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This page was generated on 2022-06-27 11:09:51 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


To the developers/maintainers of the conumee package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org: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 405/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.30.0  (landing page)
Volker Hovestadt
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/conumee
git_branch: RELEASE_3_15
git_last_commit: d79a2eb
git_last_commit_date: 2022-04-26 11:25:02 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: conumee
Version: 1.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings conumee_1.30.0.tar.gz
StartedAt: 2022-06-26 19:19:47 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 19:47:04 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 1637.2 seconds
RetCode: 0
Status:   OK  
CheckDir: conumee.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings conumee_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/conumee.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.30.0’
* 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.write           55.199  2.048  57.248
CNV.detailplot_wrap 54.489  2.352  56.842
CNV.detailplot      54.373  1.826  56.200
CNV.genomeplot      53.721  1.860  55.581
CNV.analysis-class  50.120  1.468  51.657
CNV.segment         49.406  0.480  49.886
CNV.detail          29.781  0.472  30.253
CNV.bin             29.714  0.240  29.955
CNV.fit             28.935  0.528  29.464
CNV.anno-class      24.806  0.560  25.366
CNV.create_anno     23.518  0.260  23.777
read.450k.url        7.296  0.405  11.210
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/conumee.Rcheck/00check.log’
for details.



Installation output

conumee.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL conumee
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-class50.120 1.46851.657
CNV.anno-class24.806 0.56025.366
CNV.bin29.714 0.24029.955
CNV.create_anno23.518 0.26023.777
CNV.data-class2.2370.0242.261
CNV.detail29.781 0.47230.253
CNV.detailplot54.373 1.82656.200
CNV.detailplot_wrap54.489 2.35256.842
CNV.fit28.935 0.52829.464
CNV.genomeplot53.721 1.86055.581
CNV.load2.0420.0882.129
CNV.segment49.406 0.48049.886
CNV.write55.199 2.04857.248
read.450k.url 7.296 0.40511.210