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Package 342/389HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.6.2
Biocore Team c/o BioC user list
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/ShortRead
Last Changed Rev: 46600 / Revision: 49923
Last Changed Date: 2010-04-28 10:21:31 -0700 (Wed, 28 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

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

Command output

* 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

ShortRead.Rcheck/00install.out:

* 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)

ShortRead.Rcheck/ShortRead-Ex.timings:

nameusersystemelapsed
AlignedRead-class0.680.140.83
BowtieQA-class0.020.000.02
ExperimentPath-class000
FastqQA-class000
Intensity-class0.610.010.71
MAQMapQA-class000
QA-class000
QualityScore-class000
QualityScore0.010.000.02
RochePath-class000
RocheSet-class000
RtaIntensity-class0.080.000.07
RtaIntensity0.190.000.19
SRFilter-class000
SRSet-class000
SRUtil-class0.010.000.02
ShortRead-class0.080.000.07
ShortReadQ-class0.140.000.15
SolexaExportQA-class0.020.000.01
SolexaIntensity-class0.180.020.20
SolexaPath-class0.440.250.71
SolexaSet-class0.110.000.11
accessors0.020.000.01
alphabetByCycle0.450.190.64
clean0.020.000.02
countLines0.010.010.03
deprecated000
detail0.020.000.02
dustyScore0.770.251.05
polyn000
qa000
readAligned1.480.602.08
readBaseQuality0.190.090.28
readFastq1.050.471.57
readIntensities0.150.030.18
readPrb0.110.000.11
readQseq0.310.090.40
readXStringColumns1.070.401.46
renew0.400.150.62
report0.000.020.02
srFilter0.850.361.22
srapply0.010.000.01
srdistance0.660.070.74
srduplicated0.530.210.73
tables0.450.150.61