Package: ShortRead

Version: 1.9.14

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.9.14.tar.gz

StartedAt: 2011-02-24 22:42:31 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:45:24 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 172.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ShortRead.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.9.14’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Class "AssayData" is defined (with package slot ‘Biobase’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘ShortRead’
See ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck/00install.out’ for details.
* 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 ... WARNING
Undocumented S4 classes:
  AssayData
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck/00check.log’
for details

* 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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.8-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 sampler.o util.o xsnap.o -lz -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-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, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Warning: Class "AssayData" is defined (with package slot ‘Biobase’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘ShortRead’
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.620	0.008	0.629
BAMQA-class	0.000	0.004	0.001
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.004	0.000	0.001
FastqQA-class	0.000	0.000	0.001
Intensity-class	0.464	0.004	0.466
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.004	0.000	0.001
QualityScore-class	0	0	0
QualityScore	0.008	0.000	0.007
RochePath-class	0.000	0.000	0.001
RocheSet-class	0.000	0.000	0.001
RtaIntensity-class	0.056	0.000	0.056
RtaIntensity	0.040	0.000	0.038
SRFilter-class	0.000	0.000	0.001
SRFilterResult-class	0.084	0.000	0.084
SRSet-class	0.004	0.000	0.001
SRUtil-class	0.004	0.000	0.005
Sampler-class	0.532	0.008	0.536
ShortRead-class	0.052	0.004	0.056
ShortReadQ-class	0.104	0.020	0.124
SolexaExportQA-class	0.004	0.000	0.001
SolexaIntensity-class	0.112	0.004	0.119
SolexaPath-class	0.076	0.004	0.079
SolexaSet-class	0.076	0.000	0.076
accessors	0.004	0.000	0.005
alphabetByCycle	0.020	0.008	0.027
clean	0.004	0.000	0.001
countLines	0.012	0.000	0.011
deprecated	0	0	0
dustyScore	0.316	0.000	0.314
polyn	0	0	0
qa	0.000	0.000	0.001
readAligned	0.244	0.008	0.253
readBaseQuality	0.020	0.004	0.025
readFasta	0.084	0.004	0.119
readFastq	0.416	0.004	0.421
readIntensities	0.084	0.004	0.089
readPrb	0.060	0.000	0.061
readQseq	0.016	0.000	0.015
readXStringColumns	0.160	0.000	0.162
renew	0.076	0.004	0.077
report	0.000	0.004	0.005
srFilter	0.324	0.000	0.323
srapply	0.008	0.000	0.006
srdistance	0.224	0.000	0.226
srduplicated	0.116	0.000	0.115
tables	0.144	0.000	0.146