############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MSnID_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSnID.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘MSnID/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSnID’ version ‘1.33.0’ * 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 ‘MSnID’ 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 R 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 ... NOTE Namespaces in Imports field not imported from: ‘BiocGenerics’ ‘BiocStyle’ ‘RUnit’ ‘ggplot2’ ‘msmsTests’ ‘xtable’ 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 .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘peptideRef’ Undefined global functions or variables: peptideRef * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘MSnID-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: remap_fasta_entry_names > ### Title: Remapping entries in FASTA file > ### Aliases: remap_fasta_entry_names > > ### ** Examples > > library(Biostrings) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit > fst_path <- system.file("extdata","for_phospho.fasta.gz",package="MSnID") > readAAStringSet(fst_path) AAStringSet object of length 45: width seq names [1] 715 MSSPKRSSKPSMSLAPSGSSMPT...DATTSKATLPGERSSSSSSKLA sp|B3KS81|SRRM5_H... [2] 740 MSFGRDMELEHFDERDKAQRYSR...NSESEDYSPSSSETVRSPNSPF sp|O15075|DCLK1_H... [3] 508 MTQTLKYASRVFHRVRWAPELGA...VRPKTRTVLVPERSINLQFLDR sp|O15528|CP27B_H... [4] 247 MDAFTRFTNQTQGRDRLFRATQY...GLVSSIAGMITVAYPQMKLKTR sp|O75192|PX11A_H... [5] 1304 MAKIAKTHEDIEAQIREIQGKKA...HYPRIYNDDKNTYIRYELDYIL sp|O75533|SF3B1_H... ... ... ... [41] 2752 MYNGIGLPTPRGSGTNGYVQRNL...SHKRRRETPSPRPMRHRSSRSP sp|Q9UQ35|SRRM2_H... [42] 1087 MTTESGSDSESKPDQEAEPQEAA...DMSVTKVVVHKETEITPEDGED sp|Q9Y2J2|E41L3_H... [43] 955 MSKTNKSKSGSRSSRSRSASRSR...IEDDESGTENREEKDNIQPTTE sp|Q9Y2W1|TR150_H... [44] 1467 MSDESASGSDPDLDPDVELEDAE...EVGFSSNDDEDKDDDVIEVTGK sp|Q9Y4B4|ARIP4_H... [45] 313 MSDLLLLGLIGGLTLLLLLTLLA...GTEPLGTTKWLWEPTAPEKGKE sp|Q9Y6I9|TX264_H... > conv_tab <- fetch_conversion_table("Homo sapiens", "UNIPROT", "SYMBOL") Error in readRDS(.db_index_file(x)) : error reading from connection Calls: fetch_conversion_table ... query -> query -> .local -> .db_index_load -> readRDS Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘handling_mods.Rnw’... OK ‘msnid_vignette.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/MSnID.Rcheck/00check.log’ for details.