############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ptairMS_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘ptairMS’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ See ‘/home/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck/00install.out’ for details. * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘htmlwidgets’ ‘plyr’ There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’ ‘processFileTemporalNominalMass’ ‘tofToMz’ * 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 Non-topic package-anchored link(s) in Rd file 'detectPeak.Rd': ‘[ptairMS]{ptrSet}’ 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 ... ERROR Running examples in ‘ptairMS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotTIC > ### Title: plot the Total Ion sptectrum (TIC) for one or several files. > ### Aliases: plotTIC plotTIC,ptrRaw-method plotTIC,ptrSet-method > > ### ** Examples > > ### ptrRaw object > > library(ptairData) > filePath <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', + package = 'ptairData') > raw <- readRaw(filePath) 29.013424 41.03858 203.943 330.8495excluded, not contains in the mass axis > p <- plotTIC(raw) Warning: `qplot()` was deprecated in ggplot2 3.4.0. ℹ The deprecated feature was likely used in the ptairMS package. Please report the issue at . Error in pm[[2]] : subscript out of bounds Calls: plotTIC ... .local -> -> ggplotly.ggplot -> gg2list Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed detectPeak 132.268 1.875 134.473 imputeMat 27.503 0.152 27.727 alignSamples 25.738 0.327 26.199 getPeakList 24.297 0.135 24.492 impute 23.897 0.060 24.023 annotation 23.264 0.140 23.461 defineKnots 19.750 0.056 19.861 plot 18.661 0.071 18.787 plotCalib 18.071 0.056 18.173 plotFeatures 17.925 0.052 18.020 plotRaw 17.576 0.056 17.674 convert_to_mzML 16.621 0.347 17.011 importSampleMetadata 15.920 0.048 16.009 getSampleMetadata 15.885 0.048 15.972 exportSampleMetada 15.690 0.136 15.864 getFileNames 15.705 0.052 15.795 getDirectory 15.665 0.052 15.754 changeTimeLimits 15.017 0.084 15.136 createPtrSet 13.714 0.040 13.854 * 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: 1 ERROR, 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck/00check.log’ for details.