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This page was generated on 2024-03-29 11:36:34 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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

Package 155/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.18.1  (landing page)
Julien Wollbrett
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/BgeeCall
git_branch: RELEASE_3_18
git_last_commit: 4677681
git_last_commit_date: 2023-10-31 06:43:21 -0400 (Tue, 31 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for BgeeCall on palomino4


To the developers/maintainers of the BgeeCall package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BgeeCall
Version: 1.18.1
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BgeeCall.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings BgeeCall_1.18.1.tar.gz
StartedAt: 2024-03-27 22:40:25 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 22:46:52 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 386.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BgeeCall.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BgeeCall.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings BgeeCall_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/BgeeCall.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BgeeCall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BgeeCall' version '1.18.1'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
generate_presence_absence          5.43   0.20    7.86
setAnnotationFromFile              3.65   1.39    6.52
merge_transcriptome_and_intergenic 0.54   0.05   15.76
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/BgeeCall.Rcheck/00check.log'
for details.



Installation output

BgeeCall.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL BgeeCall
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  30.46    2.67   79.39 

Example timings

BgeeCall.Rcheck/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index000
download_fasta_intergenic000
download_kallisto0.040.110.37
generate_calls_workflow000
generate_presence_absence5.430.207.86
generate_slurm_calls000
generate_slurm_indexes000
getIntergenicPrefix0.000.010.61
getIntergenicRelease0.010.020.63
getRunIds000
getSimpleArborescence000
getWorkingPath000
list_bgee_ref_intergenic_species0.050.032.19
list_community_ref_intergenic_species0.050.000.65
list_intergenic_release0.000.000.63
merge_transcriptome_and_intergenic 0.54 0.0515.76
merging_libraries000
run_kallisto000
run_tximport1.410.112.09
setAnnotationFromFile3.651.396.52
setAnnotationFromObject0.330.031.55
setIntergenicRelease0.020.000.78
setOutputDir000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence000
setTranscriptomeFromFile0.030.000.03
setTranscriptomeFromObject0.010.000.01
setWorkingPath000