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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 896/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSim 1.42.0  (landing page)
Holger Froehlich
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GOSim
git_branch: RELEASE_3_19
git_last_commit: b54cb57
git_last_commit_date: 2024-04-30 10:33:28 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GOSim on kjohnson3

To the developers/maintainers of the GOSim package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOSim.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GOSim
Version: 1.42.0
Command: /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
StartedAt: 2024-06-10 17:38:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 17:54:23 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 953.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GOSim.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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: aarch64-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 Ventura 13.6.5
* 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 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 365.599 32.484 587.376
getTermSim            10.725  0.222  16.690
getDisjCommAnc        10.308  0.324  15.773
getMinimumSubsumer     9.956  0.224  15.402
setEnrichmentFactors   8.978  0.164  13.945
* 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.


Installation output

GOSim.Rcheck/00install.out

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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-arm64/Resources/library’
* installing *source* package ‘GOSim’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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)

Tests output


Example timings

GOSim.Rcheck/GOSim-Ex.timings

nameusersystemelapsed
GOenrichment000
calcICs0.0000.0000.001
evaluateClustering0.0000.0000.001
filterGO000
getAncestors000
getChildren0.0010.0000.000
getDisjCommAnc10.308 0.32415.773
getGOGraph0.0000.0010.000
getGOInfo000
getGeneFeatures000
getGeneFeaturesPrototypes000
getGeneSim000
getGeneSimPrototypes365.599 32.484587.376
getMinimumSubsumer 9.956 0.22415.402
getOffsprings000
getParents000
getTermSim10.725 0.22216.690
selectPrototypes000
setEnrichmentFactors 8.978 0.16413.945
setEvidenceLevel000
setOntology000