############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Aerith.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Aerith_0.99.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck’ * using R Under development (unstable) (2025-11-04 r88984) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.8 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Aerith/DESCRIPTION’ ... OK * this is package ‘Aerith’ version ‘0.99.11’ * 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 ‘Aerith’ can be installed ... WARNING Found the following significant warnings: filterPSMs.cpp:23:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:24:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:25:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:26:52: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:27:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:28:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:29:51: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:30:42: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:31:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:32:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:33:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:34:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:35:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:36:53: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:37:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:38:53: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:39:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:40:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:41:56: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPSMs.cpp:42:47: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:34:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:35:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:36:45: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:85:62: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:86:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:87:62: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:88:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:89:71: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:90:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:91:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:92:67: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:93:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] filterPeptides.cpp:94:61: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] getISOpeak.cpp:344:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] getISOpeak.cpp:344:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] getISOpeak.cpp:345:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] getISOpeak.cpp:400:37: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] getISOpeak.cpp:401:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] getISOpeak.cpp:401:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:138:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:139:68: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:140:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:141:67: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:142:72: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:143:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:270:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:271:68: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:272:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:273:67: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:274:72: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] readScans.cpp:275:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] scorePSM.cpp:431:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:431:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:431:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:432:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:432:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:432:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:578:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:578:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:578:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:579:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:579:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] scorePSM.cpp:579:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference] See ‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 8.3Mb sub-directories of 1Mb or more: extdata 5.2Mb libs 1.2Mb png 1.6Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘ggnewscale’ ‘methods’ ‘tidyr’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cal_isotope_abundance_fft: no visible global function definition for ‘fft’ cal_isotope_numbers: no visible global function definition for ‘rmultinom’ getPrecursorSpectra: no visible global function definition for ‘new’ getRealScan: no visible global function definition for ‘head’ getRealScanFromList: no visible global function definition for ‘new’ getRealScanWithCharge: no visible global function definition for ‘new’ getSipBYionSpectra: no visible global function definition for ‘new’ getSipPrecursorSpectra: no visible global function definition for ‘new’ isotope_abundance_fft: no visible global function definition for ‘fft’ plotFilteredPCTIntensitySummary: no visible binding for global variable ‘log2_intensity’ plotFilteredPCTIntensitySummary: no visible binding for global variable ‘MS1IsotopicAbundances’ plotMolecularFFTisotopes: no visible binding for global variable ‘MZ’ plotMolecularFFTisotopes: no visible binding for global variable ‘Prob’ plotMolecularIsotopes: no visible binding for global variable ‘MZ’ plotMolecularIsotopes: no visible global function definition for ‘desc’ plotMolecularIsotopes: no visible binding for global variable ‘Prob’ plotMolecularIsotopes: no visible binding for global variable ‘Formula’ plotPSMannotation: no visible global function definition for ‘new’ plotPSMsipPCT: no visible global function definition for ‘read.table’ plotPSMsipPCT: no visible global function definition for ‘median’ plotPrecursorMzFrequency: no visible binding for global variable ‘mz’ plotPrecursorMzFrequency: no visible binding for global variable ‘time’ plotPrecursorMzFrequency: no visible binding for global variable ‘Frequency’ plotPrecursorMzFrequency: no visible global function definition for ‘topo.colors’ plotProSipPct: no visible global function definition for ‘read.table’ plotProSipPct: no visible global function definition for ‘median’ plotProSipPct: no visible global function definition for ‘sd’ plotProSipPct: no visible binding for global variable ‘Abundance’ plotRealScan: no visible binding for global variable ‘MZ’ plotRealScan: no visible binding for global variable ‘Prob’ plotRealScan: no visible binding for global variable ‘Kind’ plotSIPfilteredPCTIntensityBySample: no visible binding for global variable ‘log2_intensity’ plotSIPfilteredPCTIntensityBySample: no visible binding for global variable ‘MS1IsotopicAbundances’ plotScanFrequency: no visible binding for global variable ‘RetentionTime’ plotScanFrequency: no visible binding for global variable ‘Kind’ plotScoreDistribution: no visible binding for global variable ‘MassError’ plotScoreDistribution: no visible binding for global variable ‘scores’ plotScoreDistribution: no visible binding for global variable ‘IsDecoy’ plotScoreDistribution: no visible binding for global variable ‘parentCharges’ plotSipBYionLabel: no visible binding for global variable ‘Label’ plotSipBYionLabel: no visible binding for global variable ‘MZ’ plotSipBYionLabel: no visible binding for global variable ‘x’ plotSipBYionLabel: no visible binding for global variable ‘y’ plotTIC: no visible binding for global variable ‘RetentionTime’ plotTIC: no visible binding for global variable ‘RelativeTic’ readPSMtsv: no visible global function definition for ‘read.table’ readPepXMLtable: no visible global function definition for ‘across’ readPepXMLtable: no visible global function definition for ‘all_of’ readPepXMLtable: no visible binding for global variable ‘DatabaseAccess’ readPepXMLtable: no visible binding for global variable ‘DatabaseDescription’ summaryPSMsipPCT: no visible global function definition for ‘read.table’ summaryPSMsipPCT: no visible global function definition for ‘median’ summaryPSMsipPCT: no visible global function definition for ‘mad’ summaryPSMsipPCT: no visible global function definition for ‘sd’ summary_isotopic_df: no visible global function definition for ‘desc’ summary_isotopic_df: no visible binding for global variable ‘Count’ plot,AAspectra-missing: no visible binding for global variable ‘MZ’ plot,AAspectra-missing: no visible binding for global variable ‘Prob’ plot,AAspectra-missing: no visible binding for global variable ‘Kind’ Undefined global functions or variables: Abundance Count DatabaseAccess DatabaseDescription Formula Frequency IsDecoy Kind Label MS1IsotopicAbundances MZ MassError Prob RelativeTic RetentionTime across all_of desc fft head log2_intensity mad median mz new parentCharges read.table rmultinom scores sd time topo.colors x y Consider adding importFrom("grDevices", "topo.colors") importFrom("methods", "new") importFrom("stats", "fft", "mad", "median", "rmultinom", "sd", "time") importFrom("utils", "head", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Argument items with no description in Rd file 'plotRealScan.Rd': ‘linewidth’ * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/Makevars Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Aerith/libs/Aerith.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++) Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++) Found ‘_exit’, possibly from ‘exit’ (C) 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 readMgf 5.228 0.141 5.53 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 ‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck/00check.log’ for details.