Package: ShortRead

Version: 1.16.4

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.16.4.tar.gz

StartedAt: 2013-03-25 04:51:43 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:58:15 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 391.8 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ShortRead.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.16.4’
* 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 12.465  0.492  15.424
qa2             5.153  0.088   8.045
* 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-2.11-bioc/meat/ShortRead.Rcheck/00check.log’
for details.

* installing *source* package ‘ShortRead’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-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
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -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-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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	0.384	0.012	0.564
BAMQA-class	0.000	0.000	0.002
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0	0	0
FastqQA-class	0.000	0.000	0.001
GappedReads-class	0.320	0.004	0.564
Intensity-class	0.272	0.020	0.773
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.000	0.000	0.001
QualityScore-class	0	0	0
QualityScore	0.372	0.004	0.498
RochePath-class	0.000	0.000	0.001
RocheSet-class	0.000	0.000	0.001
RtaIntensity-class	0.076	0.004	0.107
RtaIntensity	0.040	0.000	0.038
SRFilter-class	0	0	0
SRFilterResult-class	0.076	0.000	0.078
SRSet-class	0.004	0.000	0.001
SRUtil-class	0.004	0.000	0.005
Sampler-class	1.456	0.000	1.484
ShortRead-class	0.076	0.000	0.075
ShortReadQ-class	0.592	0.020	0.622
Snapshot-class	12.465	0.492	15.424
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0.000	0.000	0.001
SolexaIntensity-class	0.196	0.008	0.425
SolexaPath-class	0.144	0.008	0.152
SolexaSet-class	0.120	0.000	0.119
SpTrellis-class	1.264	0.012	1.274
accessors	0.008	0.000	0.005
alphabetByCycle	0.028	0.000	0.031
clean	0.000	0.000	0.001
countLines	0.012	0.004	0.092
deprecated	0	0	0
dotQA-class	0.000	0.000	0.002
dustyScore	0.540	0.004	0.662
polyn	0	0	0
qa	0.940	0.004	1.107
qa2	5.153	0.088	8.045
readAligned	0.296	0.004	0.412
readBaseQuality	0.016	0.004	0.044
readFasta	0.096	0.004	0.222
readFastq	0.168	0.008	0.215
readIntensities	0.108	0.004	0.115
readPrb	0.076	0.004	0.138
readQseq	0.024	0.004	0.040
readXStringColumns	0.176	0.000	0.297
renew	0.108	0.000	0.183
report	0.008	0.000	0.010
spViewPerFeature	2.552	0.056	3.035
srFilter	0.500	0.008	0.508
srapply	0.008	0.000	0.007
srdistance	0.196	0.000	0.224
srduplicated	0.108	0.000	0.141
tables	0.168	0.004	0.345
trimTails	0.116	0.000	0.128