Multiple platform build/check report for BioC 3.13 - CHECK results for annotatr on tokay2

Package: annotatr

Version: 1.18.1

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings annotatr_1.18.1.tar.gz

StartedAt: 2021-10-14 19:34:06 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 19:42:52 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 526.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: annotatr.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings annotatr_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/annotatr.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 'annotatr/DESCRIPTION' ... OK
* this is package 'annotatr' version '1.18.1'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck/00install.out' for details.
* 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 LazyData ... 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 6.96   1.48    9.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
build_ah_annots   6.88   0.63    8.82
build_annotations 5.06   0.11    5.18
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/annotatr_1.18.1.tar.gz && rm -rf annotatr.buildbin-libdir && mkdir annotatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annotatr.buildbin-libdir annotatr_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL annotatr_1.18.1.zip && rm annotatr_1.18.1.tar.gz annotatr_1.18.1.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
 93 1461k   93 1364k    0     0  1657k      0 --:--:-- --:--:-- --:--:-- 1657k
100 1461k  100 1461k    0     0  1699k      0 --:--:-- --:--:-- --:--:-- 1699k

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
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
** 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
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
** 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
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
* MD5 sums
packaged installation of 'annotatr' as annotatr_1.18.1.zip
* DONE (annotatr)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'annotatr' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
Warning message:
replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr' 
> 
> test_check("annotatr")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
  46.07    3.57   70.17


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
Warning message:
replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr' 
> 
> test_check("annotatr")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
  46.17    2.10   64.17

name	user	system	elapsed
annotate_regions	1.03	0.03	1.06
annotatr_cache	2.27	1.28	3.58
build_ah_annots	6.96	1.48	9.93
build_annotations	4.31	0.19	4.50
builtin_annotations	0	0	0
builtin_genomes	0	0	0
plot_annotation	2.98	0.05	3.05
plot_categorical	2.70	0.06	2.78
plot_coannotations	0.83	0.00	0.83
plot_numerical	0.47	0.03	0.50
plot_numerical_coannotations	0.57	0.02	0.60
randomize_regions	2.96	0.01	2.96
read_annotations	0.34	0.04	0.38
read_regions	0.25	0.10	0.36
summarize_annotations	2.54	0.08	2.63
summarize_categorical	0.39	0.03	0.42
summarize_numerical	0.58	0.07	0.64

name	user	system	elapsed
annotate_regions	0.59	0.00	0.59
annotatr_cache	2.33	1.00	3.33
build_ah_annots	6.88	0.63	8.82
build_annotations	5.06	0.11	5.18
builtin_annotations	0	0	0
builtin_genomes	0.01	0.00	0.02
plot_annotation	2.86	0.03	2.89
plot_categorical	3.33	0.02	3.34
plot_coannotations	0.78	0.01	0.80
plot_numerical	0.34	0.05	0.39
plot_numerical_coannotations	0.46	0.01	0.47
randomize_regions	2.23	0.02	2.25
read_annotations	0.31	0.03	0.34
read_regions	0.3	0.0	0.3
summarize_annotations	2.36	0.03	2.39
summarize_categorical	0.59	0.02	0.60
summarize_numerical	0.47	0.04	0.52

CHECK results for annotatr on tokay2

Summary

Command output

Installation output

Tests output

Example timings