Back to Multiple platform build/check report for BioC 3.6
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for DirichletMultinomial on veracruz1

This page was generated on 2018-04-12 13:35:34 -0400 (Thu, 12 Apr 2018).

Package 371/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DirichletMultinomial 1.20.0
Martin Morgan
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DirichletMultinomial
Branch: RELEASE_3_6
Last Commit: 251529f
Last Changed Date: 2017-10-30 12:39:40 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DirichletMultinomial
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DirichletMultinomial_1.20.0.tar.gz
StartedAt: 2018-04-12 02:55:06 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:56:03 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 56.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DirichletMultinomial.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DirichletMultinomial_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DirichletMultinomial.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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 ‘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 ... NOTE
dmn: no visible global function definition for ‘runif’
dmngroup: no visible global function definition for ‘setNames’
heatmapdmn: no visible global function definition for ‘head’
heatmapdmn: no visible global function definition for ‘layout’
heatmapdmn: no visible global function definition for ‘par’
heatmapdmn: no visible global function definition for ‘image’
heatmapdmn: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis head image layout par runif setNames
Consider adding
  importFrom("graphics", "axis", "image", "layout", "par")
  importFrom("stats", "runif", "setNames")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/DirichletMultinomial.Rcheck/00check.log’
for details.



Installation output

DirichletMultinomial.Rcheck/00install.out

* installing *source* package ‘DirichletMultinomial’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC  -Wall -g -O2  -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC  -Wall -g -O2  -c dirichlet_fit.c -o dirichlet_fit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC  -Wall -g -O2  -c dirichlet_fit_main.c -o dirichlet_fit_main.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 DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/DirichletMultinomial.Rcheck/DirichletMultinomial/libs
** R
** data
** inst
** preparing 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-class0.0180.0040.022
DMNGroup-class0.0100.0020.013
cvdmngroup0.0040.0010.005
dataobjects0.0160.0040.020
dmn0.0230.0040.026
dmngroup0.0410.0020.042
fitted0.1270.0060.135
heatmapdmn0.0810.0030.087
roc0.2260.0080.237
util0.0350.0020.036