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

Package: annotatr

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2019-04-09 01:05:53 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:13:47 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 473.4 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_1.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/annotatr.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.9.0'
* 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_ah_annots 4.04   0.57     6.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
build_ah_annots 4.71   0.47    6.82
* 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_1.9.0.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_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL annotatr_1.9.0.zip && rm annotatr_1.9.0.tar.gz annotatr_1.9.0.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  19.9M      0 --:--:-- --:--:-- --:--:-- 22.3M

install for i386

* installing *source* package 'annotatr' ...
** 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_1.9.0.zip
* DONE (annotatr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'annotatr' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  34.53    3.12   55.90


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  37.51    2.21   61.75

name	user	system	elapsed
annotate_regions	0.94	0.06	1.00
annotatr_cache	1.72	0.95	2.67
build_ah_annots	4.04	0.57	6.30
build_annotations	4.50	0.17	4.67
builtin_annotations	0.02	0.00	0.01
builtin_genomes	0	0	0
plot_annotation	1.12	0.17	2.13
plot_categorical	2.03	0.12	3.19
plot_coannotations	0.66	0.13	0.78
plot_numerical	0.28	0.00	0.28
plot_numerical_coannotations	0.37	0.01	0.39
randomize_regions	0.78	0.08	1.71
read_annotations	0.44	0.02	0.48
read_regions	0.31	0.05	0.36
summarize_annotations	1.18	0.12	2.03
summarize_categorical	0.33	0.05	0.40
summarize_numerical	0.37	0.03	0.41

name	user	system	elapsed
annotate_regions	1.23	0.00	1.23
annotatr_cache	1.61	0.80	2.44
build_ah_annots	4.71	0.47	6.82
build_annotations	3.54	0.04	3.59
builtin_annotations	0	0	0
builtin_genomes	0	0	0
plot_annotation	1.18	0.11	2.16
plot_categorical	1.25	0.02	2.04
plot_coannotations	1.50	0.01	1.51
plot_numerical	0.3	0.0	0.3
plot_numerical_coannotations	0.45	0.00	0.45
randomize_regions	0.78	0.07	1.61
read_annotations	0.31	0.01	0.33
read_regions	0.28	0.02	0.30
summarize_annotations	0.95	0.11	1.82
summarize_categorical	0.41	0.06	0.47
summarize_numerical	0.45	0.06	0.53

CHECK report for annotatr on tokay2

Summary

Command output

Installation output

Tests output

Example timings