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CHECK report for gtrellis on tokay1

This page was generated on 2019-04-13 11:25:05 -0400 (Sat, 13 Apr 2019).

Package 698/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gtrellis 1.14.0
Zuguang Gu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/gtrellis
Branch: RELEASE_3_8
Last Commit: 93935fb
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gtrellis
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gtrellis.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gtrellis_1.14.0.tar.gz
StartedAt: 2019-04-13 02:56:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:59:59 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 193.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gtrellis.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gtrellis.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gtrellis_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/gtrellis.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/gtrellis_1.14.0.tar.gz && rm -rf gtrellis.buildbin-libdir && mkdir gtrellis.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gtrellis.buildbin-libdir gtrellis_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL gtrellis_1.14.0.zip && rm gtrellis_1.14.0.tar.gz gtrellis_1.14.0.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
  0  833k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  833k  100  833k    0     0  17.5M      0 --:--:-- --:--:-- --:--:-- 18.5M

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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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-3.8-bioc/tmpdir/RtmpwzIpYm/R.INSTALL1194758f649c/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_1.14.0.zip
* DONE (gtrellis)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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)
> suppressWarnings(suppressPackageStartupMessages(library(gtrellis)))
> 
> test_check("gtrellis")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.96    0.25    4.20

gtrellis.Rcheck/tests_x64/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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)
> suppressWarnings(suppressPackageStartupMessages(library(gtrellis)))
> 
> test_check("gtrellis")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.54    0.50    6.04

Example timings

gtrellis.Rcheck/examples_i386/gtrellis-Ex.timings

nameusersystemelapsed
add_heatmap_track2.670.142.81
add_ideogram_track1.580.031.61
add_lines_track1.600.031.63
add_points_track1.370.031.40
add_rect_track0.980.021.00
add_segments_track0.910.000.91
add_track1.890.011.91
current_track000
get_cell_meta_data2.550.002.54
gtrellis_layout2.830.022.85
gtrellis_show_index1.070.001.07

gtrellis.Rcheck/examples_x64/gtrellis-Ex.timings

nameusersystemelapsed
add_heatmap_track2.590.032.62
add_ideogram_track1.880.001.87
add_lines_track1.890.001.89
add_points_track1.50.01.5
add_rect_track1.080.001.08
add_segments_track1.060.001.07
add_track1.950.001.95
current_track000
get_cell_meta_data2.270.002.26
gtrellis_layout2.670.002.68
gtrellis_show_index0.910.000.90