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CHECK report for BgeeCall on merida1

This page was generated on 2021-01-17 11:55:10 -0500 (Sun, 17 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE BgeeCall PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 140/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.6.2
Julien Wollbrett
Snapshot Date: 2021-01-16 14:41:12 -0500 (Sat, 16 Jan 2021)
URL: https://git.bioconductor.org/packages/BgeeCall
Branch: RELEASE_3_12
Last Commit: 1b74dcf
Last Changed Date: 2020-12-10 05:55:05 -0500 (Thu, 10 Dec 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  ERROR  skipped 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BgeeCall
Version: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BgeeCall_1.6.2.tar.gz
StartedAt: 2021-01-16 23:34:58 -0500 (Sat, 16 Jan 2021)
EndedAt: 2021-01-16 23:42:04 -0500 (Sat, 16 Jan 2021)
EllapsedTime: 425.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BgeeCall.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BgeeCall_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BgeeCall.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.6.2’
* 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 ... 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
generate_calls_workflow: no visible binding for global variable
  ‘myUserMetadata’
Undefined global functions or variables:
  myUserMetadata
* 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          5.896  0.518  11.287
merge_transcriptome_and_intergenic 0.504  0.172   5.450
list_bgee_ref_intergenic_species   0.020  0.012   6.192
* 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-3.12-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.



Installation output

BgeeCall.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'unknown' length 4420457 bytes (4.2 MB)
==================================================
trying URL 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'unknown' length 4420457 bytes (4.2 MB)
==================================================
trying URL 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'unknown' length 4420457 bytes (4.2 MB)
==================================================
trying URL 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'unknown' length 4420457 bytes (4.2 MB)
==================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 30.183   1.736  55.991 

Example timings

BgeeCall.Rcheck/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index0.0000.0010.001
download_fasta_intergenic0.0020.0000.002
download_kallisto0.0780.0540.823
generate_calls_workflow0.0000.0010.001
generate_presence_absence 5.896 0.51811.287
generate_slurm_calls000
generate_slurm_indexes0.0000.0000.001
getIntergenicPrefix0.0060.0031.688
getIntergenicRelease0.0050.0031.822
getRunIds000
getSimpleArborescence0.0010.0010.001
getWorkingPath0.0010.0000.000
list_bgee_ref_intergenic_species0.0200.0126.192
list_community_ref_intergenic_species0.0350.0030.684
list_intergenic_release0.0090.0041.568
merge_transcriptome_and_intergenic0.5040.1725.450
run_kallisto0.0000.0020.002
run_tximport1.0950.0192.715
setAnnotationFromFile2.8960.6144.850
setAnnotationFromObject0.4740.0141.327
setIntergenicRelease0.0050.0031.613
setOutputDir0.0000.0010.001
setRNASeqLibPath000
setRunIds0.0010.0000.000
setSimpleArborescence0.0000.0000.001
setTranscriptomeFromFile0.0220.0010.023
setTranscriptomeFromObject0.0070.0010.008
setWorkingPath000