Package: maanova

Version: 1.48.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings maanova_1.48.0.tar.gz

StartedAt: 2018-04-12 00:42:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:43:34 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 35.9 seconds

RetCode: 0

Status:  OK

CheckDir: maanova.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings maanova_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/maanova.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maanova/DESCRIPTION’ ... OK
* this is package ‘maanova’ version ‘1.48.0’
* 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 ‘maanova’ can be installed ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘qvalue’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fdr: no visible global function definition for ‘qvalue’
matest: no visible global function definition for ‘makeMPIcluster’
matest: no visible global function definition for ‘clusterApply’
matest: no visible global function definition for ‘clusterEvalQ’
matest: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApply clusterEvalQ makeMPIcluster qvalue stopCluster
* 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 GNU extensions 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 files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/maanova.Rcheck/00check.log’
for details.

* installing *source* package ‘maanova’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c makeratio.c -o makeratio.o
gcc -I/home/biocbuild/bbs-3.6-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]
  /* work on a copy of x */
  ^
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
 /*#ifndef IEEE_754
 ^
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
     /* work on a copy of x */
     ^
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
  ^
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
  ^
gcc -I/home/biocbuild/bbs-3.6-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]
   int i, j, k;
             ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c util.c -o util.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.016	0.004	0.019
Rmaanova.version	0.004	0.000	0.004
abf1	0.008	0.000	0.007
adjPval	0.008	0.000	0.007
arrayview	0	0	0
consensus	0.008	0.000	0.007
dyeswapfilter	0	0	0
fill.missing	0.144	0.000	0.146
fitmaanova	0.004	0.004	0.008
fom	0.004	0.000	0.007
geneprofile	0.004	0.000	0.006
gridcheck	0.004	0.000	0.001
kidney	0.044	0.012	0.056
maanova-internal	0.040	0.004	0.043
macluster	0.004	0.000	0.007
matest	0.004	0.000	0.007
read.madata	0.000	0.000	0.001
resiplot	0.008	0.000	0.007
riplot	0.000	0.000	0.001
subset.madata	0.048	0.004	0.052
summarytable	0.008	0.000	0.007
transform.madata	0.052	0.000	0.053
varplot	0.004	0.004	0.007
volcano	0	0	0
write.madata	0.004	0.000	0.006