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CHECK report for DirichletMultinomial on malbec1

This page was generated on 2019-04-16 11:49:35 -0400 (Tue, 16 Apr 2019).

Package 416/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DirichletMultinomial 1.24.1
Martin Morgan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DirichletMultinomial
Branch: RELEASE_3_8
Last Commit: 50195d9
Last Changed Date: 2019-01-04 13:29:45 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DirichletMultinomial
Version: 1.24.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DirichletMultinomial.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DirichletMultinomial_1.24.1.tar.gz
StartedAt: 2019-04-15 23:32:04 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:32:54 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 50.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DirichletMultinomial.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DirichletMultinomial.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DirichletMultinomial_1.24.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DirichletMultinomial.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DirichletMultinomial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DirichletMultinomial’ version ‘1.24.1’
* 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 ‘DirichletMultinomial’ 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 ... 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/DirichletMultinomial.Rcheck/00check.log’
for details.



Installation output

DirichletMultinomial.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DirichletMultinomial
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DirichletMultinomial’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c dirichlet_fit.c -o dirichlet_fit.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c dirichlet_fit_main.c -o dirichlet_fit_main.o
dirichlet_fit_main.c: In function ‘dirichlet_fit_main’:
dirichlet_fit_main.c:542:17: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
     int signum, status;
                 ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/DirichletMultinomial/libs
** R
** data
** 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
* DONE (DirichletMultinomial)

Tests output


Example timings

DirichletMultinomial.Rcheck/DirichletMultinomial-Ex.timings

nameusersystemelapsed
DMN-class0.0120.0040.017
DMNGroup-class0.0120.0000.009
cvdmngroup0.0000.0040.004
dataobjects0.0160.0000.013
dmn0.0160.0000.017
dmngroup0.0040.0000.005
fitted0.1080.0040.121
heatmapdmn0.0520.0000.051
roc0.2080.0000.242
util0.020.000.02