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Package 146/553HostnameOS / ArchBUILDCHECKBUILD BIN
DEGseq 1.10.0
Likun Wang
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/DEGseq
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DEGseq
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGseq_1.10.0.tar.gz
StartedAt: 2012-09-23 23:54:14 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:55:22 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 68.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DEGseq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/DEGseq.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'DEGseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
FindDiff_FET: warning in matrix(c(o1, o2, count1 - o1, count2 - o2), nr
  = 2): partial argument match of 'nr' to 'nrow'
png_new: warning in png(file = file, units = "px", width = 480, height
  = 480): partial argument match of 'file' to 'filename'
* 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 compiled code ... NOTE
File '/Users/biocbuild/bbs-2.10-bioc/meat/DEGseq.Rcheck/DEGseq/libs/i386/DEGseq.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'getGeneExp.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from '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

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/DEGseq.Rcheck/00check.log'
for details.

DEGseq.Rcheck/00install.out:

* installing *source* package 'DEGseq' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c getGeneExp.cpp -o getGeneExp.o
g++ -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-2.10-bioc/meat/DEGseq.Rcheck/DEGseq/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DEGseq.Rnw' 
** testing if installed package can be loaded

* DONE (DEGseq)

DEGseq.Rcheck/DEGseq-Ex.timings:

nameusersystemelapsed
DEGexp2.5320.6453.224
DEGexp24.3991.5776.032
DEGseq0.8970.0590.966
getGeneExp0.3220.0180.340
readGeneExp0.0310.0040.035
samWrapper4.0240.6914.736