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CHECK report for conumee on malbec1

This page was generated on 2021-05-06 12:27:14 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the conumee package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 370/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.24.0  (landing page)
Volker Hovestadt
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/conumee
Branch: RELEASE_3_12
Last Commit: 0be6400
Last Changed Date: 2020-10-27 11:04:42 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: conumee
Version: 1.24.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings conumee_1.24.0.tar.gz
StartedAt: 2021-05-06 00:23:01 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:57:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 2064.6 seconds
RetCode: 0
Status:   OK  
CheckDir: conumee.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings conumee_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/conumee.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.24.0’
* 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.detailplot_wrap 91.408  0.448  92.019
CNV.genomeplot      88.676  0.504  94.550
CNV.write           84.856  0.696  85.700
CNV.analysis-class  82.216  1.108  84.076
CNV.detailplot      80.328  0.320  80.753
CNV.segment         75.600  0.096  75.823
CNV.fit             46.980  0.016  47.094
CNV.detail          41.692  0.096  41.835
CNV.bin             38.848  0.024  38.917
CNV.anno-class      36.048  0.128  36.226
CNV.create_anno     32.160  0.012  32.238
read.450k.url       13.488  0.276  20.298
* 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-3.12-bioc/meat/conumee.Rcheck/00check.log’
for details.



Installation output

conumee.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL conumee
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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-class82.216 1.10884.076
CNV.anno-class36.048 0.12836.226
CNV.bin38.848 0.02438.917
CNV.create_anno32.160 0.01232.238
CNV.data-class3.4120.0123.426
CNV.detail41.692 0.09641.835
CNV.detailplot80.328 0.32080.753
CNV.detailplot_wrap91.408 0.44892.019
CNV.fit46.980 0.01647.094
CNV.genomeplot88.676 0.50494.550
CNV.load4.0760.1484.226
CNV.segment75.600 0.09675.823
CNV.write84.856 0.69685.700
read.450k.url13.488 0.27620.298