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This page was generated on 2021-09-20 15:05:39 -0400 (Mon, 20 Sep 2021).

CHECK results for CTDquerier on machv2

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? here 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 420/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CTDquerier 2.0.0  (landing page)
Xavier Escribà-Montagut
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/CTDquerier
git_branch: RELEASE_3_13
git_last_commit: 54a0a69
git_last_commit_date: 2021-05-19 13:00:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    TIMEOUT  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CTDquerier
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CTDquerier_2.0.0.tar.gz
StartedAt: 2021-09-19 17:52:59 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 17:56:30 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 211.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CTDquerier.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CTDquerier_2.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CTDquerier.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.0.0’
* 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
enrich-methods     4.941  0.037  15.077
download_ctd_chem  2.523  0.103  12.592
query_ctd_dise     1.041  0.019  11.089
query_ctd_gene     1.041  0.017  11.061
load_ctd_gene      0.994  0.031  11.035
load_ctd_chem      1.001  0.023  11.077
query_ctd_chem     0.958  0.020  10.979
load_ctd_dise      0.935  0.020  11.003
download_ctd_dise  0.914  0.020  10.936
download_ctd_genes 0.908  0.019  10.933
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CTDquerier.Rcheck/00check.log’
for details.



Installation output

CTDquerier.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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_chem 2.523 0.10312.592
download_ctd_dise 0.914 0.02010.936
download_ctd_genes 0.908 0.01910.933
enrich-methods 4.941 0.03715.077
gala4.2850.0344.320
get_table-methods4.0920.0244.118
get_terms-methods3.8420.0133.858
leaf_plot0.6110.0230.635
load_ctd_chem 1.001 0.02311.077
load_ctd_dise 0.935 0.02011.003
load_ctd_gene 0.994 0.03111.035
query_ctd_chem 0.958 0.02010.979
query_ctd_dise 1.041 0.01911.089
query_ctd_gene 1.041 0.01711.061