BioC 2.13: CHECK report for maanova on zin1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/maanova.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.33.2’
* 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 ‘maanova’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘maanova.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [2s/2s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/maanova.Rcheck/00check.log’
for details.

* installing *source* package ‘maanova’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-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-2.13-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-2.13-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-2.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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)

name	user	system	elapsed
PairContrast	0.020	0.008	0.029
Rmaanova.version	0.012	0.000	0.009
abf1	0.008	0.000	0.009
adjPval	0.008	0.000	0.010
arrayview	0.004	0.000	0.003
consensus	0.012	0.000	0.012
dyeswapfilter	0.000	0.004	0.003
fill.missing	0.280	0.000	0.282
fitmaanova	0.008	0.004	0.012
fom	0.008	0.000	0.010
geneprofile	0.008	0.000	0.010
gridcheck	0.004	0.000	0.003
kidney	0.052	0.008	0.060
maanova-internal	0.008	0.000	0.010
macluster	0.008	0.004	0.012
matest	0.008	0.000	0.009
read.madata	0.004	0.000	0.005
resiplot	0.012	0.000	0.009
riplot	0.004	0.000	0.002
subset.madata	0.056	0.000	0.057
summarytable	0.008	0.000	0.010
transform.madata	0.060	0.000	0.061
varplot	0.048	0.000	0.049
volcano	0.000	0.000	0.002
write.madata	0.008	0.000	0.009

BioC 2.13: CHECK report for maanova on zin1

Summary

Command output