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Package 125/479HostnameOS / ArchBUILDCHECKBUILD BIN
DEGseq 1.7.1
Likun Wang
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGseq
Last Changed Rev: 56066 / Revision: 56603
Last Changed Date: 2011-06-08 15:07:12 -0700 (Wed, 08 Jun 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DEGseq
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGseq_1.7.1.tar.gz
StartedAt: 2011-07-07 02:39:00 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 02:43:24 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 264.1 seconds
RetCode: 0
Status:  OK 
CheckDir: DEGseq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/DEGseq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DEGseq/DESCRIPTION' ... OK
* this is package 'DEGseq' version '1.7.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DEGseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* 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 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... 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

DEGseq.Rcheck/00install.out:

* installing *source* package 'DEGseq' ...
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c getGeneExp.cpp -o getGeneExp.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DEGseq.so getGeneExp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/DEGseq.Rcheck/DEGseq/libs/i386
** R
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
Loading required package: IRanges

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

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: impute
Loading required package: matrixStats
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for help.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DEGseq.Rnw' 
** testing if installed package can be loaded

* DONE (DEGseq)

DEGseq.Rcheck/DEGseq-Ex.timings:

nameusersystemelapsed
DEGexp3.1440.7584.255
DEGexp26.0941.9958.242
DEGseq1.1660.0791.293
DEGseq.aln1.6470.1391.850
getGeneExp0.3710.0150.389
getGeneExp.aln0.6270.0450.694
readGeneExp0.0430.0030.046
samWrapper7.0341.0238.495