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This page was generated on 2021-07-21 15:05:51 -0400 (Wed, 21 Jul 2021).

CHECK results for GOSim on machv2

To the developers/maintainers of the GOSim package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 791/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSim 1.30.0  (landing page)
Holger Froehlich
Snapshot Date: 2021-07-20 04:50:13 -0400 (Tue, 20 Jul 2021)
URL: https://git.bioconductor.org/packages/GOSim
Branch: RELEASE_3_13
Last Commit: cd2c2c0
Last Changed Date: 2021-05-19 12:00:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GOSim
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOSim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOSim_1.30.0.tar.gz
StartedAt: 2021-07-20 19:27:08 -0400 (Tue, 20 Jul 2021)
EndedAt: 2021-07-20 19:35:59 -0400 (Tue, 20 Jul 2021)
EllapsedTime: 530.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GOSim.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOSim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOSim_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GOSim.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.30.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 247.137 40.580 287.923
getTermSim            14.495  0.105  14.615
getDisjCommAnc        13.418  0.372  13.801
getMinimumSubsumer    13.407  0.112  13.527
setEnrichmentFactors   9.769  0.064   9.841
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GOSim.Rcheck/00check.log’
for details.



Installation output

GOSim.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GOSim
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘GOSim’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fPIC  -Wall -g -O2  -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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
** 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
GOenrichment0.0000.0000.001
calcICs0.0000.0000.001
evaluateClustering0.0000.0000.001
filterGO000
getAncestors000
getChildren000
getDisjCommAnc13.418 0.37213.801
getGOGraph0.0000.0000.001
getGOInfo000
getGeneFeatures0.0010.0000.000
getGeneFeaturesPrototypes000
getGeneSim000
getGeneSimPrototypes247.137 40.580287.923
getMinimumSubsumer13.407 0.11213.527
getOffsprings000
getParents0.0000.0010.000
getTermSim14.495 0.10514.615
selectPrototypes0.0000.0000.001
setEnrichmentFactors9.7690.0649.841
setEvidenceLevel000
setOntology000