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CHECK report for annotatr on tokay1

This page was generated on 2020-08-12 11:45:26 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE annotatr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 65/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.15.2
Raymond G. Cavalcante
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/annotatr
Branch: master
Last Commit: 78eb300
Last Changed Date: 2020-07-07 08:56:57 -0400 (Tue, 07 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotatr
Version: 1.15.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annotatr_1.15.2.tar.gz
StartedAt: 2020-08-12 03:35:25 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 03:46:07 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 642.1 seconds
RetCode: 0
Status:  OK  
CheckDir: annotatr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annotatr_1.15.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/annotatr.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotatr/DESCRIPTION' ... OK
* this is package 'annotatr' version '1.15.2'
* 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 'annotatr' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... NOTE
plot_coannotations: no visible binding for global variable '.'
plot_numerical_coannotations: no visible binding for global variable
  '.'
Undefined global functions or variables:
  .
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
build_ah_annots 13.77   1.79   21.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
build_ah_annots 15.3    1.2   23.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/annotatr.Rcheck/00check.log'
for details.



Installation output

annotatr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/annotatr_1.15.2.tar.gz && rm -rf annotatr.buildbin-libdir && mkdir annotatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annotatr.buildbin-libdir annotatr_1.15.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL annotatr_1.15.2.zip && rm annotatr_1.15.2.tar.gz annotatr_1.15.2.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1467k  100 1467k    0     0  25.2M      0 --:--:-- --:--:-- --:--:-- 27.0M

install for i386

* installing *source* package 'annotatr' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'annotatr'
    finding HTML links ... done
    annotate_regions                        html  
    annotations                             html  
    annotatr                                html  
    annotatr_cache                          html  
    build_ah_annots                         html  
    build_annotations                       html  
    build_cpg_annots                        html  
    build_enhancer_annots                   html  
    build_gene_annots                       html  
    build_hmm_annots                        html  
    build_lncrna_annots                     html  
    builtin_annotations                     html  
    builtin_genomes                         html  
    check_annotations                       html  
    expand_annotations                      html  
    get_cellline_from_code                  html  
    get_cellline_from_shortcut              html  
    get_orgdb_name                          html  
    get_txdb_name                           html  
    plot_annotation                         html  
    plot_categorical                        html  
    plot_coannotations                      html  
    plot_numerical                          html  
    plot_numerical_coannotations            html  
    randomize_regions                       html  
    read_annotations                        html  
    read_regions                            html  
    reformat_hmm_codes                      html  
    subset_order_tbl                        html  
    summarize_annotations                   html  
    summarize_categorical                   html  
    summarize_numerical                     html  
    tidy_annotations                        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 'annotatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotatr' as annotatr_1.15.2.zip
* DONE (annotatr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'annotatr' successfully unpacked and MD5 sums checked

Tests output

annotatr.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(annotatr)
> 
> test_check("annotatr")
== testthat results  ===========================================================
[ OK: 72 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  53.62    4.67   91.06 

annotatr.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(annotatr)
> 
> test_check("annotatr")
== testthat results  ===========================================================
[ OK: 72 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.23    3.26   86.57 

Example timings

annotatr.Rcheck/examples_i386/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions0.580.030.61
annotatr_cache2.391.303.69
build_ah_annots13.77 1.7921.42
build_annotations4.700.254.95
builtin_annotations0.010.000.02
builtin_genomes000
plot_annotation2.250.002.25
plot_categorical2.350.052.39
plot_coannotations0.890.000.89
plot_numerical0.330.000.33
plot_numerical_coannotations0.580.000.58
randomize_regions2.000.032.03
read_annotations0.280.030.32
read_regions0.310.000.31
summarize_annotations2.900.082.97
summarize_categorical0.340.030.37
summarize_numerical0.440.020.45

annotatr.Rcheck/examples_x64/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions0.580.020.59
annotatr_cache2.040.832.88
build_ah_annots15.30 1.2023.84
build_annotations4.530.094.62
builtin_annotations000
builtin_genomes000
plot_annotation3.890.084.06
plot_categorical4.290.084.38
plot_coannotations1.080.011.09
plot_numerical1.770.001.77
plot_numerical_coannotations0.920.030.95
randomize_regions2.550.072.61
read_annotations0.340.010.36
read_regions0.380.010.40
summarize_annotations2.390.002.39
summarize_categorical0.390.030.42
summarize_numerical0.470.020.48