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CHECK report for maanova on malbec2

This page was generated on 2019-04-09 11:24:10 -0400 (Tue, 09 Apr 2019).

Package 884/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maanova 1.53.0
Keith Sheppard
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/maanova
Branch: master
Last Commit: c6d407f
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: maanova
Version: 1.53.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:maanova.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings maanova_1.53.0.tar.gz
StartedAt: 2019-04-09 01:39:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:39:44 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 42.8 seconds
RetCode: 0
Status:  OK 
CheckDir: maanova.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:maanova.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings maanova_1.53.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/maanova.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.53.0’
* 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 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.consensus.hc plot.consensus.kmean print.madata
  print.summary.madata print.summary.mamodel subset.madata
  summary.madata summary.mamodel transform.madata transform.rawdata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... NOTE
Note: information on .o files is not available
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/maanova.Rcheck/00check.log’
for details.



Installation output

maanova.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL maanova
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘maanova’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c makeratio.c -o makeratio.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-maanova/00new/maanova/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maanova)

Tests output


Example timings

maanova.Rcheck/maanova-Ex.timings

nameusersystemelapsed
PairContrast0.0820.0000.082
Rmaanova.version0.0050.0000.015
abf10.0080.0000.009
adjPval0.0090.0000.009
arrayview0.0010.0000.000
consensus0.0090.0000.009
dyeswapfilter000
fill.missing0.0880.0080.095
fitmaanova0.0080.0000.007
fom0.0060.0000.006
geneprofile0.0060.0000.007
gridcheck000
kidney0.0500.0000.049
maanova-internal0.0010.0000.002
macluster0.0070.0000.006
matest0.0060.0000.006
read.madata000
resiplot0.0060.0000.007
riplot000
subset.madata0.0440.0030.049
summarytable0.0060.0000.007
transform.madata0.0410.0080.049
varplot0.0060.0000.006
volcano0.0000.0000.001
write.madata0.0060.0000.006