* using log directory ‘/srv/hornik/tmp/CRAN/disambiguateR.Rcheck’ * using R Under development (unstable) (2024-03-24 r86185) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘disambiguateR/DESCRIPTION’ ... OK * this is package ‘disambiguateR’ version ‘1.1.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Hugh Salamon ’ New submission Possibly misspelled words in DESCRIPTION: Canonicalization (4:9) GL (11:6, 17:15, 18:5, 18:51, 19:74) HLA (11:56, 16:52) IMGT (13:25, 16:31) Immunogenetics (12:63) canonicalize (17:69) preconfigured (22:36) Found the following (possibly) invalid URLs: URL: http://igdawg.org/pubs/HLA_frequencies_by_accession_and_region.txt From: man/package_HLA_frequencies_by_accession.Rd Status: Error Message: SSL: certificate subject name (www.uvm.edu) does not match target host name 'igdawg.org' The Description field should not start with the package name, 'This package' or similar. * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘disambiguateR’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... 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 ... [3s/3s] NOTE disambiguate: no visible binding for global variable ‘gl_match_rules’ disambiguate: no visible binding for global variable ‘gl_HLA_frequencies_by_accession’ disambiguate: no visible binding for global variable ‘gl_HLA_deleted_alleles’ disambiguate: no visible binding for global variable ‘gl_HLA_allele_history’ disambiguate: no visible binding for global variable ‘package_HLA_frequencies_by_accession’ disambiguate: no visible binding for global variable ‘package_HLA_deleted_alleles’ disambiguate: no visible binding for global variable ‘package_HLA_allele_history’ disambiguate: no visible binding for global variable ‘region’ disambiguate: no visible binding for global variable ‘accession’ disambiguate: no visible global function definition for ‘capture.output’ disambiguate: no visible global function definition for ‘write.table’ fetchHLAfrequencies: no visible global function definition for ‘read.table’ fetchHLAhistory: no visible binding for global variable ‘fdat.raw’ fetchHLAhistory: no visible global function definition for ‘read.table’ fetchHLAnomenclature: no visible global function definition for ‘read.table’ guessimgtversion: no visible binding for global variable ‘gl_HLA_allele_history’ guessimgtversion: no visible binding for global variable ‘package_HLA_allele_history’ loadHLAdata: no visible binding for global variable ‘currentHLAnomenclature’ loadHLAdata: no visible binding for global variable ‘currentHLAfrequencies’ loadHLAdata: no visible binding for global variable ‘currentHLAhistory’ updateHLAdata: no visible binding for '<<-' assignment to ‘gl_HLA_deleted_alleles’ updateHLAdata: no visible binding for '<<-' assignment to ‘gl_HLA_frequencies_by_accession’ updateHLAdata: no visible binding for '<<-' assignment to ‘gl_HLA_allele_history’ updateHLAfrequencies: possible error in dim(fredat.fetched$data, sep = ""): unused argument (sep = "") updateHLAhistory: no visible global function definition for ‘read.table’ updateHLAhistory: possible error in dim(hisdat.fetched$data, sep = ""): unused argument (sep = "") updateHLAnomenclature: possible error in dim(nomdat.fetched$data, sep = ""): unused argument (sep = "") Undefined global functions or variables: accession capture.output currentHLAfrequencies currentHLAhistory currentHLAnomenclature fdat.raw gl_HLA_allele_history gl_HLA_deleted_alleles gl_HLA_frequencies_by_accession gl_match_rules package_HLA_allele_history package_HLA_deleted_alleles package_HLA_frequencies_by_accession read.table region write.table Consider adding importFrom("utils", "capture.output", "read.table", "write.table") to your NAMESPACE file. Found if() conditions comparing class() to string: File ‘disambiguateR/R/disambiguate.R’: if (class(imgtversion) == "try-error") ... File ‘disambiguateR/R/fetchHLAfrequencies.R’: if (class(fdat.raw) == "try-error") ... File ‘disambiguateR/R/fetchHLAfrequencies.R’: if (class(parseret) == "try-error") ... File ‘disambiguateR/R/fetchHLAhistory.R’: if (class(hdat.raw) == "try-error") ... File ‘disambiguateR/R/fetchHLAhistory.R’: if (class(parseret) == "try-error") ... File ‘disambiguateR/R/fetchHLAnomenclature.R’: if (class(ddat.raw) == "try-error") ... File ‘disambiguateR/R/loadHLAdata.R’: if (class(datadir) == "try-error") ... File ‘disambiguateR/R/loadHLAdata.R’: if (class(nomret) == "try-error") ... File ‘disambiguateR/R/loadHLAdata.R’: if (class(freret) == "try-error") ... File ‘disambiguateR/R/loadHLAdata.R’: if (class(hisret) == "try-error") ... File ‘disambiguateR/R/updateHLAfrequencies.R’: if (class(datadir) == "try-error") ... File ‘disambiguateR/R/updateHLAfrequencies.R’: if (class(saveret) == "try-error") ... File ‘disambiguateR/R/updateHLAfrequencies.R’: if (class(saveret) == "try-error") ... File ‘disambiguateR/R/updateHLAhistory.R’: if (class(datadir) == "try-error") ... File ‘disambiguateR/R/updateHLAhistory.R’: if (class(saveret) == "try-error") ... File ‘disambiguateR/R/updateHLAhistory.R’: if (class(saveret) == "try-error") ... File ‘disambiguateR/R/updateHLAnomenclature.R’: if (class(datadir) == "try-error") ... File ‘disambiguateR/R/updateHLAnomenclature.R’: if (class(saveret) == "try-error") ... File ‘disambiguateR/R/updateHLAnomenclature.R’: if (class(saveret) == "try-error") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'canonicalize.Rd': \examples lines wider than 100 characters: gls <- c("HLA-A*11011/HLA-A*11012+HLA-A*2410^HLA-C*0702/HLA-C*0710+HLA-C*0704/HLA-C*0711/HLA-C*0712|HLA-C*0703+HLA-C*0704/HLA-C*0711/HL ... [TRUNCATED] gls <- c("HLA-C*0308/HLA-C*0309+HLA-C*0702/HLA-C*0710|HLA-C*0310+HLA-C*0702/HLA-C*0710","HLA-C*0710+HLA-C*0310/HLA-C*0308/HLA-C*0309|HL ... [TRUNCATED] Rd file 'disambiguate.Rd': \examples lines wider than 100 characters: gls <- c("A*11011/A*11012+A*3303^C*03041/C*0308/C*0309+C*07011/C*07012/C*0706|C*03041/C*0308/C*0309+C*0705|C*0305+C*07011/C*07012/C*070 ... [TRUNCATED] gls.out <- disambiguate(probratio=0.5,freqbyacc=package_HLA_frequencies_by_accession,deletedalleles=package_HLA_deleted_alleles,alleleh ... [TRUNCATED] gls.out <- disambiguate(probratio=0.5,freqbyacc=package_HLA_frequencies_by_accession,deletedalleles=package_HLA_deleted_alleles,alleleh ... [TRUNCATED] # Once updated data are updated (or later simply loaded with load_HLA_data), there is no need to specify freqbyacc, deletedalleles, or ... [TRUNCATED] # gls.out <- disambiguate(probratio=0.5,region="NAF",imgtversion = "1050",dislevel=0,mode="normal",glstrings=gls,log=TRUE) # For a vector or list of GL Strings, gls, use guessimgtversion to calculate a different imgt version for each GL String, and create a ... [TRUNCATED] # ret <- lapply(1:length(gls), function(X) {print(X);imgt <- guessimgtversion(gls[X]); ret<-cbind(disambiguate(gls[X],regionstring="EUR ... [TRUNCATED] # When there is doubt about the geographic region appropriate for disambiguating GL strings, one can investigate the effect of region o ... [TRUNCATED] # sapply(unique(gl_HLA_frequencies_by_accession$data$region), function(X) {d <- disambiguate(test.glstrings,region=X,verbose="quiet",di ... [TRUNCATED] Rd file 'fetchHLAfrequencies.Rd': \examples lines wider than 100 characters: fret <- fetchHLAfrequencies("https://raw.githubusercontent.com/hughsalamon/disambiguateR/master/inst/HLA_frequencies_by_accession_and_r ... [TRUNCATED] Rd file 'fetchHLAnomenclature.Rd': \examples lines wider than 100 characters: fret <- fetchHLAnomenclature("https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/wmda/hla_nom.txt") Rd file 'guessimgtversion.Rd': \examples lines wider than 100 characters: gls <- c("A*1101/A*11012+A*3303^B*40:02:01+B*44:03:01/B*44:03:02^Cw*03041/Cw*0308/Cw*0309/Cw*0310+Cw*07011/Cw*07012/Cw*0705/Cw*0706|Cw* ... [TRUNCATED] gls <- c("A*1101/A*11012+A*3303^B*40:02:01+B*44:03:01/B*44:03:02^C*03:04:01:01/C*03:08/C*03:09/C*03:10+C*07:01:01/C*07:01:02/C*07:05/C* ... [TRUNCATED] Rd file 'updateHLAfrequencies.Rd': \usage lines wider than 90 characters: "https://raw.githubusercontent.com/hughsalamon/disambiguateR/master/inst/HLA_frequencies_by_accession_and_region.txt" These lines will be truncated in the PDF manual. * 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [9s/29s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed updateHLAdata 4.247 0.080 13.429 fetchHLAhistory 1.912 0.146 12.407 * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 5 NOTEs