Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:26 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1020/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
isobar 1.45.0 (landing page) Florian P Breitwieser
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
Package: isobar |
Version: 1.45.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings isobar_1.45.0.tar.gz |
StartedAt: 2023-04-11 21:07:33 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 21:12:36 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 302.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: isobar.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings isobar_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/isobar.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘isobar/DESCRIPTION’ ... OK * this is package ‘isobar’ version ‘1.45.0’ * 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 loading without being on the library search path ... 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’ .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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed NoiseModel-class 9.755 0.28 10.035 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘isobar-devel.Rnw’... OK ‘isobar-ptm.Rnw’ using ‘UTF-8’... OK ‘isobar-usecases.Rnw’ using ‘UTF-8’... OK ‘isobar.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/isobar.Rcheck/00check.log’ for details.
isobar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL isobar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
isobar.Rcheck/isobar-Ex.timings
name | user | system | elapsed | |
IBSpectra-class | 0.347 | 0.007 | 0.355 | |
NoiseModel-class | 9.755 | 0.280 | 10.035 | |
ProteinGroup-class | 0.228 | 0.020 | 0.249 | |
TlsParameter-class | 0.001 | 0.000 | 0.001 | |
Tlsd-class | 0.001 | 0.000 | 0.001 | |
calculate-pvalues | 0.028 | 0.000 | 0.029 | |
calculate.dNSAF | 2.100 | 0.020 | 2.121 | |
calculate.emPAI | 0.257 | 0.016 | 0.272 | |
distr-methods | 0.055 | 0.007 | 0.063 | |
fit-distr | 4.273 | 0.115 | 4.389 | |
getPtmInfo | 0 | 0 | 0 | |
groupMemberPeptides | 0.347 | 0.008 | 0.355 | |
isobar-analysis | 0.248 | 0.000 | 0.249 | |
isobar-data | 0.210 | 0.004 | 0.214 | |
isobar-import | 1.653 | 0.064 | 1.718 | |
isobar-log | 0.665 | 0.053 | 0.717 | |
isobar-plots | 0.979 | 0.062 | 1.042 | |
isobar-preprocessing | 1.037 | 0.040 | 1.077 | |
number.ranges | 0 | 0 | 0 | |
observedKnownSites | 0.185 | 0.012 | 0.197 | |
peptide.count | 1.966 | 0.036 | 2.002 | |
proteinInfo-methods | 0.177 | 0.008 | 0.185 | |
proteinNameAndDescription | 0.232 | 0.006 | 0.238 | |
ratio-summ | 0.278 | 0.009 | 0.287 | |
sanitize | 0.000 | 0.000 | 0.001 | |
spectra.count2 | 0.267 | 0.008 | 0.275 | |
subsetIBSpectra | 1.632 | 0.004 | 1.637 | |
utils | 0 | 0 | 0 | |