CRAN Package Check Results for Package HAP.ROR

Last updated on 2015-08-27 23:46:55.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 0.94 20.02 20.96 NOTE
r-devel-linux-x86_64-debian-gcc 1.0 0.96 18.92 19.89 NOTE
r-devel-linux-x86_64-fedora-clang 1.0 41.88 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 37.95 NOTE
r-devel-osx-x86_64-clang 1.0 39.07 NOTE
r-devel-windows-ix86+x86_64 1.0 5.00 38.00 43.00 NOTE
r-patched-linux-x86_64 1.0 0.98 20.38 21.36 NOTE
r-patched-solaris-sparc 1.0 265.90 NOTE
r-patched-solaris-x86 1.0 55.70 NOTE
r-release-linux-x86_64 1.0 0.98 20.20 21.18 NOTE
r-release-osx-x86_64-mavericks 1.0 NOTE
r-release-windows-ix86+x86_64 1.0 4.00 57.00 61.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0 6.00 64.00 70.00 NOTE

Check Details

Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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

Version: 1.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘ape’ which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘ape’ ‘hash’
     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: 1.0
Check: R code for possible problems
Result: NOTE
    AIC: no visible global function definition for ‘hash’
    AIC: no visible global function definition for ‘values’
    AIC: no visible global function definition for ‘contr.treatment’
    AIC: no visible global function definition for ‘values<-’
    AIC: no visible global function definition for ‘glm’
    AIC: no visible binding for global variable ‘binomial’
    AIC: no visible global function definition for ‘fitted’
    ODS.ror: no visible global function definition for ‘write.table’
    ODS.ror: no visible global function definition for ‘hash’
    ODS.ror: no visible global function definition for ‘values<-’
    ODS.ror: no visible global function definition for ‘keys’
    ODS.ror: no visible global function definition for ‘values’
    ODS.ror: no visible global function definition for ‘read.tree’
    ODS.ror: no visible global function definition for ‘colorRampPalette’
    ODS.ror: no visible global function definition for ‘plot’
    ODS.ror: no visible global function definition for ‘nodelabels’
    cc.sim: no visible global function definition for ‘hash’
    cc.sim: no visible global function definition for ‘values<-’
    cc.sim: no visible global function definition for ‘values’
    cc.sim: no visible global function definition for ‘rbinom’
    collapse: no visible global function definition for ‘hash’
    collapse: no visible global function definition for ‘values<-’
    collapse: no visible global function definition for ‘keys’
    collapse: no visible global function definition for ‘values’
    deletion: no visible global function definition for ‘hash’
    deletion: no visible global function definition for ‘values<-’
    deletion: no visible global function definition for ‘keys’
    deletion: no visible global function definition for ‘values’
    deletion: no visible global function definition for ‘pchisq’
    grp.list: no visible global function definition for ‘hash’
    grp.list: no visible global function definition for ‘values’
    Undefined global functions or variables:
     binomial colorRampPalette contr.treatment fitted glm hash keys
     nodelabels pchisq plot rbinom read.tree values values<- write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette")
     importFrom("graphics", "plot")
     importFrom("stats", "binomial", "contr.treatment", "fitted", "glm",
     "pchisq", "rbinom")
     importFrom("utils", "write.table")
    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: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'HAP.ROR-package.Rd':
     \examples lines wider than 100 characters:
     ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev ... [TRUNCATED]
    
    Rd file 'HAP.ror.Rd':
     \usage lines wider than 90 characters:
     HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha = 0.01, ref.level = NA, display.proc = TRUE)
    
    Rd file 'ODS.ror.Rd':
     \usage lines wider than 90 characters:
     ODS.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, records, dev.list, AIC.list, deleted.snps.ls, proteinf, locus = "DRB1*", ref.level = ... [TRUNCATED]
     \examples lines wider than 100 characters:
     ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev ... [TRUNCATED]
    
    Rd file 'cc.sim.Rd':
     \usage lines wider than 90 characters:
     cc.sim(n.ctrl, n.case, beta0, beta1, case.sub, ctl.sub, lib.sub, lib.sub.names, risk.type = "AA", risk.inx = 2, risk.names = c("301", " ... [TRUNCATED]
    
    Rd file 'deletion.Rd':
     \usage lines wider than 90 characters:
     deletion(lib, lib.names, case.sub, ctl.sub, aic.now, dev.now, df.now, rank = FALSE, cut = -1, delete.snp = -1, ref = "NA", alpha = 0.05 ... [TRUNCATED]
    
    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: 1.0
Check: R code for possible problems
Result: NOTE
    AIC: no visible global function definition for ‘hash’
    AIC: no visible global function definition for ‘values’
    AIC: no visible global function definition for ‘values<-’
    ODS.ror: no visible global function definition for ‘hash’
    ODS.ror: no visible global function definition for ‘values<-’
    ODS.ror: no visible global function definition for ‘keys’
    ODS.ror: no visible global function definition for ‘values’
    ODS.ror: no visible global function definition for ‘read.tree’
    ODS.ror: no visible global function definition for ‘nodelabels’
    cc.sim: no visible global function definition for ‘hash’
    cc.sim: no visible global function definition for ‘values<-’
    cc.sim: no visible global function definition for ‘values’
    collapse: no visible global function definition for ‘hash’
    collapse: no visible global function definition for ‘values<-’
    collapse: no visible global function definition for ‘keys’
    collapse: no visible global function definition for ‘values’
    deletion: no visible global function definition for ‘hash’
    deletion: no visible global function definition for ‘values<-’
    deletion: no visible global function definition for ‘keys’
    deletion: no visible global function definition for ‘values’
    grp.list: no visible global function definition for ‘hash’
    grp.list: no visible global function definition for ‘values’
    Undefined global functions or variables:
     hash keys nodelabels read.tree values values<-
Flavor: r-devel-osx-x86_64-clang

Version: 1.0
Check: R code for possible problems
Result: NOTE
    AIC: no visible global function definition for ‘hash’
    AIC: no visible global function definition for ‘values’
    AIC: no visible global function definition for ‘values<-’
    ODS.ror: no visible global function definition for ‘hash’
    ODS.ror: no visible global function definition for ‘values<-’
    ODS.ror: no visible global function definition for ‘keys’
    ODS.ror: no visible global function definition for ‘values’
    ODS.ror: no visible global function definition for ‘read.tree’
    ODS.ror: no visible global function definition for ‘nodelabels’
    cc.sim: no visible global function definition for ‘hash’
    cc.sim: no visible global function definition for ‘values<-’
    cc.sim: no visible global function definition for ‘values’
    collapse: no visible global function definition for ‘hash’
    collapse: no visible global function definition for ‘values<-’
    collapse: no visible global function definition for ‘keys’
    collapse: no visible global function definition for ‘values’
    deletion: no visible global function definition for ‘hash’
    deletion: no visible global function definition for ‘values<-’
    deletion: no visible global function definition for ‘keys’
    deletion: no visible global function definition for ‘values’
    grp.list: no visible global function definition for ‘hash’
    grp.list: no visible global function definition for ‘values’
Flavors: 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