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BioC 2.12: CHECK report for maanova on george2

This page was generated on 2013-10-09 09:37:17 -0700 (Wed, 09 Oct 2013).

Package 377/671HostnameOS / ArchBUILDCHECKBUILD BIN
maanova 1.30.0
Keith Sheppard
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/maanova
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 [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: maanova
Version: 1.30.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings maanova_1.30.0.tar.gz
StartedAt: 2013-10-09 02:58:32 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:00:00 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 87.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: maanova.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/maanova.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 ‘maanova/DESCRIPTION’ ... OK
* this is package ‘maanova’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* 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 ‘maanova’ can be installed ... [9s/9s] 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 ... WARNING
Foreign function calls with ‘PACKAGE’ argument in a base package:
  .Call("La_svd", ..., PACKAGE = "base")
  .Call("La_svd_cmplx", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
  argument match of 'r' to 'red'
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
  argument match of 'g' to 'green'
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
  argument match of 'b' to 'blue'
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘MPI.tex’, ‘Rtour.tex’, ‘abf1.tex’, ‘algorithm.tex’, ‘camda.tex’,
  ‘faq.tex’, ‘intro.tex’, ‘paigen.tex’, ‘prepfile.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [3s/3s] 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 was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/maanova.Rcheck/00check.log’
for details.

maanova.Rcheck/00install.out:

* installing *source* package ‘maanova’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c makeratio.c -o makeratio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment [-Wcomment]
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c shift.c -o shift.o
shift.c: In function ‘shift’:
shift.c:27:13: warning: unused variable ‘k’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -shared -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/maanova.Rcheck/maanova/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maanova)

maanova.Rcheck/maanova-Ex.timings:

nameusersystemelapsed
PairContrast0.0480.0040.050
Rmaanova.version0.0280.0000.027
abf10.0160.0000.016
adjPval0.0160.0040.020
arrayview0.0080.0000.010
consensus0.0200.0040.026
dyeswapfilter0.0080.0000.011
fill.missing0.6120.0080.619
fitmaanova0.0240.0040.027
fom0.0200.0000.019
geneprofile0.0160.0000.018
gridcheck0.0080.0000.008
kidney0.0600.0120.074
maanova-internal0.0440.0000.041
macluster0.0320.0000.031
matest0.0160.0000.017
read.madata0.0160.0000.018
resiplot0.0080.0080.016
riplot0.0080.0000.008
subset.madata0.0680.0080.077
summarytable0.0200.0040.025
transform.madata0.0920.0080.101
varplot0.0160.0000.016
volcano0.0080.0000.007
write.madata0.0160.0000.016