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CHECK report for BgeeCall on tokay1

This page was generated on 2020-08-11 11:49:49 -0400 (Tue, 11 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 132/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.5.3
Julien Wollbrett
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 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
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BgeeCall_1.5.3.tar.gz
StartedAt: 2020-08-11 06:08:57 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 06:16:32 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 454.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BgeeCall.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BgeeCall_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeCall.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'BgeeCall' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
generate_presence_absence 5.56   0.62   11.67
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeCall.Rcheck/00check.log'
for details.



Installation output

BgeeCall.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BgeeCall_1.5.3.tar.gz && rm -rf BgeeCall.buildbin-libdir && mkdir BgeeCall.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BgeeCall.buildbin-libdir BgeeCall_1.5.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BgeeCall_1.5.3.zip && rm BgeeCall_1.5.3.tar.gz BgeeCall_1.5.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5761k  100 5761k    0     0  52.4M      0 --:--:-- --:--:-- --:--:-- 54.6M

install for i386

* installing *source* package 'BgeeCall' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BgeeCall'
    finding HTML links ... done
    AbundanceMetadata-class                 html  
    BgeeCall                                html  
    BgeeMetadata-class                      html  
    KallistoMetadata-class                  html  
    UserMetadata-class                      html  
    create_kallisto_index                   html  
    download_fasta_intergenic               html  
    download_kallisto                       html  
    generate_calls_workflow                 html  
    generate_presence_absence               html  
    generate_slurm_calls                    html  
    generate_slurm_indexes                  html  
    getIntergenicPrefix                     html  
    getIntergenicRelease                    html  
    getRunIds                               html  
    getSimpleArborescence                   html  
    getWorkingPath                          html  
    list_bgee_ref_intergenic_species        html  
    list_community_ref_intergenic_species   html  
    list_intergenic_release                 html  
    merge_transcriptome_and_intergenic      html  
    run_kallisto                            html  
    run_tximport                            html  
    setAnnotationFromFile                   html  
    setAnnotationFromObject                 html  
    setIntergenicRelease                    html  
    setOutputDir                            html  
    setRNASeqLibPath                        html  
    setRunIds                               html  
    setSimpleArborescence                   html  
    setTranscriptomeFromFile                html  
    setTranscriptomeFromObject              html  
    setWorkingPath                          html  
** 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

install for x64

* installing *source* package 'BgeeCall' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BgeeCall' as BgeeCall_1.5.3.zip
* DONE (BgeeCall)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BgeeCall' successfully unpacked and MD5 sums checked

Tests output

BgeeCall.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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'
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downloaded 4.2 MB

== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  24.31    2.60   39.87 

BgeeCall.Rcheck/tests_x64/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-w64-mingw32/x64 (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://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_windows-v0.45.0.zip'
Content type 'application/octet-stream' length 4387130 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
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downloaded 4.2 MB

== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  36.12    2.06   50.32 

Example timings

BgeeCall.Rcheck/examples_i386/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto0.160.030.87
generate_calls_workflow000
generate_presence_absence 5.56 0.6211.67
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.000.001.04
getIntergenicRelease0.000.001.14
getRunIds000
getSimpleArborescence000
getWorkingPath000
list_bgee_ref_intergenic_species0.050.014.47
list_community_ref_intergenic_species0.140.000.63
list_intergenic_release001
merge_transcriptome_and_intergenic0.610.104.67
run_kallisto000
run_tximport0.860.001.88
setAnnotationFromFile2.110.763.89
setAnnotationFromObject0.470.021.50
setIntergenicRelease0.020.001.02
setOutputDir000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.020.000.01
setTranscriptomeFromObject0.010.000.02
setWorkingPath000

BgeeCall.Rcheck/examples_x64/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto0.010.000.02
generate_calls_workflow000
generate_presence_absence0.590.031.62
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.000.001.02
getIntergenicRelease0.000.001.01
getRunIds000
getSimpleArborescence000
getWorkingPath000
list_bgee_ref_intergenic_species0.050.014.46
list_community_ref_intergenic_species0.030.000.50
list_intergenic_release0.000.001.01
merge_transcriptome_and_intergenic0.030.001.13
run_kallisto000
run_tximport2.000.073.14
setAnnotationFromFile2.680.834.67
setAnnotationFromObject0.450.031.45
setIntergenicRelease0.000.001.01
setOutputDir000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.030.000.03
setTranscriptomeFromObject000
setWorkingPath000