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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 231/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRAIN 1.51.0  (landing page)
Piotr Dittwald
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BRAIN
git_branch: devel
git_last_commit: 2dec858
git_last_commit_date: 2024-04-30 10:27:08 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for BRAIN on kjohnson1

To the developers/maintainers of the BRAIN package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BRAIN
Version: 1.51.0
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_1.51.0.tar.gz
StartedAt: 2024-06-10 13:29:54 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 13:30:46 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 52.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BRAIN.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running 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_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BRAIN.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BRAIN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BRAIN’ version ‘1.51.0’
* 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 code 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 ... NOTE
checkRd: (-1) useBRAIN.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) useBRAIN.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) useBRAIN.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) useBRAIN.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) useBRAIN2.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'calculateIsotopicProbabilities.Rd':
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 Rd file 'useBRAIN2.Rd':
  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 ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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-package0.1490.0270.176
calculateAverageMass000
calculateIsotopicProbabilities0.0510.0080.059
calculateMonoisotopicMass000
calculateNrPeaks0.0000.0000.001
getAtomsFromSeq0.0050.0000.005
useBRAIN0.1340.0110.145
useBRAIN20.4320.0170.449