Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1589/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pviz 1.34.0  (landing page)
Renan Sauteraud
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Pviz
git_branch: RELEASE_3_17
git_last_commit: 62a5ac8
git_last_commit_date: 2023-04-25 10:33:03 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for Pviz on kjohnson2


To the developers/maintainers of the Pviz package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Pviz
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pviz_1.34.0.tar.gz
StartedAt: 2023-10-18 16:30:38 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 16:39:22 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 523.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pviz.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pviz_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Pviz.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pviz’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... 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
* 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'
plot_clade: no visible global function definition for 'tail'
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 tail unit
  viewport
Consider adding
  importFrom("utils", "assignInNamespace", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'ATrack.Rd':
  ‘GdObject’

Missing link or links in documentation object 'DTrack.Rd':
  ‘GdObject’

Missing link or links in documentation object 'ProbeTrack.Rd':
  ‘GdObject’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ATrack     3.432  0.111   5.380
ProbeTrack 3.336  0.106   5.248
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Pviz.Rcheck/00check.log’
for details.



Installation output

Pviz.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pviz
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘Pviz’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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
* DONE (Pviz)

Tests output


Example timings

Pviz.Rcheck/Pviz-Ex.timings

nameusersystemelapsed
ATrack3.4320.1115.380
CladeTrack1.2010.0291.865
DTrack0.1410.0010.218
ProbeTrack3.3360.1065.248
ProteinAxisTrack0.5030.0090.747
ProteinSequenceTrack0.2510.0090.397
plot_clade1.7230.0382.711
plot_inter0.7920.0121.196