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BioC 2.12: CHECK report for plw on george2

This page was generated on 2013-10-09 09:37:26 -0700 (Wed, 09 Oct 2013).

Package 492/671HostnameOS / ArchBUILDCHECKBUILD BIN
plw 1.20.0
Magnus Astrand
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/plw
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: plw
Version: 1.20.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings plw_1.20.0.tar.gz
StartedAt: 2013-10-09 04:06:51 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:08:18 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 87.3 seconds
RetCode: 0
Status:  OK 
CheckDir: plw.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/plw.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plw/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plw’ version ‘1.20.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘plw’ can be installed ... [6s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .C("qnorm_c", ..., PACKAGE = "affy")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [20s/21s] OK
Examples with CPU or elapsed time > 5s
     user system elapsed
plw 5.784   0.12   6.002
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/plw.Rcheck/00check.log’
for details.

plw.Rcheck/00install.out:

* installing *source* package ‘plw’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SpecialFunctions.c -o SpecialFunctions.o
SpecialFunctions.c: In function ‘getPosteriorProbsAndSigmaHatStrata0’:
SpecialFunctions.c:154:20: warning: variable ‘s2’ set but not used [-Wunused-but-set-variable]
SpecialFunctions.c:154:17: warning: variable ‘s1’ set but not used [-Wunused-but-set-variable]
SpecialFunctions.c:154:14: warning: variable ‘s0’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SpecialOptim.c -o SpecialOptim.o
gcc -std=gnu99 -shared -L/usr/local/lib -o plw.so SpecialFunctions.o SpecialOptim.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/plw.Rcheck/plw/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (plw)

plw.Rcheck/plw-Ex.timings:

nameusersystemelapsed
HowToPLW0.0120.0000.016
lmw1.8480.0641.938
logitT1.7320.0601.824
plw5.7840.1206.002
scaleParameterPlot1.9920.0562.052
statByIndex1.7200.0121.955
topRankSummary2.0370.0722.212
varHistPlot1.9960.0642.061