Package: ShortRead

Version: 1.11.23

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.11.23.tar.gz

StartedAt: 2011-07-07 02:15:56 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:19:58 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 242.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ShortRead.Rcheck

Warnings: 3

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.11.23’
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘Rmpi’ ‘multicore’
* 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-2.9-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       2.3Mb
* 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
.coverage_viewer: no visible binding for global variable ‘group’
.multicoverage_viewer: no visible global function definition for
  ‘.getData<-’
.multicoverage_viewer: no visible binding for global variable ‘lv’
.multicoverage_viewer: no visible binding for global variable ‘group’
.multicoverage_viewer: no visible binding for global variable ‘sv’
.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 ... WARNING
Missing link(s) in documentation object ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck/00_pkg_src/ShortRead/man/Snapshot-class.Rd’:
  ‘Snapshot-class’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GappedReads’ ‘qname’ ‘qseq’ ‘readGappedReads’
Undocumented S4 classes:
  ‘AssayData’ ‘GappedReads’ ‘Snapshot’ ‘trellis’
Undocumented S4 methods:
  generic 'SnapshotFunctionList' and siglist 'SnapshotFunction'
  generic '[' and siglist 'GappedReads,ANY,ANY'
  generic 'c' and siglist 'GappedReads'
  generic 'narrow' and siglist 'GappedReads'
  generic 'qname' and siglist 'GappedReads'
  generic 'qseq' and siglist 'GappedReads'
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 3 warnings, see
  ‘/loc/home/biocbuild/bbs-2.9-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-2.9-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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -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-2.9-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

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

Loading required package: RColorBrewer
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 ...
*** tangling vignette sources ...
   ‘Overview.Rnw’ 
** testing if installed package can be loaded

* DONE (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.444	0.004	0.448
BAMQA-class	0.000	0.000	0.001
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	0.812	0.004	0.816
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.000	0.000	0.001
QualityScore-class	0.000	0.004	0.001
QualityScore	0.008	0.000	0.008
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	0.044	0.008	0.054
SRFilter-class	0	0	0
SRFilterResult-class	0.084	0.004	0.087
SRSet-class	0.000	0.000	0.001
SRUtil-class	0.004	0.000	0.005
Sampler-class	0.612	0.000	0.612
ShortRead-class	0.072	0.000	0.069
ShortReadQ-class	0.612	0.012	0.424
Snapshot-class	1.928	0.020	1.933
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0.004	0.000	0.001
SolexaIntensity-class	0.140	0.016	0.156
SolexaPath-class	0.092	0.008	0.101
SolexaSet-class	0.088	0.004	0.089
SpTrellis-class	0.000	0.000	0.001
accessors	0.008	0.000	0.006
alphabetByCycle	0.028	0.004	0.030
clean	0.000	0.000	0.001
countLines	0.008	0.004	0.013
deprecated	0	0	0
dustyScore	0.388	0.000	0.388
polyn	0.004	0.000	0.001
qa	0.764	0.000	0.764
readAligned	0.280	0.008	0.288
readBaseQuality	0.020	0.004	0.021
readFasta	0.064	0.008	0.091
readFastq	0.188	0.012	0.202
readIntensities	0.108	0.008	0.117
readPrb	0.060	0.000	0.058
readQseq	0.012	0.004	0.016
readXStringColumns	0.152	0.008	0.161
renew	0.080	0.000	0.079
report	0.004	0.004	0.005
srFilter	0.452	0.008	0.463
srapply	0.004	0.000	0.007
srdistance	0.180	0.000	0.182
srduplicated	0.116	0.008	0.123
tables	0.128	0.000	0.125
trimTails	0.000	0.000	0.001