Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:29 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for timescape on tokay2


To the developers/maintainers of the timescape package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/timescape.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1958/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
timescape 1.18.0  (landing page)
Maia Smith
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/timescape
git_branch: RELEASE_3_14
git_last_commit: 79de8cc
git_last_commit_date: 2021-10-26 12:33:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: timescape
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:timescape.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings timescape_1.18.0.tar.gz
StartedAt: 2022-04-13 04:05:19 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 04:05:52 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 32.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: timescape.Rcheck
Warnings: 1

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:timescape.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings timescape_1.18.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/timescape.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'timescape/DESCRIPTION' ... OK
* this is package 'timescape' version '1.18.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .vscode
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'timescape' 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 ... NOTE
Namespaces in Imports field not imported from:
  'dplyr' 'gtools'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getMutationsData: no visible binding for global variable
  'show_warnings'
Undefined global functions or variables:
  show_warnings
* 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 ... WARNING
Duplicated \argument entries in documentation object 'timescapeOutput':
  'width' 'height' 'mutations' 'height' 'width' 'clonal_prev'
  'tree_edges' 'alpha' 'clonal_prev' 'tree_edges' 'genotype_position'
  'clone_colours' 'perturbations' 'mutations' 'tree_edges'
  'clonal_prev' 'clonal_prev' 'tree_edges' 'clone_colours' 'mutations'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/timescape.Rcheck/00check.log'
for details.



Installation output

timescape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/timescape_1.18.0.tar.gz && rm -rf timescape.buildbin-libdir && mkdir timescape.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=timescape.buildbin-libdir timescape_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL timescape_1.18.0.zip && rm timescape_1.18.0.tar.gz timescape_1.18.0.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  449k  100  449k    0     0   723k      0 --:--:-- --:--:-- --:--:--  724k

install for i386

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

install for x64

* installing *source* package 'timescape' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'timescape' as timescape_1.18.0.zip
* DONE (timescape)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'timescape' successfully unpacked and MD5 sums checked

Tests output


Example timings

timescape.Rcheck/examples_i386/timescape-Ex.timings

nameusersystemelapsed
helpers0.300.040.34
timescape0.560.191.11

timescape.Rcheck/examples_x64/timescape-Ex.timings

nameusersystemelapsed
helpers0.280.060.35
timescape0.740.190.94