CRAN Package Check Results for Package bibliospec

Last updated on 2018-05-09 22:48:07 CEST.

Check Details

Version: 0.0.4
Check: examples
Result: ERROR
    Running examples in ‘bibliospec-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: Bibliospec-class
    > ### Title: R access to Bibliospec File
    > ### Aliases: Bibliospec Bibliospec-class bibliospec blib
    >
    > ### ** Examples
    >
    >
    > library(bibliospec)
    >
    > # use the sqlite file provided in the package
    > dbfile <- file.path(path.package("bibliospec"),
    + "extdata/peptideStd.sqlite")
    >
    > # call constructor
    > BS <- Bibliospec(dbfile=dbfile)
    database connected
    >
    > # test; should return TRUE
    > BS$getNrPSM() == 137
     count(*)
    [1,] TRUE
    >
    > S <- BS$getPsmSet()
    SELECT RefSpectra.id as RefSpectraId, numPeaks, peptideSeq,
    precursorCharge, precursorMZ, retentionTime,
    peptideModSeq, score, SpectrumSourceFiles.fileName
    FROM SpectrumSourceFiles, RefSpectra
    WHERE SpectrumSourceFiles.id = RefSpectra.fileID;
    getspectra
    preparing Peaks as a list, will take a while if you blib file is large.
     extracted MZ
     extracted Intensity
    assigning 28 modifications ...
    >
    > ## Not run:
    > ##D library(specL)
    > ##D print(S)
    > ##D lapply(S[1:10], plot)
    > ## End(Not run)
    >
    > peaks <- BS$getPeaks()
    getspectra
    preparing Peaks, will take a while if you blib file is large.
     extracted MZ
     extracted Intensity
    to data frame
    Error in result_create(conn@ptr, statement) :
     attempt to write a readonly database
    Calls: <Anonymous> ... .local -> new -> initialize -> initialize -> result_create
    Execution halted
    finalize
    [1] "disconnected"
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64