CRAN Package Check Results for Package aLFQ

Last updated on 2015-06-30 11:48:07.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3.2 5.09 66.98 72.07 NOTE
r-devel-linux-x86_64-debian-gcc 1.3.2 5.01 66.34 71.35 NOTE
r-devel-linux-x86_64-fedora-clang 1.3.2 151.50 OK
r-devel-linux-x86_64-fedora-gcc 1.3.2 147.54 OK
r-devel-osx-x86_64-clang 1.3.2 138.63 OK
r-devel-windows-ix86+x86_64 1.3.2 14.00 107.00 121.00 NOTE
r-patched-linux-x86_64 1.3.2 5.00 67.73 72.73 OK
r-patched-solaris-sparc 1.3.2 957.70 ERROR
r-patched-solaris-x86 1.3.2 209.50 OK
r-release-linux-x86_64 1.3.2 5.07 68.44 73.51 OK
r-release-osx-x86_64-mavericks 1.3.2 OK
r-release-windows-ix86+x86_64 1.3.2 23.00 108.00 131.00 OK
r-oldrel-windows-ix86+x86_64 1.3.2 32.00 192.00 224.00 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’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-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:
     Mean relative difference: 0.5925926
    
     I. Failure(@test_ProteinInference.R#152): PeptideInference: topx selection criterion
     PeptideInference(transition_data, transition_topx = 1, transition_strictness = "loose", transition_summary = "sum", consensus_proteins = TRUE, consensus_transitions = FALSE)$peptide_intensity not equal to c(60, 100, 95, 55, 95, 55)
     Mean relative difference: 0.516129
    
     J. Failure(@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)
     Mean relative difference: 0.5925926
    
     Error: Test failures
     In addition: There were 31 warnings (use warnings() to see them)
     Execution halted
Flavor: r-patched-solaris-sparc