Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:12 -0400 (Wed, 22 Sep 2021).

CHECK results for CTDquerier on tokay2

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 EscribĂ -Montagut
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CTDquerier.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CTDquerier_2.0.0.tar.gz
StartedAt: 2021-09-21 21:24:14 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 21:29:45 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 331.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CTDquerier.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CTDquerier.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CTDquerier_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CTDquerier.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
enrich-methods     3.86   0.04   13.90
download_ctd_chem  2.25   0.01   12.28
load_ctd_chem      0.93   0.00   10.94
query_ctd_dise     0.90   0.02   10.94
query_ctd_chem     0.89   0.01   10.92
load_ctd_dise      0.89   0.00   10.90
load_ctd_gene      0.89   0.00   10.91
query_ctd_gene     0.88   0.00   10.89
download_ctd_dise  0.87   0.00   10.89
download_ctd_genes 0.84   0.00   10.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
enrich-methods     3.41   0.05   13.47
download_ctd_chem  2.03   0.11   12.15
query_ctd_gene     1.11   0.02   11.14
load_ctd_chem      0.97   0.03   11.02
query_ctd_chem     0.94   0.05   11.01
query_ctd_dise     0.97   0.01   11.02
load_ctd_gene      0.97   0.00   10.98
load_ctd_dise      0.94   0.00   10.95
download_ctd_genes 0.89   0.03   10.94
download_ctd_dise  0.89   0.02   10.93
* checking PDF version of manual ... OK
* DONE

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



Installation output

CTDquerier.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CTDquerier_2.0.0.tar.gz && rm -rf CTDquerier.buildbin-libdir && mkdir CTDquerier.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CTDquerier.buildbin-libdir CTDquerier_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CTDquerier_2.0.0.zip && rm CTDquerier_2.0.0.tar.gz CTDquerier_2.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 2713k    1 49975    0     0   317k      0  0:00:08 --:--:--  0:00:08  316k
100 2713k  100 2713k    0     0  2794k      0 --:--:-- --:--:-- --:--:-- 2794k

install for i386

* installing *source* package 'CTDquerier' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CTDquerier'
    finding HTML links ... done
    CTDdata-class                           html  
    CTDquerier                              html  
    download_ctd_chem                       html  
    download_ctd_dise                       html  
    download_ctd_genes                      html  
    enrich-methods                          html  
    gala                                    html  
    get_table-methods                       html  
    get_terms-methods                       html  
    leaf_plot                               html  
    load_ctd_chem                           html  
    load_ctd_dise                           html  
    load_ctd_gene                           html  
    query_ctd_chem                          html  
    query_ctd_dise                          html  
    query_ctd_gene                          html  
** 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

install for x64

* installing *source* package 'CTDquerier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CTDquerier' as CTDquerier_2.0.0.zip
* DONE (CTDquerier)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CTDquerier' successfully unpacked and MD5 sums checked

Tests output


Example timings

CTDquerier.Rcheck/examples_i386/CTDquerier-Ex.timings

nameusersystemelapsed
download_ctd_chem 2.25 0.0112.28
download_ctd_dise 0.87 0.0010.89
download_ctd_genes 0.84 0.0010.86
enrich-methods 3.86 0.0413.90
gala3.530.033.57
get_table-methods3.160.043.20
get_terms-methods3.000.043.03
leaf_plot0.430.060.50
load_ctd_chem 0.93 0.0010.94
load_ctd_dise 0.89 0.0010.90
load_ctd_gene 0.89 0.0010.91
query_ctd_chem 0.89 0.0110.92
query_ctd_dise 0.90 0.0210.94
query_ctd_gene 0.88 0.0010.89

CTDquerier.Rcheck/examples_x64/CTDquerier-Ex.timings

nameusersystemelapsed
download_ctd_chem 2.03 0.1112.15
download_ctd_dise 0.89 0.0210.93
download_ctd_genes 0.89 0.0310.94
enrich-methods 3.41 0.0513.47
gala2.420.072.50
get_table-methods2.010.032.05
get_terms-methods2.470.052.52
leaf_plot0.470.020.48
load_ctd_chem 0.97 0.0311.02
load_ctd_dise 0.94 0.0010.95
load_ctd_gene 0.97 0.0010.98
query_ctd_chem 0.94 0.0511.01
query_ctd_dise 0.97 0.0111.02
query_ctd_gene 1.11 0.0211.14