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This page was generated on 2022-01-18 11:10:44 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 ChromHeatMap on merida1


To the developers/maintainers of the ChromHeatMap package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChromHeatMap.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 308/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromHeatMap 1.49.0  (landing page)
Tim F. Rayner
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChromHeatMap
git_branch: master
git_last_commit: 6b6da2c
git_last_commit_date: 2021-10-26 11:54:52 -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    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChromHeatMap
Version: 1.49.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromHeatMap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromHeatMap_1.49.0.tar.gz
StartedAt: 2022-01-17 23:08:34 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 23:14:14 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 339.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChromHeatMap.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromHeatMap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromHeatMap_1.49.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChromHeatMap.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromHeatMap/DESCRIPTION’ ... OK
* this is package ‘ChromHeatMap’ version ‘1.49.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChromHeatMap’ 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
createChrMatrix: no visible global function definition for ‘new’
makeRangedDataList : .makeGRanges: no visible global function
  definition for ‘as’
plotChrMap: no visible global function definition for ‘new’
makeChrStrandData,matrix: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  as new
Consider adding
  importFrom("methods", "as", "new")
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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
makeRangedDataList 4.863  0.634   5.506
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChromHeatMap.Rcheck/00check.log’
for details.



Installation output

ChromHeatMap.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ChromHeatMap’ ...
** using staged installation
** R
** data
** 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 (ChromHeatMap)

Tests output


Example timings

ChromHeatMap.Rcheck/ChromHeatMap-Ex.timings

nameusersystemelapsed
ChrMapPlot-class0.9540.0581.012
ChrStrandData-class0.9470.0210.970
ChrStrandMatrix-class0.0490.0030.052
chrHeatMap0.0790.0030.083
createChrMatrix0.0410.0020.044
drawMapDendro0.0660.0040.070
grabChrMapProbes0.2930.0140.307
makeChrStrandData0.1250.0070.132
makeRangedDataList4.8630.6345.506
plotChrMap0.2330.0120.246