Florian P Breitwieser
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/isobar |
| git_branch: master |
| git_last_commit: b3b8f9b |
| git_last_commit_date: 2021-10-26 12:01:00 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 963/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| isobar 1.41.0 (landing page) Florian P Breitwieser
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: isobar |
| Version: 1.41.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:isobar.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings isobar_1.41.0.tar.gz |
| StartedAt: 2022-03-17 19:23:50 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:26:48 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 177.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: isobar.Rcheck |
| Warnings: 3 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:isobar.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings isobar_1.41.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/isobar.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.41.0'
* 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 'D:/biocbuild/bbs-3.15-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 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'
.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 ... 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NoiseModel-class 9.67 0.39 10.24
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/isobar.Rcheck/00check.log'
for details.
isobar.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL isobar
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'isobar'
finding HTML links ... done
IBSpectra-class html
finding level-2 HTML links ... done
NoiseModel-class html
ProteinGroup-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-isobar/00new/isobar/help/ProteinGroup.html
TlsParameter-class html
Tlsd-class html
calc.delta.score html
calc.startpos html
calculate-pvalues html
calculate.dNSAF html
calculate.emPAI html
correct.peptide.ratios html
distr-methods html
fit-distr html
getPeptideModifContext html
getPhosphoRSProbabilities html
getPtmInfo html
groupMemberPeptides html
human.protein.names html
isobar-analysis html
isobar-data html
isobar-import html
isobar-log html
isobar-package html
isobar-plots html
isobar-preprocessing html
isobar-reports html
maplot.protein html
number.ranges html
observedKnownSites html
peptide.count html
proteinInfo-methods html
proteinNameAndDescription html
ratio-summ html
ratiosReshapeWide html
reporter.protein-methods html
sanitize html
shared.ratios html
shared.ratios.sign html
specificities html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-isobar/00new/isobar/help/UNSPECIFIC.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-isobar/00new/isobar/help/SPECIFICITIES.html
spectra.count2 html
subsetIBSpectra html
utils html
writeHscoreData html
writeIBSpectra html
** 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)
Making 'packages.html' ... done
isobar.Rcheck/isobar-Ex.timings
| name | user | system | elapsed | |
| IBSpectra-class | 0.19 | 0.08 | 0.26 | |
| NoiseModel-class | 9.67 | 0.39 | 10.24 | |
| ProteinGroup-class | 0.25 | 0.03 | 0.28 | |
| TlsParameter-class | 0 | 0 | 0 | |
| Tlsd-class | 0 | 0 | 0 | |
| calculate-pvalues | 0.03 | 0.00 | 0.03 | |
| calculate.dNSAF | 2.69 | 0.24 | 2.92 | |
| calculate.emPAI | 0.25 | 0.05 | 0.32 | |
| distr-methods | 0.05 | 0.01 | 0.06 | |
| fit-distr | 4.00 | 0.22 | 4.22 | |
| getPtmInfo | 0 | 0 | 0 | |
| groupMemberPeptides | 0.31 | 0.00 | 0.31 | |
| isobar-analysis | 0.22 | 0.05 | 0.26 | |
| isobar-data | 0.18 | 0.00 | 0.19 | |
| isobar-import | 0.66 | 0.20 | 0.86 | |
| isobar-log | 0.83 | 0.03 | 0.86 | |
| isobar-plots | 1.28 | 0.11 | 1.42 | |
| isobar-preprocessing | 1.05 | 0.23 | 1.28 | |
| number.ranges | 0 | 0 | 0 | |
| observedKnownSites | 0.15 | 0.02 | 0.17 | |
| peptide.count | 1.80 | 0.05 | 1.85 | |
| proteinInfo-methods | 0.23 | 0.00 | 0.23 | |
| proteinNameAndDescription | 0.24 | 0.04 | 0.28 | |
| ratio-summ | 0.39 | 0.00 | 0.39 | |
| sanitize | 0 | 0 | 0 | |
| spectra.count2 | 0.23 | 0.02 | 0.25 | |
| subsetIBSpectra | 1.63 | 0.03 | 1.66 | |
| utils | 0 | 0 | 0 | |