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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 783/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneOverlap 1.36.0  (landing page)
António Miguel de Jesus Domingues, Max-Planck Institute for Cell Biology and Genetics
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GeneOverlap
git_branch: RELEASE_3_17
git_last_commit: 7b2cdf6
git_last_commit_date: 2023-04-25 10:30:00 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for GeneOverlap on kjohnson2


To the developers/maintainers of the GeneOverlap package:
- 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: GeneOverlap
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneOverlap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneOverlap_1.36.0.tar.gz
StartedAt: 2023-10-17 21:06:19 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 21:07:15 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 56.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneOverlap.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneOverlap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneOverlap_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneOverlap.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneOverlap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneOverlap’ version ‘1.36.0’
* 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 ‘GeneOverlap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
drawHeatmap,GeneOverlapMatrix: no visible global function definition
  for ‘p.adjust’
print,GeneOverlap: no visible global function definition for ‘head’
testGeneOverlap,GeneOverlap: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  head p.adjust setNames
Consider adding
  importFrom("stats", "p.adjust", "setNames")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’
Please remove them from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneOverlap.Rcheck/00check.log’
for details.



Installation output

GeneOverlap.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneOverlap
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GeneOverlap’ ...
** using staged installation
Warning in .write_description(db, file.path(outDir, "DESCRIPTION")) :
  Unknown encoding with non-ASCII data: converting to ASCII
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneOverlap)

Tests output

GeneOverlap.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("GeneOverlap")


RUNIT TEST PROTOCOL -- Tue Oct 17 21:06:58 2023 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GeneOverlap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In getPval(go.obj) : Test has not been performed yet.

2: In getOddsRatio(go.obj) : Test has not been performed yet.

> 
> proc.time()
   user  system elapsed 
  0.518   0.083   0.806 

Example timings

GeneOverlap.Rcheck/GeneOverlap-Ex.timings

nameusersystemelapsed
GeneOverlap0.0580.0050.064
GeneOverlapMatrix0.1690.0180.195
drawHeatmap0.1340.0080.146
getGenomeSize0.0660.0040.088
getList0.0430.0030.058
getReadonly0.0410.0030.058
getReadonlyMatrix0.1930.0120.258
gs.RNASeq0.0320.0020.037
hESC.ChIPSeq.list0.0360.0020.039
hESC.RNASeq.list0.0340.0020.038
newGOM0.1440.0090.169
newGeneOverlap0.0370.0020.049
testGeneOverlap0.0400.0020.045