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CHECK report for annotatr on tokay1

This page was generated on 2018-04-12 13:28:57 -0400 (Thu, 12 Apr 2018).

Package 57/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.4.1
Raymond G. Cavalcante
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/annotatr
Branch: RELEASE_3_6
Last Commit: 95415d3
Last Changed Date: 2018-01-18 11:01:04 -0400 (Thu, 18 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotatr
Version: 1.4.1
Command: rm -rf annotatr.buildbin-libdir annotatr.Rcheck && mkdir annotatr.buildbin-libdir annotatr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotatr.buildbin-libdir annotatr_1.4.1.tar.gz >annotatr.Rcheck\00install.out 2>&1 && cp annotatr.Rcheck\00install.out annotatr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=annotatr.buildbin-libdir --install="check:annotatr-install.out" --force-multiarch --no-vignettes --timings annotatr_1.4.1.tar.gz
StartedAt: 2018-04-11 22:13:35 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:22:09 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 514.7 seconds
RetCode: 0
Status:  OK  
CheckDir: annotatr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf annotatr.buildbin-libdir annotatr.Rcheck && mkdir annotatr.buildbin-libdir annotatr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotatr.buildbin-libdir annotatr_1.4.1.tar.gz >annotatr.Rcheck\00install.out 2>&1 && cp annotatr.Rcheck\00install.out annotatr-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=annotatr.buildbin-libdir --install="check:annotatr-install.out" --force-multiarch --no-vignettes --timings annotatr_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/annotatr.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.4.1'
* 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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.6-bioc/meat/annotatr.Rcheck/00check.log'
for details.

Installation output

annotatr.Rcheck/00install.out


install for i386

* installing *source* package 'annotatr' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'annotatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotatr' as annotatr_1.4.1.zip
* DONE (annotatr)
In R CMD INSTALL
In R CMD INSTALL

Tests output

annotatr.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 71 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  27.20    1.50   54.81

annotatr.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 71 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.21    1.17   50.92

Example timings

annotatr.Rcheck/examples_i386/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions0.860.070.92
annotatr_cache0.980.261.25
build_ah_annots2.980.204.26
build_annotations4.190.154.33
builtin_annotations000
builtin_genomes000
plot_annotation2.200.072.90
plot_categorical1.440.032.27
plot_coannotations1.060.021.08
plot_numerical0.440.000.44
plot_numerical_coannotations0.600.000.59
randomize_regions0.810.031.47
read_annotations0.280.000.28
read_regions0.370.010.39
summarize_annotations0.940.081.67
summarize_categorical0.640.050.69
summarize_numerical0.350.030.38

annotatr.Rcheck/examples_x64/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions1.220.001.22
annotatr_cache0.970.391.36
build_ah_annots3.360.254.88
build_annotations4.210.134.32
builtin_annotations000
builtin_genomes000
plot_annotation2.470.033.13
plot_categorical2.190.062.95
plot_coannotations0.810.000.81
plot_numerical1.030.001.03
plot_numerical_coannotations0.720.000.72
randomize_regions0.970.051.64
read_annotations0.310.010.33
read_regions0.360.020.37
summarize_annotations1.700.052.34
summarize_categorical0.340.000.35
summarize_numerical0.890.010.90