Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1063/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
isobar 1.52.0 (landing page) Florian P Breitwieser
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: isobar |
Version: 1.52.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings isobar_1.52.0.tar.gz |
StartedAt: 2024-11-20 09:09:57 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 09:14:07 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 249.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: isobar.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings isobar_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/isobar.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘isobar/DESCRIPTION’ ... OK * this is package ‘isobar’ version ‘1.52.0’ * 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 8.962 0.215 9.198 * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/isobar.Rcheck/00check.log’ for details.
isobar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL isobar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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)
isobar.Rcheck/isobar-Ex.timings
name | user | system | elapsed | |
IBSpectra-class | 0.380 | 0.004 | 0.385 | |
NoiseModel-class | 8.962 | 0.215 | 9.198 | |
ProteinGroup-class | 0.238 | 0.008 | 0.247 | |
TlsParameter-class | 0.001 | 0.000 | 0.002 | |
Tlsd-class | 0.001 | 0.000 | 0.001 | |
calculate-pvalues | 0.035 | 0.000 | 0.036 | |
calculate.dNSAF | 2.387 | 0.016 | 2.408 | |
calculate.emPAI | 0.287 | 0.004 | 0.293 | |
distr-methods | 0.057 | 0.004 | 0.063 | |
fit-distr | 3.566 | 0.080 | 3.653 | |
getPtmInfo | 0.001 | 0.000 | 0.001 | |
groupMemberPeptides | 0.289 | 0.000 | 0.289 | |
isobar-analysis | 0.940 | 0.032 | 0.973 | |
isobar-data | 0.196 | 0.004 | 0.200 | |
isobar-import | 0.855 | 0.036 | 0.893 | |
isobar-log | 1.027 | 0.067 | 1.097 | |
isobar-plots | 1.334 | 0.016 | 1.353 | |
isobar-preprocessing | 1.363 | 0.055 | 1.421 | |
number.ranges | 0.001 | 0.000 | 0.000 | |
observedKnownSites | 0.267 | 0.012 | 0.279 | |
peptide.count | 2.461 | 0.004 | 2.470 | |
proteinInfo-methods | 0.200 | 0.004 | 0.205 | |
proteinNameAndDescription | 0.266 | 0.004 | 0.270 | |
ratio-summ | 0.311 | 0.004 | 0.316 | |
sanitize | 0.001 | 0.000 | 0.001 | |
spectra.count2 | 0.264 | 0.000 | 0.265 | |
subsetIBSpectra | 2.181 | 0.032 | 2.218 | |
utils | 0.000 | 0.000 | 0.001 | |