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This page was generated on 2021-12-06 13:05:51 -0500 (Mon, 06 Dec 2021).

CHECK results for BRAIN on machv2

To the developers/maintainers of the BRAIN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BRAIN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 209/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRAIN 1.40.0  (landing page)
Piotr Dittwald
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/BRAIN
git_branch: RELEASE_3_14
git_last_commit: 1598666
git_last_commit_date: 2021-10-26 12:02:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BRAIN
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BRAIN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BRAIN_1.40.0.tar.gz
StartedAt: 2021-12-05 12:25:13 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 12:26:46 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 92.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BRAIN.Rcheck
Warnings: 2

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BRAIN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BRAIN_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BRAIN.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BRAIN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BRAIN’ version ‘1.40.0’
* 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 ‘BRAIN’ 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
Package in Depends field not imported from: ‘Biostrings’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... WARNING
Codoc mismatches from documentation object 'calculateIsotopicProbabilities':
calculateIsotopicProbabilities
  Code: function(aC, stopOption = "nrPeaks", nrPeaks = NULL, coverage =
                 NULL, abundantEstim = NULL, approx = FALSE,
                 approxStart = 1, approxParam = NULL)
  Docs: function(aC, stopOption = "nrPeaks", nrPeaks, coverage,
                 abundantEstim)
  Argument names in code not in docs:
    approx approxStart approxParam
  Mismatches in argument default values:
    Name: 'nrPeaks' Code: NULL Docs: 
    Name: 'coverage' Code: NULL Docs: 
    Name: 'abundantEstim' Code: NULL Docs: 

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'useBRAIN2':
  useBRAIN2(aC, stopOption = "nrPeaks", nrPeaks, approxStart = 1, approxParam = NULL))

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BRAIN.Rcheck/00check.log’
for details.



Installation output

BRAIN.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BRAIN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BRAIN’ ...
** 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 (BRAIN)

Tests output


Example timings

BRAIN.Rcheck/BRAIN-Ex.timings

nameusersystemelapsed
BRAIN-package0.2720.0260.297
calculateAverageMass000
calculateIsotopicProbabilities0.0480.0040.052
calculateMonoisotopicMass0.0010.0000.000
calculateNrPeaks000
getAtomsFromSeq0.0040.0000.005
useBRAIN0.3520.0160.368
useBRAIN20.1970.0260.222