Package: GOSim

Version: 1.22.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GOSim_1.22.0.tar.gz

StartedAt: 2019-10-16 02:05:43 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:13:10 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 447.0 seconds

RetCode: 0

Status:  OK

CheckDir: GOSim.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GOSim_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GOSim.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 : : no visible global function definition
  for ‘cutree’
selectPrototypes : : no visible global function definition
  for ‘hclust’
selectPrototypes : : 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getGeneSimPrototypes 235.975  1.045 238.668
getTermSim            14.433  0.000  14.490
getMinimumSubsumer    12.417  0.036  12.508
getDisjCommAnc        12.108  0.187  12.486
setEnrichmentFactors  11.167  0.001  11.219
* 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-3.9-bioc/meat/GOSim.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GOSim
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GOSim’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include `/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
GOenrichment	0	0	0
calcICs	0	0	0
evaluateClustering	0.001	0.000	0.000
filterGO	0	0	0
getAncestors	0	0	0
getChildren	0	0	0
getDisjCommAnc	12.108	0.187	12.486
getGOGraph	0	0	0
getGOInfo	0	0	0
getGeneFeatures	0	0	0
getGeneFeaturesPrototypes	0.000	0.000	0.001
getGeneSim	0	0	0
getGeneSimPrototypes	235.975	1.045	238.668
getMinimumSubsumer	12.417	0.036	12.508
getOffsprings	0	0	0
getParents	0	0	0
getTermSim	14.433	0.000	14.490
selectPrototypes	0.001	0.000	0.000
setEnrichmentFactors	11.167	0.001	11.219
setEvidenceLevel	0	0	0
setOntology	0	0	0