Package: ShortRead

Version: 1.6.2

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.6.2.tar.gz

StartedAt: 2010-10-04 19:49:55 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 19:52:47 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 171.5 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/ShortRead.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.6.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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'
* 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 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 ... OK
* checking examples ... OK
* checking tests ...
  Running 'runalltests.R'
  Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...19,22d18
< Error in checkEquals(2396L, length(aln)) : 
<   Mean relative difference: 0.0004173623
< Error in checkIdentical(1533L, sum(occurrenceFilter(withSread = TRUE)(aln))) : 
<   FALSE 
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-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-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-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-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include"   -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 util.o xsnap.o -lz -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/ShortRead.Rcheck/ShortRead/libs
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
    rbind, rep.int, table

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.252	0.008	0.258
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.000	0.000	0.001
FastqQA-class	0.000	0.000	0.001
Intensity-class	0.672	0.012	0.683
MAQMapQA-class	0.000	0.004	0.001
QA-class	0.000	0.000	0.002
QualityScore-class	0.000	0.000	0.001
QualityScore	0.008	0.000	0.009
RochePath-class	0.000	0.000	0.001
RocheSet-class	0.000	0.004	0.001
RtaIntensity-class	0.068	0.004	0.073
RtaIntensity	0.044	0.008	0.049
SRFilter-class	0	0	0
SRSet-class	0.000	0.000	0.001
SRUtil-class	0.004	0.004	0.006
ShortRead-class	0.072	0.000	0.072
ShortReadQ-class	0.136	0.000	0.138
SolexaExportQA-class	0.004	0.000	0.001
SolexaIntensity-class	0.132	0.004	0.138
SolexaPath-class	0.120	0.000	0.121
SolexaSet-class	0.092	0.000	0.091
accessors	0.004	0.000	0.004
alphabetByCycle	0.036	0.004	0.042
clean	0.000	0.000	0.001
countLines	0.012	0.000	0.012
deprecated	0	0	0
detail	0.020	0.000	0.018
dustyScore	0.552	0.004	0.555
polyn	0.000	0.000	0.001
qa	0.000	0.000	0.002
readAligned	0.328	0.016	0.347
readBaseQuality	0.056	0.000	0.055
readFastq	0.468	0.000	0.467
readIntensities	0.080	0.020	0.158
readPrb	0.084	0.000	0.087
readQseq	0.036	0.000	0.036
readXStringColumns	0.216	0.008	0.225
renew	0.108	0.000	0.108
report	0.000	0.004	0.004
srFilter	0.364	0.000	0.365
srapply	0.008	0.000	0.007
srdistance	0.256	0.004	0.258
srduplicated	0.152	0.008	0.159
tables	0.176	0.004	0.181