Multiple platform build/check report for BioC 3.11 - CHECK report for BgeeCall on tokay2

Package: BgeeCall

Version: 1.4.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BgeeCall_1.4.1.tar.gz

StartedAt: 2020-10-17 01:51:41 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 02:04:12 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 750.5 seconds

RetCode: 0

Status: OK

CheckDir: BgeeCall.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BgeeCall_1.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeCall.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.1'
* 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  9.1Mb
  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
* 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
generate_presence_absence          6.11   0.36   17.91
setAnnotationFromFile              2.61   1.28    5.89
merge_transcriptome_and_intergenic 0.75   0.06    6.90
list_bgee_ref_intergenic_species   0.01   0.02    5.59
** 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeCall.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/BgeeCall_1.4.1.tar.gz && rm -rf BgeeCall.buildbin-libdir && mkdir BgeeCall.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BgeeCall.buildbin-libdir BgeeCall_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BgeeCall_1.4.1.zip && rm BgeeCall_1.4.1.tar.gz BgeeCall_1.4.1.zip
###
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  % 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 5762k  100 5762k    0     0  52.6M      0 --:--:-- --:--:-- --:--:-- 55.1M

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  
    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  
    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_1.4.1.zip
* DONE (BgeeCall)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BgeeCall' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 
  27.45    3.75   46.21


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
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downloaded 4.2 MB

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 
  29.98    2.10   52.09

name	user	system	elapsed
create_kallisto_index	0	0	0
download_fasta_intergenic	0	0	0
download_kallisto	0.16	0.13	0.78
generate_calls_workflow	0	0	0
generate_presence_absence	6.11	0.36	17.91
getIntergenicPrefix	0.00	0.01	1.06
getIntergenicRelease	0.00	0.00	1.07
getRunIds	0	0	0
getSimpleArborescence	0	0	0
getWorkingPath	0	0	0
list_bgee_ref_intergenic_species	0.01	0.02	5.59
list_community_ref_intergenic_species	0.02	0.00	0.59
list_intergenic_release	0.02	0.00	1.10
merge_transcriptome_and_intergenic	0.75	0.06	6.90
run_kallisto	0	0	0
run_tximport	1.06	0.00	2.19
setAnnotationFromFile	2.61	1.28	5.89
setAnnotationFromObject	0.47	0.00	1.47
setIntergenicRelease	0.03	0.00	0.98
setOutputDir	0	0	0
setRNASeqLibPath	0	0	0
setRunIds	0	0	0
setSimpleArborescence	0	0	0
setTranscriptomeFromFile	0.03	0.02	0.05
setTranscriptomeFromObject	0.00	0.01	0.01
setWorkingPath	0	0	0

name	user	system	elapsed
create_kallisto_index	0	0	0
download_fasta_intergenic	0	0	0
download_kallisto	0	0	0
generate_calls_workflow	0	0	0
generate_presence_absence	1.27	0.05	2.28
getIntergenicPrefix	0.01	0.01	0.98
getIntergenicRelease	0.00	0.02	1.24
getRunIds	0	0	0
getSimpleArborescence	0	0	0
getWorkingPath	0	0	0
list_bgee_ref_intergenic_species	0.00	0.04	4.57
list_community_ref_intergenic_species	0.05	0.00	0.53
list_intergenic_release	0.02	0.00	1.05
merge_transcriptome_and_intergenic	0.01	0.00	1.08
run_kallisto	0	0	0
run_tximport	1.63	0.08	2.80
setAnnotationFromFile	2.90	1.05	4.90
setAnnotationFromObject	0.41	0.02	1.46
setIntergenicRelease	0.00	0.01	1.06
setOutputDir	0	0	0
setRNASeqLibPath	0	0	0
setRunIds	0	0	0
setSimpleArborescence	0	0	0
setTranscriptomeFromFile	0.08	0.00	0.08
setTranscriptomeFromObject	0.02	0.00	0.02
setWorkingPath	0	0	0

CHECK report for BgeeCall on tokay2

Summary

Command output

Installation output

Tests output

Example timings