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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 468/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTDquerier 2.8.0  (landing page)
Xavier Escribà-Montagut
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CTDquerier
git_branch: RELEASE_3_17
git_last_commit: b0e3527
git_last_commit_date: 2023-04-25 11:27:24 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for CTDquerier on kjohnson2


To the developers/maintainers of the CTDquerier package:
- 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: 2.8.0
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_2.8.0.tar.gz
StartedAt: 2023-10-17 13:20:41 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 13:23:37 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 176.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CTDquerier.Rcheck
Warnings: 1

Command output

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###
### 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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CTDquerier.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CTDquerier/DESCRIPTION’ ... OK
* this is package ‘CTDquerier’ version ‘2.8.0’
* 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 ... 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 ... 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  14.316  0.298  22.190
query_ctd_gene 10.944  0.239  17.904
enrich-methods  8.397  0.217  12.221
query_ctd_chem  5.394  0.138   9.002
load_ctd_chem   3.698  0.082   5.625
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CTDquerier.Rcheck/00check.log’
for details.



Installation output

CTDquerier.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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_chem1.1040.0841.815
download_ctd_dise0.1300.0090.210
download_ctd_genes0.1400.0090.227
enrich-methods 8.397 0.21712.221
gala1.8280.0412.813
get_table-methods1.1560.0301.818
get_terms-methods1.1370.0271.761
leaf_plot0.6870.0521.140
load_ctd_chem3.6980.0825.625
load_ctd_dise1.1730.0471.858
load_ctd_gene14.316 0.29822.190
query_ctd_chem5.3940.1389.002
query_ctd_dise0.8420.0591.506
query_ctd_gene10.944 0.23917.904