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CHECK report for conumee on malbec2

This page was generated on 2020-10-17 11:54:36 -0400 (Sat, 17 Oct 2020).

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 367/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.22.0
Volker Hovestadt
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/conumee
Branch: RELEASE_3_11
Last Commit: 1c77cd9
Last Changed Date: 2020-04-27 14:48:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  TIMEOUT  OK 

Summary

Package: conumee
Version: 1.22.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings conumee_1.22.0.tar.gz
StartedAt: 2020-10-17 00:13:21 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:46:09 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 1967.9 seconds
RetCode: 0
Status:  OK 
CheckDir: conumee.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings conumee_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/conumee.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.22.0’
* 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      76.227  0.604  76.891
CNV.detailplot_wrap 75.779  0.399  87.632
CNV.write           73.212  0.632  73.860
CNV.genomeplot      72.263  0.476  72.756
CNV.segment         72.448  0.232  72.711
CNV.analysis-class  71.345  0.955  72.694
CNV.bin             46.626  0.148  46.776
CNV.fit             44.896  0.128  45.024
CNV.detail          40.534  0.184  40.726
CNV.anno-class      39.477  0.005  39.493
CNV.create_anno     31.147  0.000  31.158
read.450k.url        9.324  0.233  18.511
* 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-3.11-bioc/meat/conumee.Rcheck/00check.log’
for details.



Installation output

conumee.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL conumee
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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-class71.345 0.95572.694
CNV.anno-class39.477 0.00539.493
CNV.bin46.626 0.14846.776
CNV.create_anno31.147 0.00031.158
CNV.data-class2.2870.0962.383
CNV.detail40.534 0.18440.726
CNV.detailplot76.227 0.60476.891
CNV.detailplot_wrap75.779 0.39987.632
CNV.fit44.896 0.12845.024
CNV.genomeplot72.263 0.47672.756
CNV.load2.3800.1322.513
CNV.segment72.448 0.23272.711
CNV.write73.212 0.63273.860
read.450k.url 9.324 0.23318.511