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A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BgeeCall on tokay1

This page was generated on 2021-01-17 11:52:45 -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: 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_1.6.2.tar.gz
StartedAt: 2021-01-17 00:37:57 -0500 (Sun, 17 Jan 2021)
EndedAt: 2021-01-17 00:49:34 -0500 (Sun, 17 Jan 2021)
EllapsedTime: 696.9 seconds
RetCode: 0
Status:  OK  
CheckDir: BgeeCall.Rcheck
Warnings: 0

Command output

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###
### 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_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-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 '1.6.2'
* 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 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 ... 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 5.47   0.60   27.27
setAnnotationFromFile     2.59   0.98   22.02
setIntergenicRelease      0.00   0.00   44.74
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
setAnnotationFromFile 2.12   0.77    8.85
* 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: 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_1.6.2.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_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BgeeCall_1.6.2.zip && rm BgeeCall_1.6.2.tar.gz BgeeCall_1.6.2.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  54.1M      0 --:--:-- --:--:-- --:--:-- 56.2M

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_1.6.2.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 4.0.3 (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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  22.50    2.92   48.73 

BgeeCall.Rcheck/tests_x64/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-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

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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  24.29    1.50   47.56 

Example timings

BgeeCall.Rcheck/examples_i386/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto0.200.061.34
generate_calls_workflow000
generate_presence_absence 5.47 0.6027.27
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.000.001.08
getIntergenicRelease0.020.001.20
getRunIds000
getSimpleArborescence000
getWorkingPath000
list_bgee_ref_intergenic_species0.010.034.86
list_community_ref_intergenic_species0.030.000.70
list_intergenic_release0.020.001.13
merge_transcriptome_and_intergenic0.450.064.22
run_kallisto000
run_tximport0.880.001.95
setAnnotationFromFile 2.59 0.9822.02
setAnnotationFromObject0.300.101.27
setIntergenicRelease 0.00 0.0044.74
setOutputDir000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.060.000.07
setTranscriptomeFromObject0.020.000.01
setWorkingPath000

BgeeCall.Rcheck/examples_x64/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto000
generate_calls_workflow000
generate_presence_absence1.070.033.55
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.020.001.09
getIntergenicRelease0.000.001.21
getRunIds000
getSimpleArborescence000
getWorkingPath000
list_bgee_ref_intergenic_species0.050.024.76
list_community_ref_intergenic_species0.010.000.69
list_intergenic_release0.000.001.14
merge_transcriptome_and_intergenic0.020.001.19
run_kallisto000
run_tximport1.340.032.56
setAnnotationFromFile2.120.778.85
setAnnotationFromObject0.280.001.22
setIntergenicRelease0.00.01.1
setOutputDir000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.020.000.01
setTranscriptomeFromObject0.020.000.02
setWorkingPath000