Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 160/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeCall 1.20.0  (landing page)
Julien Wollbrett
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/BgeeCall
git_branch: RELEASE_3_19
git_last_commit: 5624a94
git_last_commit_date: 2024-04-30 11:20:00 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BgeeCall on nebbiolo1

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: 1.20.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BgeeCall_1.20.0.tar.gz
StartedAt: 2024-06-16 20:55:36 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-16 21:01:20 -0400 (Sun, 16 Jun 2024)
EllapsedTime: 343.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BgeeCall.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BgeeCall_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BgeeCall.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BgeeCall’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:26: Lost braces in \itemize; meant \describe ?
* 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          3.781  0.288   8.548
merge_transcriptome_and_intergenic 0.593  0.071   5.747
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expectation did not fail
  ── Error ('test_transcriptToGene.R:33:3'): test creation of transcript to gene file ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'nrow': object 'txToGene' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(nrow(txToGene), 4278) at test_transcriptToGene.R:33:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::nrow(txToGene)
   5. └─base::.handleSimpleError(...)
   6.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.


Installation output

BgeeCall.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BgeeCall
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_transcriptToGene.R:28:3'): test creation of transcript to gene file ──
Expectation did not fail
── Error ('test_transcriptToGene.R:33:3'): test creation of transcript to gene file ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'nrow': object 'txToGene' not found
Backtrace:
    ▆
 1. ├─testthat::expect_equal(nrow(txToGene), 4278) at test_transcriptToGene.R:33:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─base::nrow(txToGene)
 5. └─base::.handleSimpleError(...)
 6.   └─base (local) h(simpleError(msg, call))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
Error: Test failures
Execution halted

Example timings

BgeeCall.Rcheck/BgeeCall-Ex.timings

nameusersystemelapsed
create_kallisto_index0.0010.0000.000
download_fasta_intergenic0.0010.0000.002
download_kallisto0.3110.0681.030
generate_calls_workflow0.0010.0000.001
generate_presence_absence3.7810.2888.548
generate_slurm_calls0.0000.0000.001
generate_slurm_indexes000
getIntergenicPrefix0.1320.0080.811
getIntergenicRelease0.1370.0080.812
getRunIds0.0010.0000.001
getSimpleArborescence0.0010.0000.001
getWorkingPath0.0000.0000.001
list_bgee_ref_intergenic_species0.5000.0462.625
list_community_ref_intergenic_species0.1070.0151.458
list_intergenic_release0.1800.0160.821
merge_transcriptome_and_intergenic0.5930.0715.747
merging_libraries000
run_kallisto000
run_tximport0.8730.0721.800
setAnnotationFromFile0.2140.0201.545
setAnnotationFromObject0.1130.0200.486
setIntergenicRelease0.1310.0041.005
setOutputDir0.0010.0000.000
setRNASeqLibPath000
setRunIds000
setSimpleArborescence0.0000.0000.001
setTranscriptomeFromFile0.0070.0000.007
setTranscriptomeFromObject0.0060.0000.005
setWorkingPath000