Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for alsace on malbec1

This page was generated on 2020-08-11 11:19:52 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE alsace PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 46/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.25.0
Ron Wehrens
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/alsace
Branch: master
Last Commit: 1b7cacd
Last Changed Date: 2020-04-27 14:38:51 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alsace
Version: 1.25.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:alsace.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings alsace_1.25.0.tar.gz
StartedAt: 2020-08-11 00:35:29 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 00:36:27 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 58.0 seconds
RetCode: 0
Status:  OK 
CheckDir: alsace.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:alsace.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings alsace_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/alsace.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alsace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alsace’ version ‘1.25.0’
* 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 ‘alsace’ 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 ... NOTE
'library' or 'require' call to ‘lattice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  ‘stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.abline’
Undefined global functions or variables:
  panel.abline panel.stripplot stripplot
* 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
components 12.36   0.02  12.412
teaMerged   6.58   0.00   6.596
doALS       5.10   0.00   5.104
* 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/alsace.Rcheck/00check.log’
for details.



Installation output

alsace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL alsace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘alsace’ ...
** using staged installation
** R
** data
** 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 (alsace)

Tests output


Example timings

alsace.Rcheck/alsace-Ex.timings

nameusersystemelapsed
components12.360 0.02012.412
correctPeaks3.7560.0003.760
correctRT2.0840.0002.088
doALS5.1000.0005.104
filterPeaks0.0280.0000.030
fitpeaks4.2800.0044.286
getAllPeaks0.0360.0000.036
getPeakTable2.2240.0002.235
opa1.0760.0041.080
preprocess0.1000.0040.102
showALSresult0.0840.0000.086
tea0.1040.0040.107
teaMerged6.5800.0006.596
windows0.1480.0040.151