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Package 371/419HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.8.2
Biocore Team c/o BioC user list
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/ShortRead
Last Changed Rev: 51020 / Revision: 54588
Last Changed Date: 2010-11-23 07:31:39 -0800 (Tue, 23 Nov 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ WARNINGS ] OK 

Summary

Package: ShortRead
Version: 1.8.2
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings ShortRead_1.8.2.tar.gz
StartedAt: 2011-04-07 13:06:07 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 13:11:10 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 302.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ShortRead.Rcheck
Warnings: 2

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/ShortRead.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.8.2'
* 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 'D:/biocbld/bbs-2.7-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* 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 ... 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 manual 'Writing R
Extensions'.
* 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  'D:/biocbld/bbs-2.7-bioc/meat/ShortRead.Rcheck/00check.log'
for details

ShortRead.Rcheck/00install.out:

* installing *source* package 'ShortRead' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c alphabet.c -o alphabet.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io.c -o io.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c pileup.c -o pileup.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include"      -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c sampler.c -o sampler.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c util.c -o util.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -I"D:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/ShortRead.Rcheck/ShortRead/libs/x64
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

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)

ShortRead.Rcheck/ShortRead-Ex.timings:

nameusersystemelapsed
AlignedRead-class0.870.441.31
BAMQA-class000
BowtieQA-class000
ExperimentPath-class000
FastqQA-class000
Intensity-class0.310.030.44
MAQMapQA-class000
QA-class000
QualityScore-class0.020.000.02
QualityScore000
RochePath-class000
RocheSet-class000
RtaIntensity-class0.060.000.06
RtaIntensity0.050.000.04
SRFilter-class000
SRSet-class000
SRUtil-class000
Sampler-class0.440.140.58
ShortRead-class0.040.000.05
ShortReadQ-class0.140.000.14
SolexaExportQA-class000
SolexaIntensity-class0.170.000.17
SolexaPath-class0.240.320.54
SolexaSet-class0.060.020.08
accessors000
alphabetByCycle0.280.540.83
clean0.020.000.01
countLines0.010.000.02
deprecated000
dustyScore0.490.220.70
polyn000
qa000
readAligned0.700.801.65
readBaseQuality0.110.090.21
readFasta0.080.003.65
readFastq0.700.631.67
readIntensities0.150.000.14
readPrb0.090.000.10
readQseq0.170.120.29
readXStringColumns0.490.641.16
renew0.200.220.44
report0.010.000.01
srFilter0.540.440.99
srapply000
srdistance0.450.170.84
srduplicated0.260.310.83
tables0.300.180.47