Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:05:27 -0500 (Fri, 03 Dec 2021).

CHECK results for Pviz on tokay2

To the developers/maintainers of the Pviz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pviz.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1490/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pviz 1.28.0  (landing page)
Renan Sauteraud
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/Pviz
git_branch: RELEASE_3_14
git_last_commit: 18cff4d
git_last_commit_date: 2021-10-26 12:14:31 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Pviz
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pviz_1.28.0.tar.gz
StartedAt: 2021-12-03 01:33:31 -0500 (Fri, 03 Dec 2021)
EndedAt: 2021-12-03 01:40:02 -0500 (Fri, 03 Dec 2021)
EllapsedTime: 390.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Pviz.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pviz_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pviz.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pviz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pviz' version '1.28.0'
* 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 'Pviz' 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
* 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
.makeParMapping: no visible global function definition for
  'assignInNamespace'
drawGD,ProbeTrack: no visible global function definition for
  'pushViewport'
drawGD,ProbeTrack: no visible global function definition for 'viewport'
drawGD,ProbeTrack: no visible global function definition for
  'popViewport'
drawGD,ProbeTrack: no visible global function definition for 'unit'
drawGD,ProbeTrack: no visible global function definition for 'gpar'
drawGD,ProbeTrack: no visible global function definition for
  'convertWidth'
drawGD,ProbeTrack: no visible global function definition for
  'stringWidth'
drawGD,ProbeTrack: no visible global function definition for
  'stringHeight'
drawGD,ProbeTrack: no visible global function definition for
  'grid.text'
drawGD,ProbeTrack: no visible global function definition for
  'grid.rect'
drawGD,ProbeTrack: no visible global function definition for
  'dataViewport'
drawGD,ProbeTrack : <anonymous>: no visible global function definition
  for 'grid.rect'
drawGD,ProbeTrack : <anonymous>: no visible global function definition
  for 'gpar'
drawGD,ProbeTrack : <anonymous>: no visible global function definition
  for 'grid.text'
drawGD,ProteinAxisTrack: no visible global function definition for
  'pushViewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  'dataViewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  'convertHeight'
drawGD,ProteinAxisTrack: no visible global function definition for
  'stringHeight'
drawGD,ProteinAxisTrack: no visible global function definition for
  'popViewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  '.getGapPos'
drawGD,ProteinAxisTrack: no visible global function definition for
  'gaps'
drawGD,ProteinAxisTrack: no visible global function definition for
  'viewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  'grid.segments'
drawGD,ProteinAxisTrack: no visible global function definition for
  'gpar'
drawGD,ProteinAxisTrack: no visible global function definition for
  'coord2ext'
drawGD,ProteinAxisTrack: no visible global function definition for
  'grid.text'
drawGD,ProteinAxisTrack: no visible global function definition for
  'convertWidth'
drawGD,ProteinAxisTrack: no visible global function definition for
  'stringWidth'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'pushViewport'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'dataViewport'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'gpar'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'popViewport'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'convertUnit'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'stringWidth'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'grid.lines'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'unit'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'grid.text'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'grid.rect'
Undefined global functions or variables:
  .getGapPos assignInNamespace convertHeight convertUnit convertWidth
  coord2ext dataViewport gaps gpar grid.lines grid.rect grid.segments
  grid.text popViewport pushViewport stringHeight stringWidth unit
  viewport
Consider adding
  importFrom("utils", "assignInNamespace")
to your NAMESPACE file.
* 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 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 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-3.14-bioc/meat/Pviz.Rcheck/00check.log'
for details.



Installation output

Pviz.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Pviz_1.28.0.tar.gz && rm -rf Pviz.buildbin-libdir && mkdir Pviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pviz.buildbin-libdir Pviz_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Pviz_1.28.0.zip && rm Pviz_1.28.0.tar.gz Pviz_1.28.0.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
100  200k  100  200k    0     0   890k      0 --:--:-- --:--:-- --:--:--  895k

install for i386

* installing *source* package 'Pviz' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Pviz'
    finding HTML links ... done
    ATrack                                  html  
    finding level-2 HTML links ... done

    CladeTrack                              html  
    DTrack                                  html  
    ProbeTrack                              html  
    ProteinAxisTrack                        html  
    ProteinSequenceTrack                    html  
    plot_clade                              html  
    plot_inter                              html  
** building package indices
** installing vignettes
   'Pviz.Rnw' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Pviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pviz' as Pviz_1.28.0.zip
* DONE (Pviz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Pviz' successfully unpacked and MD5 sums checked

Tests output


Example timings

Pviz.Rcheck/examples_i386/Pviz-Ex.timings

nameusersystemelapsed
ATrack3.050.393.44
CladeTrack1.390.201.61
DTrack0.130.000.13
ProbeTrack2.440.663.09
ProteinAxisTrack0.390.010.41
ProteinSequenceTrack0.180.020.20
plot_clade1.380.061.44
plot_inter0.930.111.08

Pviz.Rcheck/examples_x64/Pviz-Ex.timings

nameusersystemelapsed
ATrack3.380.063.45
CladeTrack1.210.021.24
DTrack0.130.000.13
ProbeTrack2.620.042.67
ProteinAxisTrack0.420.020.44
ProteinSequenceTrack0.210.020.22
plot_clade1.450.041.50
plot_inter1.030.001.03