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This page was generated on 2023-10-13 11:32:17 -0400 (Fri, 13 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4346
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 155/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.16.0  (landing page)
Julien Wollbrett
Snapshot Date: 2023-10-08 14:00:07 -0400 (Sun, 08 Oct 2023)
git_url: https://git.bioconductor.org/packages/BgeeCall
git_branch: RELEASE_3_17
git_last_commit: 74944b5
git_last_commit_date: 2023-04-25 11:14:49 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BgeeCall on kjohnson2


To the developers/maintainers of the BgeeCall 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: BgeeCall
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeCall_1.16.0.tar.gz
StartedAt: 2023-10-10 03:25:34 -0400 (Tue, 10 Oct 2023)
EndedAt: 2023-10-10 03:34:43 -0400 (Tue, 10 Oct 2023)
EllapsedTime: 549.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BgeeCall.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeCall_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BgeeCall.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 ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.16.0’
* 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 ‘BgeeCall’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
* 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
approachesMerging : <anonymous>: no visible global function definition
  for ‘p.adjust’
generate_calls_workflow: no visible binding for global variable
  ‘myUserMetadata’
generate_qValue: no visible global function definition for ‘approxfun’
generate_qValue: no visible global function definition for ‘integrate’
generate_qValue : calculate_qValue: no visible global function
  definition for ‘integrate’
generate_theoretical_pValue: no visible binding for global variable
  ‘abundance’
generate_theoretical_pValue: no visible binding for global variable
  ‘type’
generate_theoretical_pValue: no visible global function definition for
  ‘pnorm’
merging_libraries: no visible binding for global variable ‘read.delim’
should_ignore_tx_version: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  abundance approxfun complete.cases integrate myUserMetadata p.adjust
  pnorm read.delim type
Consider adding
  importFrom("stats", "approxfun", "complete.cases", "integrate",
             "p.adjust", "pnorm")
  importFrom("utils", "read.delim")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
generate_presence_absence        4.989  0.241  12.868
setAnnotationFromFile            2.258  0.690   5.761
download_kallisto                0.078  0.040   7.234
list_bgee_ref_intergenic_species 0.080  0.019   5.218
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BgeeCall.Rcheck/00check.log’
for details.



Installation output

BgeeCall.Rcheck/00install.out

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


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

Tests output

BgeeCall.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(BgeeCall)
> 
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeCall")
trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 29.278   2.092  77.437 

Example timings

BgeeCall.Rcheck/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index0.0000.0010.001
download_fasta_intergenic0.0010.0010.002
download_kallisto0.0780.0407.234
generate_calls_workflow0.0000.0010.001
generate_presence_absence 4.989 0.24112.868
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.0200.0060.794
getIntergenicRelease0.0200.0051.021
getRunIds0.0000.0010.000
getSimpleArborescence0.0010.0000.004
getWorkingPath0.0010.0000.000
list_bgee_ref_intergenic_species0.0800.0195.218
list_community_ref_intergenic_species0.0300.0031.375
list_intergenic_release0.0230.0061.052
merge_transcriptome_and_intergenic0.4480.1113.622
merging_libraries000
run_kallisto0.0000.0010.000
run_tximport1.7480.0483.927
setAnnotationFromFile2.2580.6905.761
setAnnotationFromObject0.2310.0120.956
setIntergenicRelease0.0210.0050.883
setOutputDir0.0010.0000.004
setRNASeqLibPath0.0010.0000.000
setRunIds0.0010.0000.000
setSimpleArborescence0.0010.0000.000
setTranscriptomeFromFile0.0210.0010.037
setTranscriptomeFromObject0.0060.0010.011
setWorkingPath0.0010.0000.001