Package: ShortRead

Version: 1.12.4

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.12.4.tar.gz

StartedAt: 2012-03-24 02:41:47 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:47:08 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 321.9 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.12.4’
* 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  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    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 ... NOTE
.plotCycleBaseCall: no visible binding for global variable ‘Base’
.plotNucleotideCount: no visible binding for global variable
  ‘Nucleotide’
.plotReadCount: no visible binding for global variable ‘Census’
* 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 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

* installing *source* package ‘ShortRead’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 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
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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 -DHAVE_LIBZ=1 -fpic  -g -O2 -c readBfaToc.cc -o readBfaToc.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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 -DHAVE_LIBZ=1 -fpic  -g -O2 -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck/ShortRead/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Overview.Rnw’ 
** testing if installed package can be loaded

* DONE (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.416	0.012	0.426
BAMQA-class	0.000	0.000	0.002
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.000	0.000	0.001
FastqQA-class	0.004	0.000	0.001
GappedReads-class	0.244	0.004	0.248
Intensity-class	0.680	0.008	0.687
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.000	0.000	0.001
QualityScore-class	0	0	0
QualityScore	0.008	0.000	0.008
RochePath-class	0	0	0
RocheSet-class	0.000	0.000	0.001
RtaIntensity-class	0.068	0.004	0.071
RtaIntensity	0.04	0.00	0.04
SRFilter-class	0	0	0
SRFilterResult-class	0.084	0.000	0.083
SRSet-class	0.000	0.000	0.001
SRUtil-class	0.008	0.000	0.005
Sampler-class	3.484	0.004	2.332
ShortRead-class	0.264	0.004	0.140
ShortReadQ-class	0.533	0.016	0.474
Snapshot-class	8.844	0.184	9.552
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0	0	0
SolexaIntensity-class	0.148	0.000	0.148
SolexaPath-class	0.116	0.004	0.120
SolexaSet-class	0.088	0.000	0.094
SpTrellis-class	0.812	0.020	0.831
accessors	0.000	0.004	0.005
alphabetByCycle	0.024	0.004	0.027
clean	0.004	0.000	0.002
countLines	0.008	0.004	0.013
deprecated	0.000	0.000	0.001
dustyScore	0.584	0.000	0.587
polyn	0	0	0
qa	0.908	0.004	0.914
readAligned	0.252	0.008	0.258
readBaseQuality	0.016	0.004	0.020
readFasta	0.104	0.000	0.151
readFastq	0.164	0.008	0.173
readIntensities	0.096	0.016	0.111
readPrb	0.056	0.004	0.058
readQseq	0.016	0.000	0.017
readXStringColumns	0.156	0.004	0.162
renew	0.072	0.000	0.070
report	0.004	0.000	0.005
spViewPerFeature	1.996	0.020	2.022
srFilter	0.384	0.000	0.382
srapply	0.004	0.004	0.007
srdistance	0.176	0.000	0.176
srduplicated	0.108	0.008	0.115
tables	0.124	0.000	0.124
trimTails	0.681	0.000	0.354