Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-08-04 11:32:18 -0400 (Fri, 04 Aug 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4342
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 403/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
combi 1.12.0  (landing page)
Stijn Hawinkel
Snapshot Date: 2023-07-30 14:00:08 -0400 (Sun, 30 Jul 2023)
git_url: https://git.bioconductor.org/packages/combi
git_branch: RELEASE_3_17
git_last_commit: 62c6a98
git_last_commit_date: 2023-04-25 11:16:25 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for combi on kjohnson2


To the developers/maintainers of the combi 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: combi
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:combi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings combi_1.12.0.tar.gz
StartedAt: 2023-08-01 09:14:59 -0400 (Tue, 01 Aug 2023)
EndedAt: 2023-08-01 09:27:21 -0400 (Tue, 01 Aug 2023)
EllapsedTime: 742.3 seconds
RetCode: 0
Status:   OK  
CheckDir: combi.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:combi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings combi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/combi.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 ‘combi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘combi’ version ‘1.12.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘combi’ 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 ... NOTE
Package in Depends field not imported from: ‘DBI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("spline_value", ..., PACKAGE = "cobs")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
addLink: no visible binding for global variable ‘species’
convPlot: no visible binding for global variable ‘Iteration’
convPlot: no visible binding for global variable ‘Value’
convPlot: no visible binding for global variable ‘Variable’
convPlot: no visible binding for global variable ‘Colour’
inflPlot: no visible binding for global variable ‘h’
inflPlot: no visible binding for global variable ‘LatentVariable’
inflPlot: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Colour Iteration LatentVariable Value Variable h species value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
checkMeanVarTrend 4.372  0.117   6.863
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/combi.Rcheck/00check.log’
for details.



Installation output

combi.Rcheck/00install.out

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


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

Tests output

combi.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(combi)
Loading required package: DBI
> test_check("combi")
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 21 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
239.230  10.964 376.390 

Example timings

combi.Rcheck/combi-Ex.timings

nameusersystemelapsed
addLink1.2210.0411.934
checkMeanVarTrend4.3720.1176.863
combi0.0230.0040.043
convPlot0.8220.0181.288
extractCoords0.1050.0130.179
extractData0.0320.0030.057
inflPlot1.2080.0181.895
plot.combi2.3850.0513.734
print.combi0.0510.0050.088