CRAN Package Check Results for Package pi0

Last updated on 2015-05-04 22:46:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3-250 5.10 88.35 93.45 NOTE
r-devel-linux-x86_64-debian-gcc 1.3-250 5.44 83.62 89.06 NOTE
r-devel-linux-x86_64-fedora-clang 1.3-250 175.04 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3-250 162.57 NOTE
r-devel-osx-x86_64-clang 1.3-250 134.22 NOTE
r-devel-windows-ix86+x86_64 1.3-250 22.00 180.00 202.00 NOTE
r-patched-linux-x86_64 1.3-250 5.64 82.44 88.08 NOTE
r-patched-solaris-sparc 1.3-250 1085.50 NOTE
r-patched-solaris-x86 1.3-250 245.30 NOTE
r-release-linux-x86_64 1.3-250 5.13 83.34 88.48 NOTE
r-release-osx-x86_64-mavericks 1.3-250 NOTE
r-release-osx-x86_64-snowleopard 1.3-250 ERROR
r-release-windows-ix86+x86_64 1.3-250 20.00 179.00 199.00 NOTE
r-oldrel-windows-ix86+x86_64 1.3-250 20.00 194.00 214.00 NOTE

Check Details

Version: 1.3-250
Check: package dependencies
Result: NOTE
    Package which this enhances but not available for checking: ‘OCplus’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

Version: 1.3-250
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘ToDoList.txt’
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: 1.3-250
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘LowRankQP’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.3-250
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     marginal.dt.nparncpt marginal.dt.parncpt marginal.dt.sparncpt
     sparncpF.nparncpF sparncpF.numeric sparncpF.parncpF sparncpt.nparncpt
     sparncpt.numeric sparncpt.parncpt
    See section ‘Registering S3 methods’ 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-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.3-250
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following function:
     ‘plot.subex’
    Found the platform-specific device:
     ‘x11’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    nparncpF.sqp : sqp: no visible global function definition for
     ‘LowRankQP’
    nparncpp: no visible global function definition for ‘LowRankQP’
    nparncpt.sqp : sqp: no visible global function definition for
     ‘LowRankQP’
    
    Found the following assignments to the global environment:
    File ‘pi0/R/cond.cdf.R’:
     assign(".pi0cdfp", hiddenEnv, envir = globalenv())
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.3-250
Check: Rd line widths
Result: NOTE
    Rd file 'combn2R.Rd':
     \examples lines wider than 100 characters:
     combn2R(1:4*2,2,5,1,R=5, sample.method="diff2") ### no common samples, even considering only one group
    
    Rd file 'nparncp.Rd':
     \usage lines wider than 90 characters:
     nparncpt.sqp(tstat, df, penalty=c('3rd.deriv','2nd.deriv','1st.deriv'), lambdas=10^seq(-1,5,by=1),
     starts, IC=c('BIC','CAIC','HQIC','AIC'), K=100, bounds=quantile(tstat,c(.01,.99)),
     solver=c('solve.QP','lsei','ipop','LowRankQP'),plotit=FALSE, verbose=FALSE, approx.hess=TRUE, ... )
    
    Rd file 'pt.sad.Rd':
     \usage lines wider than 90 characters:
     dt.sad(x, df, ncp = 0, log = FALSE, normalize = c("approximate", "derivative", "integral", "none"), epsilon = 1e-04)
    
    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: 1.3-250
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘OCplus’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

Version: 1.3-250
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following function:
     ‘plot.subex’
    Found the platform-specific device:
     ‘x11’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    nparncpF.sqp : sqp: no visible global function definition for
     ‘LowRankQP’
    nparncpp: no visible global function definition for ‘LowRankQP’
    nparncpt.sqp : sqp: no visible global function definition for
     ‘LowRankQP’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 1.3-250
Check: R code for possible problems
Result: NOTE
    nparncpF.sqp : sqp: no visible global function definition for
     'LowRankQP'
    nparncpp: no visible global function definition for 'LowRankQP'
    nparncpt.sqp : sqp: no visible global function definition for
     'LowRankQP'
Flavors: r-devel-windows-ix86+x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.3-250
Check: package dependencies
Result: ERROR
    Package required but not available: ‘qvalue’
    
    Packages which this enhances but not available for checking:
     ‘limma’ ‘OCplus’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64-snowleopard