Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:38 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 160/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BgeeCall 1.20.0 (landing page) Julien Wollbrett
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
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: 2024-07-07 20:55:41 -0400 (Sun, 07 Jul 2024) |
EndedAt: 2024-07-07 21:02:20 -0400 (Sun, 07 Jul 2024) |
EllapsedTime: 398.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BgeeCall.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 4.4.1 (2024-06-14) * 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 3.898 0.160 8.410 merge_transcriptome_and_intergenic 0.647 0.076 5.443 * 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 ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘bgeecall-manual.Rmd’ using rmarkdown Quitting from lines 226-227 [unnamed-chunk-18] (bgeecall-manual.Rmd) Error: processing vignette 'bgeecall-manual.Rmd' failed with diagnostics: cannot open the connection to 'https://zenodo.org/api/records/?communities=bgee_intergenic' --- failed re-building ‘bgeecall-manual.Rmd’ SUMMARY: processing the following file failed: ‘bgeecall-manual.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/BgeeCall.Rcheck/00check.log’ for details.
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)
BgeeCall.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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
BgeeCall.Rcheck/BgeeCall-Ex.timings
name | user | system | elapsed | |
create_kallisto_index | 0 | 0 | 0 | |
download_fasta_intergenic | 0.001 | 0.000 | 0.001 | |
download_kallisto | 0.356 | 0.062 | 1.024 | |
generate_calls_workflow | 0.002 | 0.000 | 0.001 | |
generate_presence_absence | 3.898 | 0.160 | 8.410 | |
generate_slurm_calls | 0 | 0 | 0 | |
generate_slurm_indexes | 0 | 0 | 0 | |
getIntergenicPrefix | 0.169 | 0.000 | 0.805 | |
getIntergenicRelease | 0.217 | 0.000 | 0.809 | |
getRunIds | 0.000 | 0.000 | 0.001 | |
getSimpleArborescence | 0.001 | 0.000 | 0.001 | |
getWorkingPath | 0.001 | 0.000 | 0.001 | |
list_bgee_ref_intergenic_species | 0.583 | 0.000 | 2.600 | |
list_community_ref_intergenic_species | 0.095 | 0.011 | 1.196 | |
list_intergenic_release | 0.125 | 0.000 | 0.796 | |
merge_transcriptome_and_intergenic | 0.647 | 0.076 | 5.443 | |
merging_libraries | 0.001 | 0.000 | 0.000 | |
run_kallisto | 0.000 | 0.000 | 0.001 | |
run_tximport | 0.991 | 0.060 | 1.889 | |
setAnnotationFromFile | 0.199 | 0.024 | 1.177 | |
setAnnotationFromObject | 0.099 | 0.000 | 0.436 | |
setIntergenicRelease | 0.163 | 0.008 | 0.760 | |
setOutputDir | 0 | 0 | 0 | |
setRNASeqLibPath | 0.000 | 0.000 | 0.001 | |
setRunIds | 0 | 0 | 0 | |
setSimpleArborescence | 0.001 | 0.000 | 0.000 | |
setTranscriptomeFromFile | 0.002 | 0.004 | 0.006 | |
setTranscriptomeFromObject | 0.005 | 0.000 | 0.005 | |
setWorkingPath | 0.001 | 0.000 | 0.000 | |