Package: ShortRead

Version: 1.10.4

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.10.4.tar.gz

StartedAt: 2011-10-20 14:29:24 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:33:00 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 215.4 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 2.13.2 (2011-09-30)
* 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 ‘1.10.4’
* 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 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 installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    doc       2.4Mb
* 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’
* 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 the 'Writing R
Extensions' manual.
* 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 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

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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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"/loc/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include" -I"/loc/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
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	0.740	0.016	0.772
BAMQA-class	0.004	0.000	0.002
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.004	0.000	0.000
FastqQA-class	0.000	0.000	0.001
Intensity-class	0.300	0.004	0.307
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.000	0.000	0.002
QualityScore-class	0	0	0
QualityScore	0.008	0.000	0.009
RochePath-class	0.000	0.000	0.001
RocheSet-class	0.000	0.000	0.001
RtaIntensity-class	0.068	0.000	0.068
RtaIntensity	0.048	0.000	0.051
SRFilter-class	0	0	0
SRFilterResult-class	0.112	0.000	0.171
SRSet-class	0.000	0.000	0.001
SRUtil-class	0.004	0.000	0.011
Sampler-class	0.580	0.000	0.894
ShortRead-class	0.064	0.004	0.068
ShortReadQ-class	0.124	0.012	0.148
SolexaExportQA-class	0.000	0.000	0.001
SolexaIntensity-class	0.108	0.020	0.143
SolexaPath-class	0.092	0.000	0.093
SolexaSet-class	0.076	0.004	0.092
accessors	0.000	0.004	0.005
alphabetByCycle	0.024	0.004	0.030
clean	0.000	0.000	0.001
countLines	0.016	0.000	0.016
deprecated	0.000	0.000	0.001
dustyScore	0.324	0.000	0.326
polyn	0	0	0
qa	0.000	0.000	0.001
readAligned	0.260	0.004	0.264
readBaseQuality	0.024	0.000	0.025
readFasta	0.084	0.004	0.118
readFastq	0.432	0.004	0.452
readIntensities	0.080	0.012	0.096
readPrb	0.068	0.000	0.072
readQseq	0.012	0.004	0.016
readXStringColumns	0.172	0.004	0.183
renew	0.076	0.004	0.080
report	0.004	0.000	0.005
srFilter	0.420	0.000	0.421
srapply	0.008	0.000	0.006
srdistance	0.224	0.000	0.227
srduplicated	0.132	0.000	0.133
tables	0.152	0.004	0.159