CRAN Package Check Results for Package AnalyzeFMRI

Last updated on 2017-11-17 22:46:58.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-16 13.42 45.07 58.49 NOTE
r-devel-linux-x86_64-debian-gcc 1.1-16 14.11 43.35 57.46 NOTE
r-devel-linux-x86_64-fedora-clang 1.1-16 101.37 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1-16 99.02 NOTE
r-devel-windows-ix86+x86_64 1.1-16 65.00 144.00 209.00 NOTE
r-patched-linux-x86_64 1.1-16 11.85 44.69 56.53 NOTE
r-patched-solaris-x86 1.1-16 141.50 NOTE
r-release-linux-x86_64 1.1-16 12.20 44.19 56.38 NOTE
r-release-windows-ix86+x86_64 1.1-16 43.00 134.00 177.00 NOTE
r-release-osx-x86_64 1.1-16 NOTE
r-oldrel-windows-ix86+x86_64 1.1-16 42.00 123.00 165.00 NOTE
r-oldrel-osx-x86_64 1.1-16 WARN

Check Details

Version: 1.1-16
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-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.1-16
Check: top-level files
Result: NOTE
    Non-standard files/directories found at top level:
     ‘niftidoc’ ‘tst.hdr’ ‘tst.img’
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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1-16
Check: R code for possible problems
Result: NOTE
    ICAspat: no visible global function definition for ‘rnorm’
    ICAtemp: no visible global function definition for ‘rnorm’
    N2G.Class.Probability: no visible global function definition for
     ‘dnorm’
    N2G.Class.Probability: no visible global function definition for
     ‘dgamma’
    N2G.Density: no visible global function definition for ‘dnorm’
    N2G.Density: no visible global function definition for ‘dgamma’
    N2G.Fit: no visible global function definition for ‘optim’
    N2G.Likelihood.Ratio: no visible global function definition for
     ‘dgamma’
    N2G.Likelihood.Ratio: no visible global function definition for ‘dnorm’
    N2G.Region : f1: no visible global function definition for ‘dnorm’
    N2G.Region : f1: no visible global function definition for ‘dgamma’
    N2G.Region : f2: no visible global function definition for ‘dnorm’
    N2G.Region : f2: no visible global function definition for ‘dgamma’
    N2G.Region: no visible global function definition for ‘optim’
    N2G.Spatial.Mixture: no visible global function definition for ‘optim’
    Sim.3D.GammaRF: no visible global function definition for ‘qgamma’
    Sim.3D.GammaRF: no visible global function definition for ‘pnorm’
    Threshold.Bonferroni: no visible global function definition for ‘qnorm’
    Threshold.Bonferroni: no visible global function definition for ‘qt’
    Threshold.Bonferroni: no visible global function definition for ‘qf’
    Threshold.FDR: no visible global function definition for ‘pnorm’
    Threshold.FDR: no visible global function definition for ‘pt’
    Threshold.FDR: no visible global function definition for ‘pf’
    Threshold.FDR: no visible global function definition for ‘qnorm’
    Threshold.FDR: no visible global function definition for ‘qt’
    Threshold.FDR: no visible global function definition for ‘qf’
    Threshold.RF: no visible global function definition for ‘optimize’
    eigenvalues: no visible global function definition for ‘par’
    eigenvalues: no visible global function definition for ‘plot’
    eigenvalues: no visible global function definition for ‘abline’
    f.ica.fmri: no visible global function definition for ‘rnorm’
    f.icast.fmri: no visible global function definition for ‘write.table’
    f.icast.fmri: no visible global function definition for ‘dev.off’
    f.plot.ica.fmri: no visible global function definition for
     ‘heat.colors’
    f.plot.ica.fmri: no visible global function definition for ‘par’
    f.plot.ica.fmri: no visible global function definition for ‘plot’
    f.plot.ica.fmri: no visible global function definition for ‘text’
    f.plot.ica.fmri: no visible global function definition for ‘image’
    f.plot.ica.fmri: no visible global function definition for ‘box’
    f.plot.ica.fmri: no visible global function definition for ‘fft’
    f.plot.ica.fmri.jpg: no visible global function definition for
     ‘heat.colors’
    f.plot.ica.fmri.jpg: no visible global function definition for ‘jpeg’
    f.plot.ica.fmri.jpg: no visible global function definition for
     ‘dev.off’
    f.spectral.summary: no visible global function definition for ‘fft’
    f.spectral.summary: no visible global function definition for ‘median’
    f.spectral.summary: no visible binding for global variable ‘quantile’
    f.spectral.summary: no visible global function definition for ‘plot’
    f.spectral.summary: no visible global function definition for ‘axis’
    f.spectral.summary: no visible global function definition for ‘points’
    f.spectral.summary.nifti: no visible global function definition for
     ‘fft’
    f.spectral.summary.nifti: no visible global function definition for
     ‘median’
    f.spectral.summary.nifti: no visible binding for global variable
     ‘quantile’
    f.spectral.summary.nifti: no visible global function definition for
     ‘plot’
    f.spectral.summary.nifti: no visible global function definition for
     ‘axis’
    f.spectral.summary.nifti: no visible global function definition for
     ‘points’
    model.2.est.gamma: no visible global function definition for ‘optimize’
    reduction: no visible binding for global variable ‘sd’
    threeDto4D: no visible global function definition for ‘glob2rx’
    Undefined global functions or variables:
     abline axis box dev.off dgamma dnorm fft glob2rx heat.colors image
     jpeg median optim optimize par pf plot pnorm points pt qf qgamma
     qnorm qt quantile rnorm sd text write.table
    Consider adding
     importFrom("grDevices", "dev.off", "heat.colors", "jpeg")
     importFrom("graphics", "abline", "axis", "box", "image", "par", "plot",
     "points", "text")
     importFrom("stats", "dgamma", "dnorm", "fft", "median", "optim",
     "optimize", "pf", "pnorm", "pt", "qf", "qgamma", "qnorm",
     "qt", "quantile", "rnorm", "sd")
     importFrom("utils", "glob2rx", "write.table")
    to your NAMESPACE file.
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, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-16
Check: Rd line widths
Result: NOTE
    Rd file 'GaussSmoothArray.Rd':
     \usage lines wider than 90 characters:
     GaussSmoothArray(x, voxdim=c(1, 1, 1), ksize=5, sigma=diag(3, 3), mask=NULL, var.norm=FALSE)
    
    Rd file 'N2G.Spatial.Mixture.Rd':
     \usage lines wider than 90 characters:
     N2G.Spatial.Mixture(data, par.start = c(4, 2, 4, 2, 0.9, 0.05), ksize, ktype = c("2D", "3D"), mask = NULL)
     \examples lines wider than 100 characters:
     ans <- N2G.Spatial.Mixture(y, par.start = c(4, 2, 4, 2, 0.9, 0.05), ksize = 3, ktype = "2D", mask = m)
    
    Rd file 'SmoothEst.Rd':
     \examples lines wider than 100 characters:
     grf <- Sim.3D.GRF(d = d, voxdim = voxdim, sigma = sigma, ksize = ksize, mask = mask, type = "field")$mat
     grf <- Sim.3D.GRF(d = d, voxdim = voxdim, sigma = sigma, ksize = ksize, mask = mask, type = "field")$mat
    
    Rd file 'Threshold.RF.Rd':
     \usage lines wider than 90 characters:
     Threshold.RF(p.val, sigma, voxdim = c(1, 1, 1), num.vox, type = c("Normal", "t"), df = NULL)
    
    Rd file 'analyze2nifti.Rd':
     \usage lines wider than 90 characters:
     analyze2nifti(file.in,path.in=".",path.out=".",file.out=NULL,is.nii=TRUE,qform.code=2,sform.code=2,data.type=rawToChar(raw(10)),db.name ... [TRUNCATED]
     \examples lines wider than 100 characters:
     analyze2nifti(path.in=system.file(package="AnalyzeFMRI"),file.in="example",file.out="nifti-tmp",is.nii=TRUE)
    
    Rd file 'cov.est.Rd':
     \examples lines wider than 100 characters:
     mat <- Sim.3D.GRF(d = d, voxdim = voxdim, sigma = sigma, ksize = ksize, mask = mask, type = "field")$mat
    
    Rd file 'f.complete.hdr.nifti.list.create.Rd':
     \usage lines wider than 90 characters:
     f.complete.hdr.nifti.list.create(file,dim.info=character(1),dim,intent.p1=single(1),intent.p2=single(1),intent.p3=single(1),intent.code ... [TRUNCATED]
    
    Rd file 'threeDto4D.Rd':
     \usage lines wider than 90 characters:
     threeDto4D(outputfile,path.in=NULL,prefix=NULL,regexp=NULL,times=NULL,list.of.in.files=NULL,path.out=NULL,is.nii.pair=FALSE,hdr.number= ... [TRUNCATED]
     \examples lines wider than 100 characters:
     # path.fonc <- "/network/home/lafayep/Stage/Data/map284/functional/MondrianApril2007/preprocessing/1801/smoothed/"
    
    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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1-16
Check: compiled code
Result: NOTE
    File ‘AnalyzeFMRI/libs/AnalyzeFMRI.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1-16
Check: dependencies in R code
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: S3 generic/method consistency
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: replacement functions
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: foreign function calls
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: R code for possible problems
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 keyICAspat: no visible global function definition for ‘rnorm’
    ICAtemp: no visible global function definition for ‘rnorm’
    N2G.Class.Probability: no visible global function definition for
     ‘dnorm’
    N2G.Class.Probability: no visible global function definition for
     ‘dgamma’
    N2G.Density: no visible global function definition for ‘dnorm’
    N2G.Density: no visible global function definition for ‘dgamma’
    N2G.Fit: no visible global function definition for ‘optim’
    N2G.Likelihood.Ratio: no visible global function definition for
     ‘dgamma’
    N2G.Likelihood.Ratio: no visible global function definition for ‘dnorm’
    N2G.Region : f1: no visible global function definition for ‘dnorm’
    N2G.Region : f1: no visible global function definition for ‘dgamma’
    N2G.Region : f2: no visible global function definition for ‘dnorm’
    N2G.Region : f2: no visible global function definition for ‘dgamma’
    N2G.Region: no visible global function definition for ‘optim’
    N2G.Spatial.Mixture: no visible global function definition for ‘optim’
    Sim.3D.GammaRF: no visible global function definition for ‘qgamma’
    Sim.3D.GammaRF: no visible global function definition for ‘pnorm’
    Threshold.Bonferroni: no visible global function definition for ‘qnorm’
    Threshold.Bonferroni: no visible global function definition for ‘qt’
    Threshold.Bonferroni: no visible global function definition for ‘qf’
    Threshold.FDR: no visible global function definition for ‘pnorm’
    Threshold.FDR: no visible global function definition for ‘pt’
    Threshold.FDR: no visible global function definition for ‘pf’
    Threshold.FDR: no visible global function definition for ‘qnorm’
    Threshold.FDR: no visible global function definition for ‘qt’
    Threshold.FDR: no visible global function definition for ‘qf’
    Threshold.RF: no visible global function definition for ‘optimize’
    eigenvalues: no visible global function definition for ‘par’
    eigenvalues: no visible global function definition for ‘plot’
    eigenvalues: no visible global function definition for ‘abline’
    f.ica.fmri: no visible global function definition for ‘rnorm’
    f.icast.fmri: no visible global function definition for ‘write.table’
    f.icast.fmri: no visible global function definition for ‘dev.off’
    f.plot.ica.fmri: no visible global function definition for
     ‘heat.colors’
    f.plot.ica.fmri: no visible global function definition for ‘par’
    f.plot.ica.fmri: no visible global function definition for ‘plot’
    f.plot.ica.fmri: no visible global function definition for ‘text’
    f.plot.ica.fmri: no visible global function definition for ‘image’
    f.plot.ica.fmri: no visible global function definition for ‘box’
    f.plot.ica.fmri: no visible global function definition for ‘fft’
    f.plot.ica.fmri.jpg: no visible global function definition for
     ‘heat.colors’
    f.plot.ica.fmri.jpg: no visible global function definition for ‘jpeg’
    f.plot.ica.fmri.jpg: no visible global function definition for
     ‘dev.off’
    f.spectral.summary: no visible global function definition for ‘fft’
    f.spectral.summary: no visible global function definition for ‘median’
    f.spectral.summary: no visible binding for global variable ‘quantile’
    f.spectral.summary: no visible global function definition for ‘plot’
    f.spectral.summary: no visible global function definition for ‘axis’
    f.spectral.summary: no visible global function definition for ‘points’
    f.spectral.summary.nifti: no visible global function definition for
     ‘fft’
    f.spectral.summary.nifti: no visible global function definition for
     ‘median’
    f.spectral.summary.nifti: no visible binding for global variable
     ‘quantile’
    f.spectral.summary.nifti: no visible global function definition for
     ‘plot’
    f.spectral.summary.nifti: no visible global function definition for
     ‘axis’
    f.spectral.summary.nifti: no visible global function definition for
     ‘points’
    model.2.est.gamma: no visible global function definition for ‘optimize’
    reduction: no visible binding for global variable ‘sd’
    threeDto4D: no visible global function definition for ‘glob2rx’
    Undefined global functions or variables:
     abline axis box dev.off dgamma dnorm fft glob2rx heat.colors image
     jpeg median optim optimize par pf plot pnorm points pt qf qgamma
     qnorm qt quantile rnorm sd text write.table
    Consider adding
     importFrom("grDevices", "dev.off", "heat.colors", "jpeg")
     importFrom("graphics", "abline", "axis", "box", "image", "par", "plot",
     "points", "text")
     importFrom("stats", "dgamma", "dnorm", "fft", "median", "optim",
     "optimize", "pf", "pnorm", "pt", "qf", "qgamma", "qnorm",
     "qt", "quantile", "rnorm", "sd")
     importFrom("utils", "glob2rx", "write.table")
    to your NAMESPACE file.
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: for missing documentation entries
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: for code/documentation mismatches
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 1.1-16
Check: Rd \usage sections
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64