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This page was generated on 2022-01-24 13:05:55 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BgeeCall on tokay2


To the developers/maintainers of the BgeeCall package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BgeeCall.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 140/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.10.0  (landing page)
Julien Wollbrett
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/BgeeCall
git_branch: RELEASE_3_14
git_last_commit: 45c649c
git_last_commit_date: 2021-10-26 12:56:46 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BgeeCall
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BgeeCall_1.10.0.tar.gz
StartedAt: 2022-01-23 15:48:02 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 15:56:33 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 511.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BgeeCall.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BgeeCall_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeCall.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.10.0'
* 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  9.3Mb
  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
approachesMerging : <anonymous>: no visible global function definition
  for 'p.adjust'
generate_calls_workflow: no visible binding for global variable
  'myUserMetadata'
generate_qValue: no visible global function definition for 'approxfun'
generate_qValue: no visible global function definition for 'integrate'
generate_qValue : calculate_qValue: no visible global function
  definition for 'integrate'
generate_theoretical_pValue: no visible binding for global variable
  'abundance'
generate_theoretical_pValue: no visible binding for global variable
  'type'
generate_theoretical_pValue: no visible global function definition for
  'pnorm'
merging_libraries: no visible binding for global variable 'read.delim'
should_ignore_tx_version: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  abundance approxfun complete.cases integrate myUserMetadata p.adjust
  pnorm read.delim type
Consider adding
  importFrom("stats", "approxfun", "complete.cases", "integrate",
             "p.adjust", "pnorm")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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          6.34   0.38   18.15
setAnnotationFromFile              3.06   1.00    5.47
merge_transcriptome_and_intergenic 0.77   0.09   10.19
list_bgee_ref_intergenic_species   0.03   0.02    7.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
generate_presence_absence        4.94   0.22    7.86
setAnnotationFromFile            3.08   1.22    5.87
list_bgee_ref_intergenic_species 0.04   0.00    7.74
* 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-3.14-bioc/meat/BgeeCall.Rcheck/00check.log'
for details.



Installation output

BgeeCall.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BgeeCall_1.10.0.tar.gz && rm -rf BgeeCall.buildbin-libdir && mkdir BgeeCall.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BgeeCall.buildbin-libdir BgeeCall_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BgeeCall_1.10.0.zip && rm BgeeCall_1.10.0.tar.gz BgeeCall_1.10.0.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
 71 5798k   71 4156k    0     0  4371k      0  0:00:01 --:--:--  0:00:01 4370k
100 5798k  100 5798k    0     0  4786k      0  0:00:01  0:00:01 --:--:-- 4791k

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  
    get_summary_stats                       html  
    list_bgee_ref_intergenic_species        html  
    list_community_ref_intergenic_species   html  
    list_intergenic_release                 html  
    merge_transcriptome_and_intergenic      html  
    merging_libraries                       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_1.10.0.zip
* DONE (BgeeCall)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BgeeCall' successfully unpacked and MD5 sums checked

Tests output

BgeeCall.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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'
 length 4420457 bytes (4.2 MB)
==================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  27.21    3.26   52.18 

BgeeCall.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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'
 length 4420457 bytes (4.2 MB)
==================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  28.28    1.68   52.76 

Example timings

BgeeCall.Rcheck/examples_i386/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto0.300.101.24
generate_calls_workflow000
generate_presence_absence 6.34 0.3818.15
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.010.002.64
getIntergenicRelease0.020.002.65
getRunIds000
getSimpleArborescence000
getWorkingPath000
list_bgee_ref_intergenic_species0.030.027.97
list_community_ref_intergenic_species0.150.000.75
list_intergenic_release0.000.002.64
merge_transcriptome_and_intergenic 0.77 0.0910.19
merging_libraries000
run_kallisto000
run_tximport1.280.113.89
setAnnotationFromFile3.061.005.47
setAnnotationFromObject0.520.081.56
setIntergenicRelease0.000.002.64
setOutputDir000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.040.000.03
setTranscriptomeFromObject000
setWorkingPath000

BgeeCall.Rcheck/examples_x64/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto000
generate_calls_workflow000
generate_presence_absence4.940.227.86
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.000.002.64
getIntergenicRelease0.010.002.64
getRunIds000
getSimpleArborescence0.020.000.01
getWorkingPath000
list_bgee_ref_intergenic_species0.040.007.74
list_community_ref_intergenic_species0.020.000.59
list_intergenic_release0.000.002.63
merge_transcriptome_and_intergenic0.020.002.64
merging_libraries000
run_kallisto000
run_tximport1.780.094.44
setAnnotationFromFile3.081.225.87
setAnnotationFromObject0.480.021.43
setIntergenicRelease0.000.002.64
setOutputDir000
setRNASeqLibPath0.020.000.01
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.030.000.03
setTranscriptomeFromObject0.020.000.02
setWorkingPath000