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This page was generated on 2024-03-27 11:36:47 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1057/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.48.0  (landing page)
Florian P Breitwieser
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/isobar
git_branch: RELEASE_3_18
git_last_commit: b67e33a
git_last_commit_date: 2023-10-24 09:48:32 -0400 (Tue, 24 Oct 2023)
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 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for isobar on palomino4


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: 1.48.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:isobar.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings isobar_1.48.0.tar.gz
StartedAt: 2024-03-26 02:05:04 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 02:08:56 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 231.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: isobar.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:isobar.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings isobar_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/isobar.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.48.0'
* 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 whether package 'isobar' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") 
See 'F:/biocbuild/bbs-3.18-bioc/meat/isobar.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 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'
.plot.pairs: possible error in
  png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise
  Correlation plot", width = 1000, height = 1000, pointsize = 14):
  unused argument (title = "Pairwise Correlation plot")
.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
* 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 20.3   0.68   20.97
* 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: 3 WARNINGs, 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/isobar.Rcheck/00check.log'
for details.



Installation output

isobar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL isobar
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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"
Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") 
** 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-class0.420.040.47
NoiseModel-class20.30 0.6820.97
ProteinGroup-class0.230.000.23
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.030.000.03
calculate.dNSAF2.810.012.83
calculate.emPAI0.300.000.31
distr-methods0.060.000.11
fit-distr3.950.054.00
getPtmInfo000
groupMemberPeptides0.470.010.48
isobar-analysis0.250.000.25
isobar-data0.280.020.29
isobar-import1.720.001.72
isobar-log0.750.060.82
isobar-plots1.170.031.20
isobar-preprocessing1.330.031.36
number.ranges000
observedKnownSites0.250.020.26
peptide.count3.220.053.26
proteinInfo-methods0.200.030.24
proteinNameAndDescription0.270.000.26
ratio-summ0.340.030.38
sanitize000
spectra.count20.210.000.20
subsetIBSpectra1.570.041.62
utils000