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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GOSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GOSim_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GOSim.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.42.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Auto-generated content requiring editing in Rd file 'evaluateClustering.Rd':
  \details: ‘If necessary, more details than the description above’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getGeneSimPrototypes 236.520 38.164 305.082
getTermSim            10.637  0.239  10.997
getDisjCommAnc         9.693  0.376  10.226
getMinimumSubsumer     9.824  0.233  10.164
setEnrichmentFactors   8.428  0.188   8.699
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/GOSim.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GOSim
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GOSim’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fPIC  -falign-functions=64 -Wall -g -O2   -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GOSim.so OAWrapper.o hungarian2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Loading required package: Rcpp
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
Warning in fun(libname, pkgname) :
  Package 'GOSim' is deprecated and will be removed from Bioconductor
  version 3.20
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'GOSim' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (GOSim)