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This page was generated on 2021-10-22 12:04:17 -0400 (Fri, 22 Oct 2021).

CHECK results for annotatr on riesling1

To the developers/maintainers of the annotatr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotatr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 66/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.19.1  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/annotatr
git_branch: master
git_last_commit: d6b7760
git_last_commit_date: 2021-07-12 11:04:21 -0400 (Mon, 12 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: annotatr
Version: 1.19.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings annotatr_1.19.1.tar.gz
StartedAt: 2021-10-21 23:55:50 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-22 00:04:43 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 532.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: annotatr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotatr.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings annotatr_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-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 '1.19.1'
* 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 'D:/biocbuild/bbs-3.14-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 4.05   0.36    5.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
build_ah_annots 8.89   0.69   10.84
* 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 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/annotatr.Rcheck/00check.log'
for details.



Installation output

annotatr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/annotatr_1.19.1.tar.gz && rm -rf annotatr.buildbin-libdir && mkdir annotatr.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annotatr.buildbin-libdir annotatr_1.19.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL annotatr_1.19.1.zip && rm annotatr_1.19.1.tar.gz annotatr_1.19.1.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
 23 1463k   23  340k    0     0  1298k      0  0:00:01 --:--:--  0:00:01 1293k
100 1463k  100 1463k    0     0  2771k      0 --:--:-- --:--:-- --:--:-- 2771k

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_1.19.1.zip
* DONE (annotatr)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'annotatr' successfully unpacked and MD5 sums checked

Tests output

annotatr.Rcheck/tests_i386/testthat.Rout


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 
  24.85    1.59   44.31 

annotatr.Rcheck/tests_x64/testthat.Rout


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 
  25.73    1.85   42.32 

Example timings

annotatr.Rcheck/examples_i386/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions0.820.000.83
annotatr_cache1.440.752.19
build_ah_annots4.050.365.53
build_annotations2.700.182.89
builtin_annotations0.010.000.01
builtin_genomes000
plot_annotation1.750.041.79
plot_categorical1.540.011.54
plot_coannotations0.550.000.54
plot_numerical0.330.000.33
plot_numerical_coannotations0.370.010.39
randomize_regions1.110.031.14
read_annotations0.270.100.36
read_regions0.280.010.30
summarize_annotations1.900.051.95
summarize_categorical0.200.060.27
summarize_numerical0.300.050.34

annotatr.Rcheck/examples_x64/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions0.260.020.29
annotatr_cache1.280.812.09
build_ah_annots 8.89 0.6910.84
build_annotations2.290.122.41
builtin_annotations000
builtin_genomes000
plot_annotation1.340.041.37
plot_categorical2.060.032.10
plot_coannotations0.530.000.53
plot_numerical0.250.000.25
plot_numerical_coannotations0.360.000.36
randomize_regions1.100.011.11
read_annotations0.210.030.25
read_regions0.220.000.22
summarize_annotations1.30.01.3
summarize_categorical0.230.030.27
summarize_numerical0.280.040.31