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BioC 3.2: CHECK report for maanova on oaxaca

This page was generated on 2016-04-23 10:23:10 -0700 (Sat, 23 Apr 2016).

Package 580/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maanova 1.40.0
Keith Sheppard
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/maanova
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: maanova
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maanova_1.40.0.tar.gz
StartedAt: 2016-04-23 01:38:58 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:39:46 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 47.5 seconds
RetCode: 0
Status:  OK 
CheckDir: maanova.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maanova_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/maanova.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maanova/DESCRIPTION’ ... OK
* this is package ‘maanova’ version ‘1.40.0’
* 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 ... [3s/4s] 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’
* 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 ... [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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/maanova.Rcheck/00check.log’
for details.


maanova.Rcheck/00install.out:

* installing *source* package ‘maanova’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c makeratio.c -o makeratio.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c masvd.c -o masvd.o
masvd.c:114:2: warning: '/*' within block comment [-Wcomment]
        /* work on a copy of x */
        ^
masvd.c:154:1: warning: '/*' within block comment [-Wcomment]
/*#ifndef IEEE_754
^
masvd.c:161:5: warning: '/*' within block comment [-Wcomment]
    /* work on a copy of x */
    ^
masvd.c:165:2: warning: '/*' within block comment [-Wcomment]
        /* ask for optimal size of work array */
        ^
masvd.c:189:2: warning: '/*' within block comment [-Wcomment]
        /* ask for optimal size of work array */
        ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c shift.c -o shift.o
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
  int i, j, k;
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c util.c -o util.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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
PairContrast0.0280.0040.032
Rmaanova.version0.0060.0010.007
abf10.0080.0010.010
adjPval0.0080.0020.010
arrayview0.0000.0000.001
consensus0.0070.0020.009
dyeswapfilter0.0010.0000.001
fill.missing0.2170.0100.227
fitmaanova0.0070.0010.008
fom0.0080.0020.010
geneprofile0.0080.0020.010
gridcheck0.0010.0000.001
kidney0.0630.0050.068
maanova-internal0.0030.0000.004
macluster0.0090.0020.011
matest0.0080.0020.011
read.madata0.0010.0000.001
resiplot0.0080.0030.010
riplot0.0000.0000.001
subset.madata0.0640.0040.068
summarytable0.0080.0030.011
transform.madata0.1070.0050.111
varplot0.0090.0030.012
volcano0.0010.0000.001
write.madata0.0090.0030.011