Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 472/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTDquerier 2.14.0  (landing page)
Xavier Escribà-Montagut
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CTDquerier
git_branch: RELEASE_3_20
git_last_commit: fc48ee3
git_last_commit_date: 2024-10-29 10:56:39 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for CTDquerier on kjohnson1

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: 2.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CTDquerier_2.14.0.tar.gz
StartedAt: 2024-12-20 16:25:16 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 16:27:24 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 128.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CTDquerier.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CTDquerier_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CTDquerier.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CTDquerier/DESCRIPTION’ ... OK
* this is package ‘CTDquerier’ version ‘2.14.0’
* 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 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 ... NOTE
  Note: found 176 marked UTF-8 strings
* 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
load_ctd_gene  18.236  0.285  18.602
query_ctd_gene 12.991  0.248  16.504
enrich-methods 10.880  0.145  11.922
query_ctd_chem  7.996  0.119   9.842
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CTDquerier.Rcheck/00check.log’
for details.


Installation output

CTDquerier.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CTDquerier
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘CTDquerier’ ...
** 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_chem1.1530.0691.231
download_ctd_dise0.1250.0080.133
download_ctd_genes0.1140.0080.122
enrich-methods10.880 0.14511.922
gala1.4590.0241.482
get_table-methods1.3340.0161.352
get_terms-methods1.3020.0111.314
leaf_plot0.7400.0240.764
load_ctd_chem4.8720.0654.944
load_ctd_dise0.7200.0440.766
load_ctd_gene18.236 0.28518.602
query_ctd_chem7.9960.1199.842
query_ctd_dise1.6540.0552.360
query_ctd_gene12.991 0.24816.504