Multiple platform build/check report for BioC 3.9 - CHECK report for annotatr on tokay2

Package: annotatr

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings annotatr_1.10.0.tar.gz

StartedAt: 2019-10-16 01:56:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:04:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 496.8 seconds

RetCode: 0

Status: OK

CheckDir: annotatr.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings annotatr_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/annotatr.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.10.0'
* 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 or elapsed time > 5s
                  user system elapsed
build_annotations 4.92   0.14    5.06
build_ah_annots   3.87   0.76    6.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
build_annotations 6.25   0.15    6.43
build_ah_annots   4.55   0.49    6.56
* 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-3.9-bioc/meat/annotatr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/annotatr_1.10.0.tar.gz && rm -rf annotatr.buildbin-libdir && mkdir annotatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annotatr.buildbin-libdir annotatr_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL annotatr_1.10.0.zip && rm annotatr_1.10.0.tar.gz annotatr_1.10.0.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 1462k  100 1462k    0     0  16.3M      0 --:--:-- --:--:-- --:--:-- 17.6M

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_1.10.0.zip
* DONE (annotatr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'annotatr' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  32.76    2.56   63.84


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  36.46    2.23   70.42

name	user	system	elapsed
annotate_regions	1.01	0.06	1.08
annotatr_cache	1.90	0.77	2.67
build_ah_annots	3.87	0.76	6.06
build_annotations	4.92	0.14	5.06
builtin_annotations	0	0	0
builtin_genomes	0	0	0
plot_annotation	1.87	0.13	3.47
plot_categorical	1.25	0.12	2.81
plot_coannotations	0.77	0.02	0.79
plot_numerical	0.45	0.01	0.47
plot_numerical_coannotations	0.5	0.0	0.5
randomize_regions	0.78	0.16	1.89
read_annotations	0.34	0.01	0.36
read_regions	0.45	0.03	0.49
summarize_annotations	0.97	0.18	1.81
summarize_categorical	0.49	0.04	0.53
summarize_numerical	0.41	0.03	0.43

name	user	system	elapsed
annotate_regions	1.57	0.02	1.59
annotatr_cache	1.93	0.76	2.72
build_ah_annots	4.55	0.49	6.56
build_annotations	6.25	0.15	6.43
builtin_annotations	0.02	0.00	0.01
builtin_genomes	0	0	0
plot_annotation	1.55	0.02	2.31
plot_categorical	2.68	0.04	3.74
plot_coannotations	1.19	0.22	1.42
plot_numerical	0.49	0.00	0.48
plot_numerical_coannotations	0.51	0.00	0.52
randomize_regions	0.78	0.11	1.52
read_annotations	0.36	0.03	0.41
read_regions	0.29	0.05	0.34
summarize_annotations	1.22	0.05	1.91
summarize_categorical	0.39	0.08	0.48
summarize_numerical	0.36	0.01	0.38

CHECK report for annotatr on tokay2

Summary

Command output

Installation output

Tests output

Example timings