Package: ShortRead

Version: 1.10.4

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch ShortRead_1.10.4.tar.gz

StartedAt: 2011-10-20 16:37:17 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:40:56 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 219.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ShortRead.Rcheck

Warnings: 3

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/ShortRead.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.10.4'
* checking package namespace 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 'D:/biocbld/bbs-2.8-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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' ... WARNING
Package vignette(s) without corresponding PDF:
   Overview.Rnw

* 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
  'D:/biocbld/bbs-2.8-bioc/meat/ShortRead.Rcheck/00check.log'
for details

* installing *source* package 'ShortRead' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c alphabet.c -o alphabet.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io.c -o io.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io_bowtie.c -o io_bowtie.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io_soap.c -o io_soap.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c pileup.c -o pileup.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c sampler.c -o sampler.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c util.c -o util.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"    -I"D:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c xsnap.c -o xsnap.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def 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 -lRzlib -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/ShortRead.Rcheck/ShortRead/libs/x64
** 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	0.72	0.27	0.99
BAMQA-class	0	0	0
BowtieQA-class	0	0	0
ExperimentPath-class	0	0	0
FastqQA-class	0	0	0
Intensity-class	0.29	0.00	0.36
MAQMapQA-class	0	0	0
QA-class	0	0	0
QualityScore-class	0	0	0
QualityScore	0	0	0
RochePath-class	0	0	0
RocheSet-class	0	0	0
RtaIntensity-class	0.06	0.00	0.06
RtaIntensity	0.05	0.00	0.05
SRFilter-class	0	0	0
SRFilterResult-class	0.08	0.00	0.08
SRSet-class	0	0	0
SRUtil-class	0	0	0
Sampler-class	0.36	0.17	0.54
ShortRead-class	0.05	0.00	0.05
ShortReadQ-class	0.12	0.03	0.15
SolexaExportQA-class	0	0	0
SolexaIntensity-class	0.16	0.02	0.18
SolexaPath-class	0.22	0.30	0.51
SolexaSet-class	0.08	0.00	0.08
accessors	0	0	0
alphabetByCycle	0.20	0.26	0.48
clean	0	0	0
countLines	0.01	0.02	0.04
deprecated	0	0	0
dustyScore	0.55	0.28	0.82
polyn	0	0	0
qa	0	0	0
readAligned	0.81	0.75	1.57
readBaseQuality	0.13	0.06	0.18
readFasta	0.09	0.00	0.22
readFastq	0.75	0.50	1.25
readIntensities	0.13	0.02	0.14
readPrb	0.08	0.00	0.08
readQseq	0.16	0.14	0.29
readXStringColumns	0.56	0.47	1.04
renew	0.27	0.14	0.40
report	0.00	0.01	0.02
srFilter	0.57	0.38	0.95
srapply	0	0	0
srdistance	0.32	0.19	0.50
srduplicated	0.26	0.31	0.58
tables	0.28	0.22	0.50