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CHECK report for GOSim on malbec2

This page was generated on 2020-10-17 11:54:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GOSim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 756/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSim 1.26.0
Holger Froehlich
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GOSim
Branch: RELEASE_3_11
Last Commit: ccc475e
Last Changed Date: 2020-04-27 14:36:28 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOSim
Version: 1.26.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GOSim_1.26.0.tar.gz
StartedAt: 2020-10-17 01:55:10 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:01:32 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 381.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GOSim.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GOSim_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GOSim.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.26.0’
* 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 ‘GOSim’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
GOGraph: no visible global function definition for ‘new’
GOenrichment: no visible global function definition for ‘new’
calc.diffusion.kernel: no visible global function definition for ‘as’
evaluateClustering: no visible global function definition for ‘median’
evaluateClustering: no visible global function definition for ‘mad’
evaluateClustering: no visible global function definition for ‘as.dist’
norm: no visible global function definition for ‘dist’
pca: no visible global function definition for ‘prcomp’
selectPrototypes : <anonymous>: no visible global function definition
  for ‘cutree’
selectPrototypes : <anonymous>: no visible global function definition
  for ‘hclust’
selectPrototypes : <anonymous>: no visible global function definition
  for ‘dist’
selectPrototypes: no visible binding for global variable ‘BIC’
setEvidenceLevel: no visible global function definition for ‘is’
Undefined global functions or variables:
  BIC as as.dist cutree dist hclust is mad median new prcomp
Consider adding
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "BIC", "as.dist", "cutree", "dist", "hclust",
             "mad", "median", "prcomp")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getGeneSimPrototypes 200.472  1.015 201.528
getTermSim            11.793  0.000  11.793
getMinimumSubsumer    11.369  0.028  11.411
getDisjCommAnc         9.823  0.191  10.015
setEnrichmentFactors   8.014  0.004   8.030
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/GOSim.Rcheck/00check.log’
for details.



Installation output

GOSim.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GOSim
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘GOSim’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include  `/home/biocbuild/bbs-3.11-bioc/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fpic  -g -O2  -Wall -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-GOSim/00new/GOSim/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 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 (GOSim)

Tests output


Example timings

GOSim.Rcheck/GOSim-Ex.timings

nameusersystemelapsed
GOenrichment000
calcICs000
evaluateClustering000
filterGO000
getAncestors000
getChildren000
getDisjCommAnc 9.823 0.19110.015
getGOGraph0.0010.0010.000
getGOInfo000
getGeneFeatures000
getGeneFeaturesPrototypes000
getGeneSim000
getGeneSimPrototypes200.472 1.015201.528
getMinimumSubsumer11.369 0.02811.411
getOffsprings0.0000.0000.001
getParents000
getTermSim11.793 0.00011.793
selectPrototypes0.0000.0000.001
setEnrichmentFactors8.0140.0048.030
setEvidenceLevel000
setOntology0.0000.0000.001