CRAN Package Check Results for Package seqinr

Last updated on 2014-08-22 08:49:20.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.0-7 7.37 63.19 70.56 NOTE
r-devel-linux-x86_64-debian-gcc 3.0-7 9.13 63.11 72.24 NOTE
r-devel-linux-x86_64-fedora-clang 3.0-7 144.11 NOTE
r-devel-linux-x86_64-fedora-gcc 3.0-7 142.53 NOTE
r-devel-osx-x86_64-clang 3.0-7 118.30 NOTE
r-devel-windows-ix86+x86_64 3.0-7 41.00 146.00 187.00 NOTE
r-patched-linux-x86_64 3.0-7 9.28 66.26 75.54 NOTE
r-patched-solaris-sparc 3.0-7 565.20 ERROR
r-patched-solaris-x86 3.0-7 175.10 NOTE
r-release-linux-ix86 3.0-7 12.14 83.27 95.41 NOTE
r-release-linux-x86_64 3.0-7 9.19 62.42 71.61 NOTE
r-release-osx-x86_64-mavericks 3.0-7 NOTE
r-release-windows-ix86+x86_64 3.0-7 41.00 141.00 182.00 NOTE
r-oldrel-windows-ix86+x86_64 3.0-7 40.00 153.00 193.00 NOTE

Check Details

Version: 3.0-7
Check: installed package size
Result: NOTE
     installed size is 9.6Mb
     sub-directories of 1Mb or more:
     data 1.8Mb
     sequences 6.1Mb
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.0-7
Check: R code for possible problems
Result: NOTE
    Found the following assignments to the global environment:
    File ‘seqinr/R/choosebank.R’:
     assign("banknameSocket", res, .GlobalEnv)
    File ‘seqinr/R/extract.breakpoints.R’:
     assign("x.breaks", x.breaks, envir = globalenv())
     assign("y.breaks", y.breaks, envir = globalenv())
    File ‘seqinr/R/modifylist.R’:
     assign(modlistname, result, envir = .GlobalEnv)
    File ‘seqinr/R/query.r’:
     assign(listname, result, envir = .GlobalEnv)
    
    Found the following calls to data() loading into the global environment:
    File ‘seqinr/R/plotabif.R’:
     data(list = allele.names)
    File ‘seqinr/R/plotladder.R’:
     data(list = allele.names)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 3.0-7
Check: R code for possible problems
Result: NOTE
    AAstat: no visible binding for global variable ‘SEQINR.UTIL’
    computePI: no visible binding for global variable ‘SEQINR.UTIL’
    recstat: no visible global function definition for ‘dudi.coa’
    summary.SeqFastaAA: no visible binding for global variable
     ‘SEQINR.UTIL’
    tablecode: no visible binding for global variable ‘SEQINR.UTIL’
    translate: no visible binding for global variable ‘SEQINR.UTIL’
    uco: no visible binding for global variable ‘SEQINR.UTIL’
    ucoweight: no visible binding for global variable ‘SEQINR.UTIL’
    
    Found the following assignments to the global environment:
    File ‘seqinr/R/choosebank.R’:
     assign("banknameSocket", res, .GlobalEnv)
    File ‘seqinr/R/extract.breakpoints.R’:
     assign("x.breaks", x.breaks, envir = globalenv())
     assign("y.breaks", y.breaks, envir = globalenv())
    File ‘seqinr/R/modifylist.R’:
     assign(modlistname, result, envir = .GlobalEnv)
    File ‘seqinr/R/query.r’:
     assign(listname, result, envir = .GlobalEnv)
    
    Found the following calls to data() loading into the global environment:
    File ‘seqinr/R/plotabif.R’:
     data(list = allele.names)
    File ‘seqinr/R/plotladder.R’:
     data(list = allele.names)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang

Version: 3.0-7
Check: Rd line widths
Result: NOTE
    Rd file 'AAstat.Rd':
     \examples lines wider than 100 characters:
     seqAA <- read.fasta(file = system.file("sequences/seqAA.fasta", package = "seqinr"), seqtype = "AA")
    
    Rd file 'GC.Rd':
     \examples lines wider than 100 characters:
     legend("topleft", inset = 0.01, legend = c("forceToLower = TRUE", "forceToLower = FALSE"), col = c("black", "red"), lty = c(1,3))
    
    Rd file 'acnucopen.Rd':
     \usage lines wider than 90 characters:
     clientid(id = paste("seqinr_", packageDescription("seqinr")$Version, sep = ""), socket, verbose = FALSE)
    
    Rd file 'as.matrix.alignment.Rd':
     \examples lines wider than 100 characters:
     phylip <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
    
    Rd file 'col2alpha.Rd':
     \examples lines wider than 100 characters:
     mtext("Effect of alpha on some colors\nNote: need alpha transparency channel", side = 3, outer = TRUE)
    
    Rd file 'computePI.Rd':
     \examples lines wider than 100 characters:
     myProts <- read.fasta(file = system.file("sequences/seqAA.fasta", package = "seqinr"), seqtype = "AA")
    
    Rd file 'count.Rd':
     \usage lines wider than 90 characters:
     count(seq, wordsize, start = 0, by = 1, freq = FALSE, alphabet = s2c("acgt"), frame = start)
     \examples lines wider than 100 characters:
     alldiaa <- "aaxxzxbxvxyxwxtxsxpxfxmxkxlxixhxgxexqxcxdxnxrxazzbzvzyzwztzszpzfzmzkzlzizhzgzezqzczdznzrzabbvbybwbtbsbpbfbmbkblbibhbgbebqbc ... [TRUNCATED]
    
    Rd file 'crelistfromclientdata.Rd':
     \usage lines wider than 90 characters:
     crelistfromclientdata(listname, file, type, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
     clfcd(listname, file, type, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
    
    Rd file 'dinucl.Rd':
     \examples lines wider than 100 characters:
     legend("bottomright", inset = 0.02, legend = paste(substr(x,1,1), "p", substr(x,2,2), " bias", sep = ""), cex = 1.25, bg = "white")
    
    Rd file 'dotPlot.Rd':
     \examples lines wider than 100 characters:
     dotPlot(dna[1:200], dna[1:200], main = "Dot plot of a nucleic acid sequence\nwsize = 1, wstep = 1, nmatch = 1")
    
    Rd file 'draw.rearranged.oriloc.Rd':
     \usage lines wider than 90 characters:
     draw.rearranged.oriloc(rearr.ori, breaks.gcfw = NA, breaks.gcrev = NA, breaks.atfw = NA, breaks.atrev = NA)
     \examples lines wider than 100 characters:
     breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"), nbreaks = c(2, 2), gridsize = 50, it.max = 100)
     ### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###
    
    Rd file 'extract.breakpoints.Rd':
     \usage lines wider than 90 characters:
     extract.breakpoints(rearr.ori,type = c("atfw", "atrev", "gcfw", "gcrev"), nbreaks, gridsize = 100, it.max = 500)
     \examples lines wider than 100 characters:
     ## Not run: breaks <- extract.breakpoints(r.ori,type = c("gcfw", "gcrev"), nbreaks = c(2, 2), gridsize = 50, it.max = 100)
     ### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###
     ## Not run: draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev$breaks)
    
    Rd file 'extractseqs.Rd':
     \usage lines wider than 90 characters:
     extractseqs(listname,socket = autosocket(), format="fasta",operation="simple",feature="xx", bounds="xx", minbounds="xx", verbose = FALS ... [TRUNCATED]
     exseq(listname,socket = autosocket(), format="fasta",operation="simple", feature="xx", bounds="xx", minbounds="xx", verbose = FALSE, n ... [TRUNCATED]
    
    Rd file 'gb2fasta.Rd':
     \usage lines wider than 90 characters:
     "ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Agrobacterium_tumefaciens_C58_Cereon/NC_003065.gbk",
    
    Rd file 'get.db.growth.Rd':
     \usage lines wider than 90 characters:
     get.db.growth(where = "http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt" )
    
    Rd file 'getTrans.Rd':
     \usage lines wider than 90 characters:
     getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = "auto", numcode = "auto")
     getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
     getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
    
    Rd file 'ghelp.Rd':
     \usage lines wider than 90 characters:
     ghelp(item = c("GENERAL", "SELECT", "SPECIES", "KEYWORD"), file = c("HELP", "HELP_WIN"), socket = autosocket(), catresult = TRUE)
    
    Rd file 'kaks.Rd':
     \examples lines wider than 100 characters:
     s <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
     Anouk <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
     Darren <- read.alignment(file = system.file("sequences/DarrenObbard.fasta", package = "seqinr"), format = "fasta")
    
    Rd file 'm16j.Rd':
     \examples lines wider than 100 characters:
     title(xlab = "position (Kbp)", ylab = "(C-G)/(C+G) [percent]", main = expression(paste("GC skew in ", italic(Escherichia~coli))))
    
    Rd file 'modifylist.Rd':
     \usage lines wider than 90 characters:
     modifylist(listname, modlistname = listname, operation, type = c("length", "date", "scan"), socket = autosocket(), virtual = FALSE, ver ... [TRUNCATED]
    
    Rd file 'permutation.Rd':
     \usage lines wider than 90 characters:
     permutation(sequence,modele='base',frame=0,replace=FALSE,prot=FALSE,numcode=1,ucoweight = NULL)
    
    Rd file 'query.Rd':
     \usage lines wider than 90 characters:
     query(listname, query, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
    
    Rd file 'read.abif.Rd':
     \usage lines wider than 90 characters:
     read.abif(filename, max.bytes.in.file = file.info(filename)$size, pied.de.pilote = 1.2, verbose = FALSE)
    
    Rd file 'read.alignment.Rd':
     \examples lines wider than 100 characters:
     mase.res <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
     clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
     phylip.res <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
     msf.res <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
     fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
    
    Rd file 'rearranged.oriloc.Rd':
     \examples lines wider than 100 characters:
     ## Not run: breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"), nbreaks =c(2, 2), gridsize = 50, it.max = 100)
     ### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###
     ## Not run: draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev$breaks)
    
    Rd file 'savelist.Rd':
     \usage lines wider than 90 characters:
     filename = paste(gln(lrank), ifelse(type == "N", "mne", "acc"), sep = "."),
    
    Rd file 'stutterabif.Rd':
     \usage lines wider than 90 characters:
     stutterabif(abifdata, chanel, poswild, datapointbefore = 70, datapointafter = 20, datapointsigma = 3.5, chanel.names = c(1:4, 105), DAT ... [TRUNCATED]
    
    Rd file 'trimSpace.Rd':
     \examples lines wider than 100 characters:
     stopifnot(all( trimSpace(testspace, trailing = FALSE) == c("with leading space", "with trailing space ", "with both ")))
     stopifnot(all( trimSpace(testspace, leading = FALSE) == c(" with leading space", "with trailing space", " with both")))
    
    Rd file 'words.Rd':
     \examples lines wider than 100 characters:
     c("aaa", "aac", "aag", "aat", "aca", "acc", "acg", "act", "aga", "agc", "agg", "agt", "ata", "atc", "atg", "att",
     "caa", "cac", "cag", "cat", "cca", "ccc", "ccg", "cct", "cga", "cgc", "cgg", "cgt", "cta", "ctc", "ctg", "ctt",
     "gaa", "gac", "gag", "gat", "gca", "gcc", "gcg", "gct", "gga", "ggc", "ggg", "ggt", "gta", "gtc", "gtg", "gtt",
     "taa", "tac", "tag", "tat", "tca", "tcc", "tcg", "tct", "tga", "tgc", "tgg", "tgt", "tta", "ttc", "ttg", "ttt")))
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 3.0-7
Check: R code for possible problems
Result: NOTE
    AAstat: no visible binding for global variable ‘SEQINR.UTIL’
    computePI: no visible binding for global variable ‘SEQINR.UTIL’
    recstat: no visible global function definition for ‘dudi.coa’
    summary.SeqFastaAA: no visible binding for global variable
     ‘SEQINR.UTIL’
    tablecode: no visible binding for global variable ‘SEQINR.UTIL’
    translate: no visible binding for global variable ‘SEQINR.UTIL’
    uco: no visible binding for global variable ‘SEQINR.UTIL’
    ucoweight: no visible binding for global variable ‘SEQINR.UTIL’
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 3.0-7
Check: examples
Result: ERROR
    Running examples in ‘seqinr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: read.abif
    > ### Title: Read ABIF formatted files
    > ### Aliases: read.abif
    >
    > ### ** Examples
    >
    > #
    > # Quality check:
    > #
    >
    > data(JLO)
    > JLO.check <- read.abif(system.file("abif/2_FAC321_0000205983_B02_004.fsa",
    + package = "seqinr"))
    > stopifnot(identical(JLO, JLO.check))
    Error: identical(JLO, JLO.check) is not TRUE
    Execution halted
Flavor: r-patched-solaris-sparc