Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:04 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for CTDquerier on lconway


To the developers/maintainers of the CTDquerier package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 451/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTDquerier 2.6.0  (landing page)
Xavier Escribà-Montagut
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/CTDquerier
git_branch: RELEASE_3_16
git_last_commit: 97cf629
git_last_commit_date: 2022-11-01 11:24:12 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CTDquerier
Version: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2023-04-10 19:41:17 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:45:04 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 227.6 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_2.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/CTDquerier.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CTDquerier/DESCRIPTION’ ... OK
* this is package ‘CTDquerier’ version ‘2.6.0’
* 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  10.927  0.221  11.178
query_ctd_gene  8.957  0.249  21.661
enrich-methods  7.976  0.233  32.880
query_ctd_chem  5.285  0.159  39.779
query_ctd_dise  1.899  0.148  57.693
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/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_chem1.0310.0671.115
download_ctd_dise0.1340.0090.143
download_ctd_genes0.1160.0080.124
enrich-methods 7.976 0.23332.880
gala1.2340.0241.268
get_table-methods1.0320.0171.052
get_terms-methods0.9810.0080.992
leaf_plot0.8920.0490.946
load_ctd_chem2.7370.0752.821
load_ctd_dise0.5050.0300.540
load_ctd_gene10.927 0.22111.178
query_ctd_chem 5.285 0.15939.779
query_ctd_dise 1.899 0.14857.693
query_ctd_gene 8.957 0.24921.661