############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSnbase_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSnbase.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSnbase/DESCRIPTION’ ... OK * this is package ‘MSnbase’ version ‘2.26.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘MSnbase’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: R 1.8Mb data 1.9Mb * 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] () Johannes Rainer [aut, cre] () Sebastian Gibb [aut, cre] () * 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 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 ... OK * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed chromatogram-MSnExp-method 12.396 0.271 21.747 MSnSet-class 9.276 0.278 14.613 OnDiskMSnExp-class 8.314 0.172 12.914 averageMSnSet 5.921 0.427 9.574 estimateMzResolution 5.456 0.192 8.590 aggvar 4.369 0.078 6.815 combineSpectra 4.101 0.065 6.350 plot-methods 3.789 0.093 7.039 imageNA2 3.432 0.142 5.514 missing-data 3.420 0.141 5.802 quantify-methods 3.085 0.040 5.640 MzTab-class 0.543 0.047 5.939 * 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: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_MSmap.R:7:1'): (code run outside of `test_that()`) ───────────── Error in `.local(object, ...)`: No files to download. Backtrace: ▆ 1. ├─rpx::pxget(px1, "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML") at test_MSmap.R:7:0 2. └─rpx::pxget(px1, "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML") 3. └─rpx (local) .local(object, ...) [ FAIL 1 | WARN 1092 | SKIP 12 | PASS 2372 ] Error: Test failures In addition: Warning message: In for (i in seq_len(n)) { : closing unused connection 4 (/tmp/Rtmp0y38FK/file10ac47b97fb76) Execution halted * 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: 1 ERROR, 4 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSnbase.Rcheck/00check.log’ for details.