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CHECK report for PROcess on celaya2

This page was generated on 2019-10-16 12:44:59 -0400 (Wed, 16 Oct 2019).

Package 1252/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PROcess 1.60.0
Xiaochun Li
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PROcess
Branch: RELEASE_3_9
Last Commit: 08e2abe
Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PROcess
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PROcess.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PROcess_1.60.0.tar.gz
StartedAt: 2019-10-16 05:44:28 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:45:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 81.4 seconds
RetCode: 0
Status:  OK 
CheckDir: PROcess.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PROcess.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PROcess_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PROcess.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PROcess/DESCRIPTION’ ... OK
* this is package ‘PROcess’ version ‘1.60.0’
* 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 ‘PROcess’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Icens’
A package should be listed in only one of these fields.
* 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
gelmap: warning in axis(1, at = at.mz, lab = at.mz, las = 2, lty = 0,
  cex.axis = 0.8): partial argument match of 'lab' to 'labels'
gelmap: warning in axis(2, at = at.col, lab = sampLab[at.col], las = 2,
  lty = 0, cex.axis = cexCol): partial argument match of 'lab' to
  'labels'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
quality 5.729  0.284   6.015
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/PROcess.Rcheck/00check.log’
for details.



Installation output

PROcess.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PROcess
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PROcess’ ...
** using staged installation
** R
** 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 (PROcess)

Tests output


Example timings

PROcess.Rcheck/PROcess-Ex.timings

nameusersystemelapsed
aveSpec0.3880.0550.445
bslnoff0.4530.0210.475
getPeaks4.3980.1834.585
intg0.0020.0010.002
is.multiple0.0010.0010.002
isPeak2.9370.1303.070
peaks0.0550.0020.058
pk2bmkr4.2560.1394.396
quality5.7290.2846.015
renorm0.8000.0150.814
rmBaseline0.7090.0110.721
specZoom2.6980.1042.805