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This page was generated on 2022-06-24 12:07:38 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for isobar on merida1


To the developers/maintainers of the isobar package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/isobar.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 985/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.42.0  (landing page)
Florian P Breitwieser
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/isobar
git_branch: RELEASE_3_15
git_last_commit: 98ed1a6
git_last_commit_date: 2022-04-26 11:09:31 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: isobar
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:isobar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings isobar_1.42.0.tar.gz
StartedAt: 2022-06-24 04:17:11 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:23:27 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 376.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: isobar.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:isobar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings isobar_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/isobar.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.42.0’
* 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 ‘isobar’ 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.as.matrix’ ‘.as.vect’ ‘.convertPeptideModif’
  ‘.proteinGroupAsConciseDataFrame’ ‘.read.idfile’ ‘.sum.bool’
* checking S3 generic/method consistency ... WARNING
sequence:
  function(nvec, ...)
sequence.coverage:
  function(protein.group, protein.g, specificity, simplify, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  as.data.frame.IBSpectra as.data.frame.ProteinGroup plot.NoiseModel
  sequence.coverage summary.ProteinGroup
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcProbXGreaterThanY.orig: no visible global function definition for
  ‘d’
.read.peaklist: no visible binding for global variable ‘type’
.round.distr: no visible global function definition for ‘param’
.write.summarized.table: no visible binding for global variable ‘name’
distrprint: no visible global function definition for ‘param’
distrprint : <anonymous>: no visible global function definition for
  ‘param’
shared.ratios.sign: no visible binding for global variable ‘ratio’
shared.ratios.sign: no visible binding for global variable ‘g’
spectra.count2: no visible binding for global variable ‘peptide’
twodistr.plot: no visible global function definition for ‘d’
ProteinGroup,data.frame-missing: no visible binding for global variable
  ‘peptide’
coerce,IBSpectra-MSnSet: no visible global function definition for ‘mz’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘o’
coerce,MSnSet-IBSpectra: no visible global function definition for
  ‘qual’
df,Tlsd: no visible global function definition for ‘param’
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
  visible binding for global variable ‘i’
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
  visible binding for global variable ‘i’
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
  global variable ‘center.var’
location,Tlsd: no visible global function definition for ‘param’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘pch’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘noise.model.col’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘pch.p’
scale,Tlsd: no visible global function definition for ‘param’
Undefined global functions or variables:
  center.var d g i mz name noise.model.col o param pch pch.p peptide
  qual ratio type
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IBSpectra-class.Rd':
  ‘[MSnbase]{MSnbase}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'peptide.count':
  ‘sequence.coverage’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
NoiseModel-class 13.273  0.419  14.104
fit-distr         4.877  0.097   5.007
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/isobar.Rcheck/00check.log’
for details.



Installation output

isobar.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL isobar
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘isobar’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘coerce’ with signature ‘"MSnSet","IBSpectra"’: no definition for class “MSnSet”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “MSnSet”
** 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 (isobar)

Tests output


Example timings

isobar.Rcheck/isobar-Ex.timings

nameusersystemelapsed
IBSpectra-class0.5930.0200.621
NoiseModel-class13.273 0.41914.104
ProteinGroup-class0.3940.0050.406
TlsParameter-class0.0010.0010.002
Tlsd-class0.0010.0000.002
calculate-pvalues0.0550.0000.056
calculate.dNSAF3.7640.0953.972
calculate.emPAI0.4470.0050.466
distr-methods0.0860.0050.091
fit-distr4.8770.0975.007
getPtmInfo000
groupMemberPeptides0.5880.0120.605
isobar-analysis0.4190.0060.427
isobar-data0.3680.0050.380
isobar-import2.2470.0232.287
isobar-log1.6370.0531.701
isobar-plots1.8240.0651.901
isobar-preprocessing1.8510.0851.956
number.ranges000
observedKnownSites0.5870.0200.610
peptide.count3.8700.1334.053
proteinInfo-methods0.3150.0030.320
proteinNameAndDescription0.4160.0040.428
ratio-summ0.4850.0090.504
sanitize0.0000.0010.001
spectra.count20.4400.0050.447
subsetIBSpectra3.2230.0193.308
utils0.0000.0000.001