Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2023-10-20 09:38:11 -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 1769/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rrvgo 1.12.2  (landing page)
Sergi Sayols
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/rrvgo
git_branch: RELEASE_3_17
git_last_commit: 3db56c8
git_last_commit_date: 2023-09-06 17:14:29 -0400 (Wed, 06 Sep 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for rrvgo on kjohnson2


To the developers/maintainers of the rrvgo 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: rrvgo
Version: 1.12.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rrvgo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rrvgo_1.12.2.tar.gz
StartedAt: 2023-10-18 20:38:08 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 20:54:25 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 976.8 seconds
RetCode: 0
Status:   OK  
CheckDir: rrvgo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rrvgo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rrvgo_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rrvgo.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 ‘rrvgo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rrvgo’ version ‘1.12.2’
* package encoding: UTF-8
* 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:
  .travis.yml
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 ‘rrvgo’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘GOSemSim:::getAncestors’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scatterPlot: no visible binding for global variable ‘V1’
scatterPlot: no visible binding for global variable ‘V2’
scatterPlot: no visible binding for global variable ‘parentTerm’
scatterPlot: no visible binding for global variable ‘parent’
Undefined global functions or variables:
  V1 V2 parent parentTerm
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
heatmapPlot        74.434  2.769 117.120
reduceSimMatrix    72.197  2.458 114.242
wordcloudPlot      72.501  2.112 109.904
scatterPlot        70.564  2.568 111.213
calculateSimMatrix 68.911  2.292 103.590
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rrvgo.Rcheck/00check.log’
for details.



Installation output

rrvgo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rrvgo
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘rrvgo’ ...
** using staged installation
** R
** 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 (rrvgo)

Tests output

rrvgo.Rcheck/tests/testthat.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.

> library(testthat)
> library(rrvgo)

> 
> test_check("rrvgo")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
129.814   5.057 199.682 

Example timings

rrvgo.Rcheck/rrvgo-Ex.timings

nameusersystemelapsed
calculateSimMatrix 68.911 2.292103.590
gg_color_hue0.0000.0010.004
heatmapPlot 74.434 2.769117.120
reduceSimMatrix 72.197 2.458114.242
scatterPlot 70.564 2.568111.213
treemapPlot0.0000.0000.001
wordcloudPlot 72.501 2.112109.904