Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:50 -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 conumee on machv2


To the developers/maintainers of the conumee package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/conumee.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 392/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.28.0  (landing page)
Volker Hovestadt
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/conumee
git_branch: RELEASE_3_14
git_last_commit: 49326cb
git_last_commit_date: 2021-10-26 12:20:09 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: conumee
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:conumee.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings conumee_1.28.0.tar.gz
StartedAt: 2022-04-12 11:55:10 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 12:34:46 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 2375.7 seconds
RetCode: 0
Status:   OK  
CheckDir: conumee.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:conumee.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings conumee_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/conumee.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘conumee’ 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
CNV.load,GenomicRatioSet: no visible global function definition for
  ‘assays’
CNV.load,matrix: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  anno assays
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
CNV.genomeplot      105.801  4.602 116.980
CNV.detailplot_wrap 103.570  3.348 107.144
CNV.detailplot      102.697  3.411 106.363
CNV.write           100.671  3.286 104.150
CNV.analysis-class   93.891  3.308  97.305
CNV.segment          93.448  1.325  94.894
CNV.fit              67.182  1.185  71.094
CNV.detail           60.212  1.935  62.290
CNV.bin              55.877  1.539  57.468
CNV.anno-class       50.202  1.729  51.985
CNV.create_anno      48.043  1.567  49.648
read.450k.url         9.136  0.730  16.197
* 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-3.14-bioc/meat/conumee.Rcheck/00check.log’
for details.



Installation output

conumee.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL conumee
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘conumee’ ...
** using staged installation
** R
** data
** 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 (conumee)

Tests output


Example timings

conumee.Rcheck/conumee-Ex.timings

nameusersystemelapsed
CNV.analysis-class93.891 3.30897.305
CNV.anno-class50.202 1.72951.985
CNV.bin55.877 1.53957.468
CNV.create_anno48.043 1.56749.648
CNV.data-class2.8220.1132.937
CNV.detail60.212 1.93562.290
CNV.detailplot102.697 3.411106.363
CNV.detailplot_wrap103.570 3.348107.144
CNV.fit67.182 1.18571.094
CNV.genomeplot105.801 4.602116.980
CNV.load1.7270.0133.127
CNV.segment93.448 1.32594.894
CNV.write100.671 3.286104.150
read.450k.url 9.136 0.73016.197