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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GOSim_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GOSim.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.37.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... NOTE
checkRd: (-1) setEvidenceLevel.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) setEvidenceLevel.Rd:41: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:43: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:46: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:49: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:52: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:54: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:58: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:61: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:64: Escaped LaTeX specials: \$
checkRd: (-1) setEvidenceLevel.Rd:66: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:68: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:71: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:74: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:78: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:80: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:84: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:87: Escaped LaTeX specials: \$ \$ \$
* 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 ... ERROR
Running examples in ‘GOSim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGeneSimPrototypes
> ### Title: Compute functional similarity of genes with respect to a feature
> ###   vector representation.
> ### Aliases: getGeneSimPrototypes
> ### Keywords: file
> 
> ### ** Examples
> 
> #\donttest{ may take some time ...
>  proto=selectPrototypes(n=5) # --> returns a character vector of 5 genes with the highest number of annotations
initializing GOSim package ...
-> retrieving GO information for all available genes for organism 'human' in GO database
-> filtering GO terms according to evidence levels 'all'
-> loading files with information content for corresponding GO category (human)
finished.
>  getGeneSimPrototypes(c("207","208"),prototypes=proto, similarityTerm="Resnik")
filtering out genes not mapping to the currently set GO category ... ===> list of  2 genes reduced to  2 
filtering out genes not mapping to the currently set GO category ... ===> list of  5 genes reduced to  5 
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GOSim.Rnw’ using ‘latin1’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘GOSim.Rnw’
  ...
          8614      2852
8614 1.0000000 0.3226752
2852 0.3226752 1.0000000

> getGeneSim(c("8614", "2852"), similarity = "max", 
+     similarityTerm = "Lin", verbose = FALSE)
filtering out genes not mapping to the currently set GO category ... ===> list of  2 genes reduced to  2 
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GOSim.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GOSim
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GOSim’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include   `/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-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++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.17-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)