############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ProteoDisco_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ProteoDisco.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 ‘ProteoDisco/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ProteoDisco’ version ‘1.12.0’ * 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 ‘ProteoDisco’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ProteoDisco.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘ProteoDisco’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 ... OK * checking Rd files ... NOTE checkRd: (-1) checkProteotypicFragments.Rd:25: Lost braces; missing escapes or markup? 25 | \item{x}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) checkProteotypicFragments.Rd:39: Lost braces; missing escapes or markup? 39 | {ProteoDiscography} with an additional column specifying the number of proteotypic fragments per record. | ^ checkRd: (-1) generateJunctionModels.Rd:36: Lost braces; missing escapes or markup? 36 | of the given {ProteoDiscography}; strand-information is taken into account. If no strand-information is given, the nearest (or overlapping) known | ^ checkRd: (-1) importGenomicVariants.MAF.Rd:17: Lost braces; missing escapes or markup? 17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) importGenomicVariants.Rd:40: Lost braces; missing escapes or markup? 40 | into the {ProteoDiscography} as a {VRanges}. This genomic variants can later be incorporated within transcript | ^ checkRd: (-1) importGenomicVariants.Rd:40: Lost braces; missing escapes or markup? 40 | into the {ProteoDiscography} as a {VRanges}. This genomic variants can later be incorporated within transcript | ^ checkRd: (-1) importGenomicVariants.Rd:19: Lost braces; missing escapes or markup? 19 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) importGenomicVariants.VCF.Rd:17: Lost braces; missing escapes or markup? 17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) importSpliceJunctions.Rd:39: Lost braces; missing escapes or markup? 39 | Input should be a {tibble} containing the following columns: | ^ checkRd: (-1) importSpliceJunctions.Rd:18: Lost braces; missing escapes or markup? 18 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) importTranscriptSequences.Rd:15: Lost braces; missing escapes or markup? 15 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) incorporateGenomicVariants.Rd:34: Lost braces; missing escapes or markup? 34 | \code{incorporateMutations} Incorporates SNV, MNV and InDels present in the {ProteoDiscography} on the transcripts. | ^ checkRd: (-1) incorporateGenomicVariants.Rd:17: Lost braces; missing escapes or markup? 17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'ProteoDiscography' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE Error loading dataset 'ProteoDiscographyExample.hg19': Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed incorporateGenomicVariants 28.471 0.626 29.206 generateJunctionModels 10.731 0.381 15.472 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ProteoDisco.Rcheck/00check.log’ for details.