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CHECK report for gtrellis on tokay2

This page was generated on 2018-10-17 08:40:12 -0400 (Wed, 17 Oct 2018).

Package 664/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gtrellis 1.12.1
Zuguang Gu
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/gtrellis
Branch: RELEASE_3_7
Last Commit: 7f3941a
Last Changed Date: 2018-06-19 10:10:20 -0400 (Tue, 19 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gtrellis
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gtrellis.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings gtrellis_1.12.1.tar.gz
StartedAt: 2018-10-17 02:37:25 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:40:13 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 168.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gtrellis.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gtrellis.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings gtrellis_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/gtrellis.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gtrellis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gtrellis' version '1.12.1'
* 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 'gtrellis' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_heatmap_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_lines_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_points_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_rect_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_segments_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/gtrellis_layout.rd:44: file link 'I' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/gtrellis_layout.rd:57: file link 'grob' in package 'grid' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/gtrellis.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 ... OK
* 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 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 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/gtrellis.Rcheck/00check.log'
for details.

Installation output

gtrellis.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/gtrellis_1.12.1.tar.gz && rm -rf gtrellis.buildbin-libdir && mkdir gtrellis.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gtrellis.buildbin-libdir gtrellis_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL gtrellis_1.12.1.zip && rm gtrellis_1.12.1.tar.gz gtrellis_1.12.1.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
100  834k  100  834k    0     0  13.7M      0 --:--:-- --:--:-- --:--:-- 15.3M

install for i386

* installing *source* package 'gtrellis' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gtrellis'
    finding HTML links ... done
    add_heatmap_track                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_heatmap_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    add_ideogram_track                      html  
    add_lines_track                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_lines_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    add_points_track                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_points_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    add_rect_track                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_rect_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    add_segments_track                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/add_segments_track.rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    add_track                               html  
    current_track                           html  
    get_cell_meta_data                      html  
    gtrellis_layout                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/gtrellis_layout.rd:44: file link 'I' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6fxvQo/R.INSTALL17c43bda46d7/gtrellis/man/gtrellis_layout.rd:57: file link 'grob' in package 'grid' does not exist and so has been treated as a topic
    gtrellis_show_index                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gtrellis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gtrellis' as gtrellis_1.12.1.zip
* DONE (gtrellis)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'gtrellis' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

gtrellis.Rcheck/tests_i386/test-all.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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)
> suppressWarnings(suppressPackageStartupMessages(library(gtrellis)))
> 
> test_check("gtrellis")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.23    0.31    4.53

gtrellis.Rcheck/tests_x64/test-all.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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)
> suppressWarnings(suppressPackageStartupMessages(library(gtrellis)))
> 
> test_check("gtrellis")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.82    0.26    5.07

Example timings

gtrellis.Rcheck/examples_i386/gtrellis-Ex.timings

nameusersystemelapsed
add_heatmap_track3.840.093.94
add_ideogram_track2.710.032.73
add_lines_track2.690.022.70
add_points_track2.670.032.71
add_rect_track1.610.001.61
add_segments_track1.330.011.34
add_track2.620.072.69
current_track000
get_cell_meta_data3.260.003.27
gtrellis_layout3.830.013.84
gtrellis_show_index1.30.01.3

gtrellis.Rcheck/examples_x64/gtrellis-Ex.timings

nameusersystemelapsed
add_heatmap_track4.700.024.71
add_ideogram_track3.050.043.09
add_lines_track2.990.023.00
add_points_track1.940.011.95
add_rect_track1.980.001.98
add_segments_track1.770.041.80
add_track2.730.032.76
current_track000
get_cell_meta_data3.120.003.13
gtrellis_layout3.710.003.70
gtrellis_show_index1.140.001.14