CRAN Package Check Results for Package aLFQ

Last updated on 2015-07-28 23:47:22.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3.2 5.58 67.92 73.50 NOTE
r-devel-linux-x86_64-debian-gcc 1.3.2 5.09 66.76 71.85 NOTE
r-devel-linux-x86_64-fedora-clang 1.3.2 153.80 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3.2 146.91 NOTE
r-devel-osx-x86_64-clang 1.3.2 128.66 OK
r-devel-windows-ix86+x86_64 1.3.2 15.00 100.00 115.00 NOTE
r-patched-linux-x86_64 1.3.2 5.00 67.88 72.88 OK
r-patched-solaris-sparc 1.3.2 968.90 ERROR
r-patched-solaris-x86 1.3.2 209.60 OK
r-release-linux-x86_64 1.3.2 5.22 68.89 74.11 OK
r-release-osx-x86_64-mavericks 1.3.2 OK
r-release-windows-ix86+x86_64 1.3.2 23.00 104.00 127.00 OK
r-oldrel-windows-ix86+x86_64 1.3.2 34.00 179.00 213.00 OK

Check Details

Version: 1.3.2
Check: R code for possible problems
Result: NOTE
    ALF.default: no visible global function definition for ‘pdf’
    ALF.default: no visible global function definition for ‘predict’
    ALF.default: no visible global function definition for ‘dev.off’
    APEX.default: no visible binding for global variable ‘formula’
    AbsoluteQuantification.default: no visible global function definition
     for ‘lm’
    AbsoluteQuantification.default: no visible global function definition
     for ‘predict’
    AbsoluteQuantification.default: no visible global function definition
     for ‘sd’
    PeptideInference.default: no visible global function definition for
     ‘median’
    abacus_converter.import: no visible binding for global variable
     ‘read.csv’
    cval.APEX: no visible global function definition for ‘predict’
    cval.AbsoluteQuantification: no visible global function definition for
     ‘lm’
    cval.AbsoluteQuantification: no visible global function definition for
     ‘formula’
    cval.AbsoluteQuantification: no visible global function definition for
     ‘predict’
    export.AbsoluteQuantification: no visible global function definition
     for ‘write.csv’
    hist.AbsoluteQuantification: no visible global function definition for
     ‘hist’
    hist.AbsoluteQuantification: no visible global function definition for
     ‘sd’
    hist.AbsoluteQuantification: no visible global function definition for
     ‘dnorm’
    hist.AbsoluteQuantification: no visible global function definition for
     ‘lines’
    import.default: no visible global function definition for ‘read.csv’
    openmslfq_converter.import: no visible binding for global variable
     ‘read.csv’
    plot.AbsoluteQuantification: no visible global function definition for
     ‘abline’
    plot.AbsoluteQuantification: no visible global function definition for
     ‘title’
    plot.AbsoluteQuantification: no visible global function definition for
     ‘points’
    predict.APEX: no visible global function definition for ‘predict’
    predict.AbsoluteQuantification: no visible global function definition
     for ‘predict’
    protein_inference.ProteinInference: no visible global function
     definition for ‘median’
    protein_inference.ProteinInference: no visible global function
     definition for ‘predict’
    proteotypic.default: no visible global function definition for
     ‘predict’
    read_table.import: no visible global function definition for ‘read.csv’
    skyline_converter.import: no visible binding for global variable
     ‘read.csv’
    strictnessfilter.ProteinInference: no visible global function
     definition for ‘na.omit’
    Undefined global functions or variables:
     abline dev.off dnorm formula hist lines lm median na.omit pdf points
     predict read.csv sd title write.csv
    Consider adding
     importFrom("grDevices", "dev.off", "pdf")
     importFrom("graphics", "abline", "hist", "lines", "points", "title")
     importFrom("stats", "dnorm", "formula", "lm", "median", "na.omit",
     "predict", "sd")
     importFrom("utils", "read.csv", "write.csv")
    to your NAMESPACE.
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-windows-ix86+x86_64

Version: 1.3.2
Check: tests
Result: ERROR
    Running the tests in ‘tests/units.R’ failed.
    Last 13 lines of output:
     6 55 100 -45
    
     J. Failure (at test_ProteinInference.R#156): PeptideInference: loose / strict selection criterion
     PeptideInference(transition_data, transition_topx = 3, transition_strictness = "loose", transition_summary = "sum", consensus_proteins = TRUE, consensus_transitions = FALSE)$peptide_intensity not equal to c(100, 180, 170, 90, 170, 90)
     4/6 mismatches (average diff: 80).
     First 4:
     pos x y diff
     1 100 170 -70
     2 180 90 90
     5 170 100 70
     6 90 180 -90
     Error: Test failures
     Execution halted
Flavor: r-patched-solaris-sparc