008	0.478
BAMQA-class	0.012	0.000	0.011
BowtieQA-class	0.016	0.000	0.015
ExperimentPath-class	0.012	0.000	0.012
FastqQA-class	0.012	0.000	0.011
GappedReads-class	0.316	0.000	0.318
Intensity-class	0.672	0.004	0.679
MAQMapQA-class	0.016	0.000	0.013
QA-class	0.008	0.004	0.015
QualityScore-class	0.024	0.000	0.025
QualityScore	0.024	0.004	0.024
RochePath-class	0.008	0.000	0.011
RocheSet-class	0.008	0.000	0.009
RtaIntensity-class	0.092	0.000	0.089
RtaIntensity	0.048	0.000	0.045
SRFilter-class	0.012	0.000	0.010
SRFilterResult-class	0.092	0.000	0.092
SRSet-class	0.012	0.000	0.011
SRUtil-class	0.024	0.000	0.023
Sampler-class	4.549	0.000	2.897
ShortRead-class	0.320	0.008	0.180
ShortReadQ-class	0.340	0.028	0.369
Snapshot-class	11.632	0.168	11.941
SnapshotFunction-class	0.016	0.000	0.018
SolexaExportQA-class	0.008	0.000	0.005
SolexaIntensity-class	0.188	0.000	0.189
SolexaPath-class	0.156	0.004	0.160
SolexaSet-class	0.136	0.000	0.133
SpTrellis-class	0.884	0.012	0.898
accessors	0.008	0.000	0.010
alphabetByCycle	0.032	0.012	0.043
clean	0.004	0.000	0.005
countLines	0.016	0.004	0.019
deprecated	0.016	0.000	0.016
dotQA-class	0.004	0.000	0.004
dustyScore	0.640	0.004	0.643
polyn	0.528	0.000	0.526
qa	0.484	0.008	0.492
qa2	5.853	0.040	5.400
readAligned	0.288	0.016	0.303
readBaseQuality	0.028	0.000	0.028
readFasta	0.136	0.004	0.164
readFastq	0.152	0.008	0.161
readIntensities	0.120	0.004	0.128
readPrb	0.056	0.000	0.061
readQseq	0.016	0.004	0.020
readXStringColumns	0.148	0.008	0.157
renew	0.092	0.000	0.091
report	0.012	0.000	0.012
spViewPerFeature	1.944	0.028	1.974
srFilter	0.600	0.008	0.606
srapply	0.012	0.004	0.016
srdistance	0.196	0.004	0.198
srduplicated	0.144	0.000	0.146
tables	0.140	0.004	0.146
trimTails	0.736	0.004	0.382