############################################################################## ############################################################################## ### ### 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_1.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/isobar.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘isobar/DESCRIPTION’ ... OK * this is package ‘isobar’ version ‘1.53.0’ * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/isobar.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 .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 : : 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(s) in Rd file 'IBSpectra-class.Rd': ‘[MSnbase]{MSnbase}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: IBSpectra-class.Rd: eSet, AssayData, AnnotatedDataFrame-class, fData, AnnotatedDataFrame, MIAME TlsParameter-class.Rd: OptionalParameter-class Tlsd-class.Rd: AcDcLcDistribution-class, UnivDistrListOrDistribution-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... WARNING Output for data("noise.model.hcd", package = "isobar"): Warning: program compiled against libxml 212 using older 211 * checking data for non-ASCII characters ... WARNING Warning: program compiled against libxml 212 using older 211 * 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 8.691 0.343 9.048 * 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: 9 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/isobar.Rcheck/00check.log’ for details.