CRAN Package Check Results for Package PAGI

Last updated on 2015-08-30 09:47:34.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 1.53 254.72 256.26 NOTE
r-devel-linux-x86_64-debian-gcc 1.0 1.62 257.69 259.32 NOTE
r-devel-linux-x86_64-fedora-clang 1.0 253.72 NOTE --no-build-vignettes
r-devel-linux-x86_64-fedora-gcc 1.0 234.02 NOTE --no-build-vignettes
r-devel-osx-x86_64-clang 1.0 200.60 NOTE --no-build-vignettes
r-devel-windows-ix86+x86_64 1.0 8.00 387.00 395.00 NOTE
r-patched-linux-x86_64 1.0 1.48 274.97 276.45 NOTE
r-patched-solaris-sparc 1.0 189.40 NOTE --no-vignettes
r-patched-solaris-x86 1.0 433.30 NOTE --no-build-vignettes
r-release-linux-x86_64 1.0 1.60 276.87 278.47 NOTE
r-release-osx-x86_64-mavericks 1.0 NOTE
r-release-windows-ix86+x86_64 1.0 7.00 480.00 487.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0 8.00 456.00 464.00 NOTE

Check Details

Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    CalGIF: no visible binding for global variable ‘PAGIData’
    CalGIF2: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible global function definition for ‘p.adjust’
    PAGI.Main: no visible global function definition for ‘pt’
    getclass.labels: no visible binding for global variable ‘ExampleData’
    getdataset: no visible binding for global variable ‘ExampleData’
    Undefined global functions or variables:
     ExampleData PAGIData p.adjust pt
    Consider adding
     importFrom("stats", "p.adjust", "pt")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'CalGIF.Rd':
     \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data.
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data.
    
    Rd file 'PAGI.Main.Rd':
     \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
    
    These lines will be truncated in the PDF manual.
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

Version: 1.0
Flags: --no-build-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-solaris-x86

Version: 1.0
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    CalGIF: no visible binding for global variable ‘PAGIData’
    CalGIF2: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible global function definition for ‘p.adjust’
    PAGI.Main: no visible global function definition for ‘pt’
    getclass.labels: no visible binding for global variable ‘ExampleData’
    getdataset: no visible binding for global variable ‘ExampleData’
    Undefined global functions or variables:
     ExampleData PAGIData p.adjust pt
    Consider adding
     importFrom("stats", "p.adjust", "pt")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0
Flags: --no-build-vignettes
Check: Rd line widths
Result: NOTE
    Rd file 'CalGIF.Rd':
     \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data.
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data.
    
    Rd file 'PAGI.Main.Rd':
     \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
    
    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: 1.0
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    CalGIF: no visible binding for global variable ‘PAGIData’
    CalGIF2: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible binding for global variable ‘PAGIData’
    getclass.labels: no visible binding for global variable ‘ExampleData’
    getdataset: no visible binding for global variable ‘ExampleData’
    Undefined global functions or variables:
     ExampleData PAGIData
Flavor: r-devel-osx-x86_64-clang

Version: 1.0
Check: R code for possible problems
Result: NOTE
    CalGIF: no visible binding for global variable ‘PAGIData’
    CalGIF2: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible binding for global variable ‘PAGIData’
    getclass.labels: no visible binding for global variable ‘ExampleData’
    getdataset: no visible binding for global variable ‘ExampleData’
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 5.1Mb
     sub-directories of 1Mb or more:
     data 1.6Mb
     localdata 3.1Mb
Flavor: r-patched-solaris-sparc

Version: 1.0
Flags: --no-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
Flavor: r-patched-solaris-sparc

Version: 1.0
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    CalGIF: no visible binding for global variable ‘PAGIData’
    CalGIF2: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible binding for global variable ‘PAGIData’
    getclass.labels: no visible binding for global variable ‘ExampleData’
    getdataset: no visible binding for global variable ‘ExampleData’
Flavor: r-patched-solaris-sparc

Version: 1.0
Flags: --no-build-vignettes
Check: installed package size
Result: NOTE
     installed size is 5.1Mb
     sub-directories of 1Mb or more:
     data 1.6Mb
     localdata 3.1Mb
Flavor: r-patched-solaris-x86

Version: 1.0
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    CalGIF: no visible binding for global variable ‘PAGIData’
    CalGIF2: no visible binding for global variable ‘PAGIData’
    PAGI.Main: no visible binding for global variable ‘PAGIData’
    getclass.labels: no visible binding for global variable ‘ExampleData’
    getdataset: no visible binding for global variable ‘ExampleData’
Flavor: r-patched-solaris-x86

Version: 1.0
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: igraph
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'tools' is missing or broken
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'stats' is missing or broken
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'graphics' is missing or broken
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'grDevices' is missing or broken
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'utils' is missing or broken
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'datasets' is missing or broken
    Warning in FUN(X[[i]], ...) :
     DESCRIPTION file of package 'methods' is missing or broken
    
    Error: processing vignette 'PAGI.Rnw' failed with diagnostics:
     chunk 4 (label = sessionInfo)
    Error : $ operator is invalid for atomic vectors
    Execution halted
Flavor: r-release-osx-x86_64-mavericks