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This page was generated on 2022-01-27 11:07:14 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 geneplotter on riesling1


To the developers/maintainers of the geneplotter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geneplotter.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 728/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneplotter 1.73.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/geneplotter
git_branch: master
git_last_commit: a1bbcd2
git_last_commit_date: 2021-10-26 11:45:33 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: geneplotter
Version: 1.73.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneplotter.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings geneplotter_1.73.0.tar.gz
StartedAt: 2022-01-26 18:59:22 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 19:01:09 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 107.8 seconds
RetCode: 0
Status:   OK  
CheckDir: geneplotter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneplotter.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings geneplotter_1.73.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/geneplotter.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneplotter/DESCRIPTION' ... OK
* this is package 'geneplotter' version '1.73.0'
* 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 'geneplotter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to 'annotate' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'Rgraphviz' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotExpressionGraph: no visible global function definition for
  'selectMethod'
Undefined global functions or variables:
  selectMethod
Consider adding
  importFrom("methods", "selectMethod")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package 'prada' in Rd xrefs
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/geneplotter.Rcheck/00check.log'
for details.



Installation output

geneplotter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL geneplotter
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'geneplotter' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneplotter'
    finding HTML links ... done
    GetColor                                html  
    Makesense                               html  
    alongChrom                              html  
    amplicon.plot                           html  
    cColor                                  html  
    cPlot                                   html  
    cScale                                  html  
    eset133a                                html  
    groupedHeatmap                          html  
    histStack                               html  
    imageMap                                html  
    make.chromOrd                           html  
    multiecdf                               html  
    openHtmlPage                            html  
    plotChr                                 html  
    plotExpressionGraph                     html  
    plotMA                                  html  
    savepng                                 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
* DONE (geneplotter)
Making 'packages.html' ... done

Tests output


Example timings

geneplotter.Rcheck/geneplotter-Ex.timings

nameusersystemelapsed
GetColor000
Makesense0.930.050.99
alongChrom0.710.030.73
amplicon.plot000
cColor0.820.000.83
cPlot0.470.020.48
cScale0.420.010.44
eset133a0.100.000.09
groupedHeatmap0.030.000.04
histStack000
imageMap0.030.000.03
make.chromOrd0.090.000.09
multiecdf0.050.000.05
openHtmlPage000
plotChr0.650.030.69
plotExpressionGraph0.500.020.51
plotMA0.030.000.03
savepng0.090.000.14