Package: ShortRead

Version: 1.6.2

Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings ShortRead_1.6.2.tar.gz

StartedAt: 2010-10-04 20:08:18 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 20:11:51 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 212.8 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/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 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' ...19,25d18
< Error in checkEquals(srorder(sread(rfq)), order(as.character(sread(rfq)))) : 
<   Mean relative difference: 0.4435591
< Error in checkIdentical(exp, res) : FALSE 
< 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' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c alphabet.c -o alphabet.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c io.c -o io.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c io_bowtie.c -o io_bowtie.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c io_soap.c -o io_soap.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c pileup.c -o pileup.o
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c util.c -o util.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c xsnap.c -o xsnap.o
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 util.o xsnap.o -lRzlib -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/ShortRead.Rcheck/ShortRead/libs
  ... done
** 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	0.68	0.14	0.83
BowtieQA-class	0.02	0.00	0.02
ExperimentPath-class	0	0	0
FastqQA-class	0	0	0
Intensity-class	0.61	0.01	0.71
MAQMapQA-class	0	0	0
QA-class	0	0	0
QualityScore-class	0	0	0
QualityScore	0.01	0.00	0.02
RochePath-class	0	0	0
RocheSet-class	0	0	0
RtaIntensity-class	0.08	0.00	0.07
RtaIntensity	0.19	0.00	0.19
SRFilter-class	0	0	0
SRSet-class	0	0	0
SRUtil-class	0.01	0.00	0.02
ShortRead-class	0.08	0.00	0.07
ShortReadQ-class	0.14	0.00	0.15
SolexaExportQA-class	0.02	0.00	0.01
SolexaIntensity-class	0.18	0.02	0.20
SolexaPath-class	0.44	0.25	0.71
SolexaSet-class	0.11	0.00	0.11
accessors	0.02	0.00	0.01
alphabetByCycle	0.45	0.19	0.64
clean	0.02	0.00	0.02
countLines	0.01	0.01	0.03
deprecated	0	0	0
detail	0.02	0.00	0.02
dustyScore	0.77	0.25	1.05
polyn	0	0	0
qa	0	0	0
readAligned	1.48	0.60	2.08
readBaseQuality	0.19	0.09	0.28
readFastq	1.05	0.47	1.57
readIntensities	0.15	0.03	0.18
readPrb	0.11	0.00	0.11
readQseq	0.31	0.09	0.40
readXStringColumns	1.07	0.40	1.46
renew	0.40	0.15	0.62
report	0.00	0.02	0.02
srFilter	0.85	0.36	1.22
srapply	0.01	0.00	0.01
srdistance	0.66	0.07	0.74
srduplicated	0.53	0.21	0.73
tables	0.45	0.15	0.61