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CHECK report for mBPCR on malbec1

This page was generated on 2021-05-06 12:28:09 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the mBPCR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1018/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mBPCR 1.44.0  (landing page)
P.M.V. Rancoita
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/mBPCR
Branch: RELEASE_3_12
Last Commit: d64dedf
Last Changed Date: 2020-10-27 10:36:15 -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  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: mBPCR
Version: 1.44.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:mBPCR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings mBPCR_1.44.0.tar.gz
StartedAt: 2021-05-06 03:07:36 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:11:45 -0400 (Thu, 06 May 2021)
EllapsedTime: 248.7 seconds
RetCode: 0
Status:   OK  
CheckDir: mBPCR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:mBPCR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings mBPCR_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/mBPCR.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 ‘mBPCR/DESCRIPTION’ ... OK
* this is package ‘mBPCR’ version ‘1.44.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mBPCR’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotEstProfile      10.396  0.020  10.434
estProfileWithMBPCR  5.024  0.044   5.072
* 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: OK


Installation output

mBPCR.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL mBPCR
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘mBPCR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path
* DONE (mBPCR)

Tests output


Example timings

mBPCR.Rcheck/mBPCR-Ex.timings

nameusersystemelapsed
centromere0.0040.0000.006
computeMBPCR2.6040.0402.648
estGlobParam0.0080.0000.007
estProfileWithMBPCR5.0240.0445.072
estProfileWithMBPCRforOligoSnpSet0.0000.0000.001
importCNData0.0920.0000.127
logAdd0.0000.0000.001
plotEstProfile10.396 0.02010.434
writeEstProfile4.0240.0044.035