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CHECK report for BgeeCall on malbec1

This page was generated on 2020-08-06 11:47:02 -0400 (Thu, 06 Aug 2020).

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 132/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.5.3
Julien Wollbrett
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BgeeCall
Branch: master
Last Commit: cc52b16
Last Changed Date: 2020-06-15 13:41:33 -0400 (Mon, 15 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BgeeCall
Version: 1.5.3
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BgeeCall_1.5.3.tar.gz
StartedAt: 2020-08-06 05:16:52 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 05:22:18 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 326.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BgeeCall.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BgeeCall_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BgeeCall.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.3’
* 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   8.7Mb
* 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 ... WARNING
Undocumented arguments in documentation object 'generate_slurm_calls'
  ‘kallistoMetadata’ ‘userMetadata’
Documented arguments not in \usage in documentation object 'generate_slurm_calls':
  ‘abundanceMetadata’

Undocumented arguments in documentation object 'generate_slurm_indexes'
  ‘kallistoMetadata’ ‘userMetadata’
Documented arguments not in \usage in documentation object 'generate_slurm_indexes':
  ‘abundanceMetadata’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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          5.108  0.228   9.751
merge_transcriptome_and_intergenic 0.512  0.032   5.455
list_bgee_ref_intergenic_species   0.012  0.012   8.772
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.



Installation output

BgeeCall.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BgeeCall
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
==================================================
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 28.540   0.788  54.694 

Example timings

BgeeCall.Rcheck/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic0.0040.0000.001
download_kallisto0.4080.1281.314
generate_calls_workflow0.0000.0000.001
generate_presence_absence5.1080.2289.751
generate_slurm_calls0.0000.0000.001
generate_slurm_indexes000
getIntergenicPrefix0.0040.0001.832
getIntergenicRelease0.0040.0001.706
getRunIds0.0000.0000.001
getSimpleArborescence000
getWorkingPath0.0000.0000.001
list_bgee_ref_intergenic_species0.0120.0128.772
list_community_ref_intergenic_species0.1280.0040.560
list_intergenic_release0.0040.0041.913
merge_transcriptome_and_intergenic0.5120.0325.455
run_kallisto000
run_tximport1.1080.0002.809
setAnnotationFromFile2.4720.1124.014
setAnnotationFromObject0.2480.0001.312
setIntergenicRelease0.0040.0001.513
setOutputDir000
setRNASeqLibPath0.0000.0000.001
setRunIds0.0000.0000.001
setSimpleArborescence000
setTranscriptomeFromFile0.0240.0000.026
setTranscriptomeFromObject0.0080.0000.009
setWorkingPath000