############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSnbase.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MSnbase_2.33.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MSnbase.Rcheck' * using R Under development (unstable) (2025-01-21 r87610 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MSnbase/DESCRIPTION' ... OK * this is package 'MSnbase' version '2.33.2' * package encoding: UTF-8 * 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 'MSnbase' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... INFO installed size is 6.4Mb sub-directories of 1Mb or more: R 2.4Mb data 1.7Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Laurent Gatto [aut, cre] (ORCID: ) Johannes Rainer [aut, cre] (ORCID: ) Sebastian Gibb [aut, cre] (ORCID: ) * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE ':::' calls which should be '::': 'S4Vectors:::makeClassinfoRowForCompactPrinting' 'S4Vectors:::makePrettyMatrixForCompactPrinting' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'Biobase:::.showAnnotatedDataFrame' 'MALDIquant:::.estimateNoise' 'MALDIquant:::.localMaxima' 'MALDIquant:::.movingAverage' 'MALDIquant:::.savitzkyGolay' 'mzR:::.hasChromatograms' 'mzR:::.hasSpectra' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Chromatogram-class.Rd: closest FeaturesOfInterest-class.Rd: Versioned-class MIAPE-class.Rd: MIAME-class, MIAxE-class, Versioned-class MSnExp-class.Rd: AnnotatedDataFrame-class, phenoData, eSet-class, featureData, experimentData, protocolData, Versions-class, VersionedBiobase-class, Versioned-class, isolationWindow MSnProcess-class.Rd: Versioned-class MSnSet-class.Rd: eSet-class, ExpressionSet-class, AnnotatedDataFrame-class, AssayData-class, exprs, assayData, phenoData, featureData, experimentData, protocolData, Versions-class, VersionedBiobase-class, Versioned-class, impute, meanSdPlot, ma.plot, mva.pairs MSnSetList-class.Rd: AnnotatedDataFrame-class MSpectra.Rd: mcols, DataFrame, SimpleList OnDiskMSnExp-class.Rd: AnnotatedDataFrame-class, phenoData, featureData, experimentData, eSet-class, protocolData, Versions-class, VersionedBiobase-class, Versioned-class ProcessingStep-class.Rd: Versioned-class ReporterIons-class.Rd: Versioned-class Spectrum-class.Rd: Versioned-class Spectrum1-class.Rd: Versioned-class Spectrum2-class.Rd: Versioned-class combineFeatures.Rd: impute combineSpectra.Rd: bpparam extractSpectraData.Rd: DataFrame normToReference.Rd: exprs normalise-methods.Rd: vsn2 pSet-class.Rd: eSet-class, AnnotatedDataFrame-class, phenoData, featureData, experimentData, protocolData, Versions-class, VersionedBiobase-class, Versioned-class plotMzDelta-methods.Rd: geom_histogram readMSData.Rd: AnnotatedDataFrame-class readMSnSet.Rd: readExpressionSet, read.AnnotatedDataFrame, read.MIAME readMgfData.Rd: AnnotatedDataFrame-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/MSnbase/libs/x64/MSnbase.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed chromatogram-MSnExp-method 12.80 0.36 13.15 OnDiskMSnExp-class 8.80 0.18 9.25 averageMSnSet 6.21 0.51 8.72 estimateMzResolution 5.45 0.43 5.84 imageNA2 5.09 0.41 5.50 MSnSet-class 4.93 0.34 5.27 aggvar 5.16 0.07 5.23 plot-methods 5.10 0.06 5.16 combineSpectra 4.72 0.11 5.55 extractSpectraData 3.72 0.24 5.11 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: ── Error ('test_MSmap.R:6:1'): (code run outside of `test_that()`) ───────────── Error in `fix_issue_17(x)`: Can't access URL(s): Backtrace: ▆ 1. └─rpx::PXDataset("PXD000001") at test_MSmap.R:6:1 2. └─rpx:::get_url(px_metadata[["_links"]]$datasetFtpUrl$href) 3. └─rpx:::fix_issue_17(x) [ FAIL 1 | WARN 1092 | SKIP 12 | PASS 2355 ] Error: Test failures In addition: Warning message: In for (i in seq_len(n)) { : closing unused connection 4 (E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpKg8RlB\file30c022863033) Execution halted * 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: 1 ERROR, 4 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/MSnbase.Rcheck/00check.log' for details.