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This page was generated on 2025-03-19 11:40 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 475/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTDquerier 2.15.0  (landing page)
Xavier Escribà-Montagut
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/CTDquerier
git_branch: devel
git_last_commit: b79a567
git_last_commit_date: 2024-10-29 10:56:39 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for CTDquerier on nebbiolo1

To the developers/maintainers of the CTDquerier package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CTDquerier.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: CTDquerier
Version: 2.15.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CTDquerier_2.15.0.tar.gz
StartedAt: 2025-03-18 21:18:13 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 21:20:53 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 160.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CTDquerier.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CTDquerier_2.15.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CTDquerier.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CTDquerier/DESCRIPTION’ ... OK
* this is package ‘CTDquerier’ version ‘2.15.0’
* 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 ‘CTDquerier’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘batch_query.Rmd’ ‘biomed-central.csl’ ‘case_study.Rmd’
  ‘case_study.bib’ ‘img/01_CTDbase.png’ ‘img/02_XKR4_keyword.png’
  ‘img/03_BatchQuery.png’ ‘vignette.Rmd’
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
download_ctd_chem  1.743  0.146  11.890
enrich-methods     1.702  0.110  11.814
download_ctd_dise  0.802  0.201  11.005
query_ctd_dise     0.566  0.049  10.617
query_ctd_chem     0.589  0.007  10.598
download_ctd_genes 0.556  0.013  10.571
load_ctd_dise      0.559  0.008  10.569
load_ctd_chem      0.536  0.012  10.552
load_ctd_gene      0.539  0.009  10.550
query_ctd_gene     0.528  0.005  10.533
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CTDquerier.Rcheck/00check.log’
for details.


Installation output

CTDquerier.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CTDquerier
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CTDquerier’ ...
** this is package ‘CTDquerier’ version ‘2.15.0’
** using staged installation
** R
** data
** 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 (CTDquerier)

Tests output


Example timings

CTDquerier.Rcheck/CTDquerier-Ex.timings

nameusersystemelapsed
download_ctd_chem 1.743 0.14611.890
download_ctd_dise 0.802 0.20111.005
download_ctd_genes 0.556 0.01310.571
enrich-methods 1.702 0.11011.814
gala1.1400.0591.198
get_table-methods0.9960.0431.041
get_terms-methods0.9440.0360.980
leaf_plot0.5700.0240.593
load_ctd_chem 0.536 0.01210.552
load_ctd_dise 0.559 0.00810.569
load_ctd_gene 0.539 0.00910.550
query_ctd_chem 0.589 0.00710.598
query_ctd_dise 0.566 0.04910.617
query_ctd_gene 0.528 0.00510.533