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Package 408/462HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.11.1
Biocore Team c/o BioC user list
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead
Last Changed Rev: 55040 / Revision: 55359
Last Changed Date: 2011-04-22 03:57:05 -0700 (Fri, 22 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ShortRead
Version: 1.11.1
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings ShortRead_1.11.1.tar.gz
StartedAt: 2011-05-09 15:34:58 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 15:38:55 -0700 (Mon, 09 May 2011)
EllapsedTime: 236.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ShortRead.Rcheck
Warnings: 2

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-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 '1.11.1'
* 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 'E:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.3Mb
* 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 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 2 warnings, see
  'E:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00check.log'
for details

ShortRead.Rcheck/00install.out:

* installing *source* package 'ShortRead' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-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˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c alphabet.c -o alphabet.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c io.c -o io.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c io_bowtie.c -o io_bowtie.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c io_soap.c -o io_soap.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c pileup.c -o pileup.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c sampler.c -o sampler.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -c util.c -o util.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-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 sampler.o util.o xsnap.o -lRzlib -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/ShortRead/libs/i386
** 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

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)

ShortRead.Rcheck/ShortRead-Ex.timings:

nameusersystemelapsed
AlignedRead-class1.040.211.23
BAMQA-class000
BowtieQA-class000
ExperimentPath-class000
FastqQA-class000
Intensity-class0.500.000.53
MAQMapQA-class000
QA-class000
QualityScore-class000
QualityScore0.020.000.01
RochePath-class000
RocheSet-class000
RtaIntensity-class0.060.000.07
RtaIntensity0.030.000.03
SRFilter-class000
SRFilterResult-class0.060.000.07
SRSet-class000
SRUtil-class000
Sampler-class0.410.120.55
ShortRead-class0.060.000.06
ShortReadQ-class0.130.000.13
SolexaExportQA-class000
SolexaIntensity-class0.150.030.18
SolexaPath-class0.460.250.71
SolexaSet-class0.110.000.11
accessors0.010.000.01
alphabetByCycle0.570.140.71
clean000
countLines0.010.000.07
deprecated000
dustyScore0.700.251.02
polyn000
qa000
readAligned1.600.522.16
readBaseQuality0.190.050.23
readFasta0.070.000.12
readFastq0.990.391.40
readIntensities0.340.000.34
readPrb0.080.000.08
readQseq0.300.110.40
readXStringColumns1.200.311.52
renew0.440.150.59
report0.010.000.02
srFilter1.030.291.31
srapply000
srdistance0.490.170.66
srduplicated0.580.150.73
tables0.450.190.64