############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hdxmsqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hdxmsqc_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/hdxmsqc.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hdxmsqc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hdxmsqc’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘hdxmsqc’ can be installed ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE chargeCorrelationHdx: no visible global function definition for ‘assay’ chargeCorrelationHdx: no visible binding for global variable ‘x’ chargeCorrelationHdx: no visible binding for global variable ‘z’ chargeCorrelationHdx: no visible binding for global variable ‘peptide’ chargeCorrelationHdx: no visible binding for global variable ‘y’ compatibleUptake: no visible global function definition for ‘rowData’ compatibleUptake: no visible global function definition for ‘assay’ computeMassError: no visible global function definition for ‘rowData’ computeMassError: no visible global function definition for ‘assay’ computeMonotoneStats: no visible global function definition for ‘assay’ computeMonotoneStats: no visible binding for global variable ‘x’ computeMonotoneStats: no visible binding for global variable ‘y’ imTimeOutlier: no visible global function definition for ‘rowData’ imTimeOutlier: no visible global function definition for ‘rowMedians’ imTimeOutlier: no visible binding for global variable ‘Experiment’ imTimeOutlier: no visible binding for global variable ‘IMS_shift’ intensityOutliers: no visible global function definition for ‘rowData’ isMissingAtRandom: no visible global function definition for ‘assay’ isMissingAtRandom: no visible global function definition for ‘rowData’ plotImTimeOutlier: no visible binding for global variable ‘Experiment’ plotImTimeOutlier: no visible binding for global variable ‘IMS_shift’ plotImTimeOutlier: no visible global function definition for ‘brewer.pal’ plotIntensityOutliers: no visible binding for global variable ‘x’ plotIntensityOutliers: no visible binding for global variable ‘y’ plotIntensityOutliers: no visible binding for global variable ‘outlier’ plotIntensityOutliers: no visible global function definition for ‘brewer.pal’ plotMassError: no visible binding for global variable ‘x’ plotMassError: no visible binding for global variable ‘y’ plotMassError: no visible global function definition for ‘brewer.pal’ plotMissing: no visible global function definition for ‘assay’ plotMissing: no visible global function definition for ‘pheatmap’ plotMissing: no visible global function definition for ‘brewer.pal’ plotMonotoneStat : : no visible binding for global variable ‘x’ plotMonotoneStat : : no visible binding for global variable ‘y’ plotMonotoneStat : : no visible binding for global variable ‘outlier’ plotMonotoneStat : : no visible global function definition for ‘brewer.pal’ plotrTimeOutliers: no visible binding for global variable ‘Experiment’ plotrTimeOutliers: no visible binding for global variable ‘RT_shift’ plotrTimeOutliers: no visible global function definition for ‘brewer.pal’ processHDE: no visible binding for global variable ‘Deut.Time’ processHDE: no visible binding for global variable ‘Sequence’ processHDE: no visible binding for global variable ‘Protein.State’ processHDE: no visible binding for global variable ‘Charge’ qualityControl: no visible global function definition for ‘rowData’ rTimeOutliers: no visible global function definition for ‘rowData’ rTimeOutliers: no visible global function definition for ‘rowMedians’ rTimeOutliers: no visible binding for global variable ‘Experiment’ rTimeOutliers: no visible binding for global variable ‘RT_shift’ replicateCorrelation: no visible global function definition for ‘assay’ replicateCorrelation: no visible binding for global variable ‘x’ replicateCorrelation: no visible binding for global variable ‘y’ replicateOutlier: no visible global function definition for ‘assay’ replicateOutlier: no visible binding for global variable ‘x’ replicateOutlier: no visible binding for global variable ‘y’ spectraSimilarity: no visible global function definition for ‘bpparam’ spectraSimilarity: no visible binding for global variable ‘timepoints’ spectraSimilarity: no visible binding for global variable ‘Sequence’ spectraSimilarity: no visible global function definition for ‘bplapply’ spectraSimilarity: no visible global function definition for ‘spectraData’ spectraSimilarity: no visible binding for global variable ‘Charge’ spectraSimilarity: no visible binding for global variable ‘DeutTime’ Undefined global functions or variables: Charge Deut.Time DeutTime Experiment IMS_shift Protein.State RT_shift Sequence assay bplapply bpparam brewer.pal outlier peptide pheatmap rowData rowMedians spectraData timepoints x y z * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/hdxmsqc.Rcheck/00check.log’ for details.