############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PSMatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PSMatch_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PSMatch.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PSMatch/DESCRIPTION’ ... OK * this is package ‘PSMatch’ version ‘1.9.0’ * 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 ‘PSMatch’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘PSMatch-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: PSM > ### Title: A class for peptide-spectrum matches > ### Aliases: PSM PSM-class reducePSMs readPSMs psmVariables PSM,character > ### PSM,data.frame PSM,PSM reduced reduced<- adjacencyMatrix,PSM-method > > ### ** Examples > > > ## --------------------------------- > ## Example with a single mzid file > ## --------------------------------- > > f <- msdata::ident(full.names = TRUE, pattern = "TMT") > basename(f) [1] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid" > > ## mzR parser (default) > psm <- PSM(f) > psm PSM with 5802 rows and 35 columns. names(35): sequence spectrumID ... subReplacementResidue subLocation > > ## PSM variables > psmVariables(psm) spectrum peptide protein decoy "spectrumID" "sequence" "DatabaseAccess" "isDecoy" rank score fdr "rank" NA NA > > ## mzID parser > psm_mzid <- PSM(f, parser = "mzID") Loading required namespace: mzID reading TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid...Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE Warning in type.convert.default(...) : 'as.is' should be specified by the caller; using TRUE DONE! > psm_mzid PSM with 5759 rows and 30 columns. names(30): spectrumid scan number(s) ... spectrumFile databaseFile > > ## different PSM variables > psmVariables(psm_mzid) spectrum peptide protein decoy rank score "spectrumid" "pepseq" "accession" "isdecoy" "rank" NA fdr NA > > ## Reducing the PSM data > (i <- which(duplicated(psm$spectrumID))[1:2]) [1] 9 24 > (i <- which(psm$spectrumID %in% psm$spectrumID[i])) [1] 8 9 23 24 25 26 > psm2 <- psm[i, ] > reduced(psm2) [1] NA > > ## Peptide sequence CIDRARHVEVQIFGDGKGRVVALGERDCSLQRR with > ## Carbamidomethyl modifications at positions 1 and 28. > DataFrame(psm2[, c("sequence", "spectrumID", "modName", "modLocation")]) DataFrame with 6 rows and 4 columns sequence spectrumID modName modLocation 1 CIDRARHVEV... controller... Carbamidom... 1 2 CIDRARHVEV... controller... Carbamidom... 28 3 KCNQCLKVAC... controller... Carbamidom... 2 4 KCNQCLKVAC... controller... Carbamidom... 5 5 KCNQCLKVAC... controller... Carbamidom... 10 6 KCNQCLKVAC... controller... Carbamidom... 15 > reduced(psm2) <- FALSE > reduced(psm2) [1] FALSE > > ## uses by default the spectrum PSM variable, as defined during > ## the construction - see psmVariables() > rpsm2 <- reducePSMs(psm2) > rpsm2 Reduced PSM with 2 rows and 35 columns. names(35): sequence spectrumID ... subReplacementResidue subLocation > DataFrame(rpsm2[, c("sequence", "spectrumID", "modName", "modLocation")]) DataFrame with 2 rows and 4 columns sequence spectrumID controllerType=0 controllerNumber=1 scan=5490 KCNQCLKVAC... controller... controllerType=0 controllerNumber=1 scan=6518 CIDRARHVEV... controller... modName modLocation controllerType=0 controllerNumber=1 scan=5490 Carbamidom... 2,5,10,... controllerType=0 controllerNumber=1 scan=6518 Carbamidom... 1,28 > reduced(rpsm2) [1] TRUE > > ## --------------------------------- > ## Multiple mzid files > ## --------------------------------- > > library(rpx) > PXD022816 <- PXDataset("PXD022816") Querying ProteomeXchange for PXD022816. Error in open.connection(con, open = mode) : Timeout was reached: [ftp.pride.ebi.ac.uk] Calls: PXDataset ... curl_connection -> withCallingHandlers -> open -> open.connection Execution halted * 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 See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PSMatch.Rcheck/00check.log’ for details.