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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1072/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.50.0  (landing page)
Florian P Breitwieser
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/isobar
git_branch: RELEASE_3_19
git_last_commit: 2f05a5d
git_last_commit_date: 2024-04-30 10:26:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 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 isobar on nebbiolo1

To the developers/maintainers of the isobar package:
- 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 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: isobar
Version: 1.50.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings isobar_1.50.0.tar.gz
StartedAt: 2024-06-20 00:25:44 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 00:29:51 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 246.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: isobar.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings isobar_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/isobar.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.50.0’
* 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 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* 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 ... WARNING
checkRd: (5) ProteinGroup-class.Rd:119-128: \item in \describe must have non-empty label
checkRd: (-1) getPhosphoRSProbabilities.Rd:83: Lost braces; missing escapes or markup?
    83 |     spectrum -> {peptide 1, peptides 2, ...} -> {peptide}.
       |                 ^
checkRd: (-1) getPhosphoRSProbabilities.Rd:83: Lost braces; missing escapes or markup?
    83 |     spectrum -> {peptide 1, peptides 2, ...} -> {peptide}.
       |                                                 ^
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file '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 Rd file 'peptide.count.Rd':
  ‘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 ... NOTE
Argument items with no description in Rd file 'maplot.protein.Rd':
  ‘add’
* 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
NoiseModel-class 9.022  0.991  10.013
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/isobar.Rcheck/00check.log’
for details.


Installation output

isobar.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL isobar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-class0.3410.0160.357
NoiseModel-class 9.022 0.99110.013
ProteinGroup-class0.2230.0210.243
TlsParameter-class0.0010.0000.001
Tlsd-class0.0010.0000.001
calculate-pvalues0.0240.0000.023
calculate.dNSAF1.9960.0282.024
calculate.emPAI0.2540.0110.265
distr-methods0.0330.0150.050
fit-distr3.1940.0993.294
getPtmInfo0.0010.0010.000
groupMemberPeptides0.2250.0150.240
isobar-analysis0.2220.0130.235
isobar-data0.1700.0190.189
isobar-import0.7380.0160.755
isobar-log0.6720.0470.720
isobar-plots1.0110.0711.082
isobar-preprocessing1.1050.0241.129
number.ranges0.0010.0000.001
observedKnownSites0.1960.0040.200
peptide.count2.2020.0402.242
proteinInfo-methods0.1890.0010.190
proteinNameAndDescription0.2190.0100.229
ratio-summ0.2960.0080.305
sanitize0.0010.0000.000
spectra.count20.2350.0120.246
subsetIBSpectra1.5710.0601.631
utils0.0010.0000.000