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BioC 3.4: CHECK report for maanova on zin1

This page was generated on 2016-09-21 03:35:58 -0700 (Wed, 21 Sep 2016).

Package 675/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maanova 1.43.0
Keith Sheppard
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maanova
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: maanova
Version: 1.43.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings maanova_1.43.0.tar.gz
StartedAt: 2016-09-20 08:44:31 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:45:02 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 31.5 seconds
RetCode: 0
Status:  OK 
CheckDir: maanova.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings maanova_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/maanova.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.43.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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-3.4-bioc/meat/maanova.Rcheck/00check.log’
for details.


maanova.Rcheck/00install.out:

* installing *source* package ‘maanova’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c makeratio.c -o makeratio.o
gcc -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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
PairContrast0.0120.0080.021
Rmaanova.version0.0040.0000.004
abf10.0080.0000.006
adjPval0.0080.0000.007
arrayview000
consensus0.0080.0000.007
dyeswapfilter000
fill.missing0.1520.0080.157
fitmaanova0.0080.0000.007
fom0.0040.0040.007
geneprofile0.0080.0000.007
gridcheck000
kidney0.0560.0000.054
maanova-internal0.0040.0000.003
macluster0.0080.0000.007
matest0.0080.0000.007
read.madata0.0000.0000.001
resiplot0.0080.0000.007
riplot000
subset.madata0.0520.0000.051
summarytable0.0080.0000.007
transform.madata0.0880.0000.088
varplot0.0080.0000.007
volcano0.0040.0000.001
write.madata0.0040.0000.007