Last updated on 2018-02-24 09:51:30 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.03 | 2.25 | 24.21 | 26.46 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.03 | 1.44 | 18.62 | 20.06 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.03 | 33.27 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.03 | 31.23 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.03 | 5.00 | 44.00 | 49.00 | NOTE | |
| r-patched-linux-x86_64 | 1.03 | 0.77 | 24.81 | 25.58 | NOTE | |
| r-patched-solaris-x86 | 1.03 | 39.70 | NOTE | |||
| r-release-linux-x86_64 | 1.03 | 0.78 | 24.49 | 25.27 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.03 | 2.00 | 34.00 | 36.00 | NOTE | |
| r-release-osx-x86_64 | 1.03 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.03 | 3.00 | 34.00 | 37.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.03 | NOTE |
Version: 1.03
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-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: 1.03
Check: dependencies in R code
Result: NOTE
'library' or 'require' call to ‘impute’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested 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-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: 1.03
Check: S3 generic/method consistency
Result: NOTE
Found the following apparent S3 methods exported but not registered:
print.GSA print.GSA.func summary.GSA.genesets
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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 1.03
Check: R code for possible problems
Result: NOTE
GSA: no visible global function definition for ‘impute.knn’
GSA.correlate: no visible global function definition for ‘quantile’
GSA.func: no visible global function definition for ‘quantile’
GSA.func: no visible global function definition for ‘var’
GSA.func: no visible global function definition for ‘qnorm’
GSA.func: no visible global function definition for ‘pt’
GSA.plot: no visible global function definition for ‘plot’
GSA.plot: no visible global function definition for ‘points’
GSA.plot: no visible global function definition for ‘legend’
GSA.xl.correlate: no visible global function definition for ‘quantile’
GSA.xl.plot: no visible global function definition for ‘runif’
GSA.xl.summary.genesets: no visible global function definition for
‘quantile’
est.s0: no visible global function definition for ‘quantile’
est.s0: no visible global function definition for ‘mad’
est.s0: no visible global function definition for ‘var’
paired.perm: no visible global function definition for ‘runif’
paired.ttest.func: no visible global function definition for ‘var’
tCorr.func: no visible global function definition for ‘cor’
taCorr.func: no visible global function definition for ‘cor’
Undefined global functions or variables:
cor impute.knn legend mad plot points pt qnorm quantile runif var
Consider adding
importFrom("graphics", "legend", "plot", "points")
importFrom("stats", "cor", "mad", "pt", "qnorm", "quantile", "runif",
"var")
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, r-oldrel-osx-x86_64
Version: 1.03
Check: Rd line widths
Result: NOTE
Rd file 'GSA.Rd':
\usage lines wider than 90 characters:
method=c("maxmean","mean","absmean"), resp.type=c("Quantitative","Two class unpaired","Survival","Multiclass", "Two class paired", "tCo ... [TRUNCATED]
\examples lines wider than 100 characters:
GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets, resp.type="Two class unpaired", nperms=100)
# GSA.obj<-GSA(x,y, genenames=genenames, genesets=geneset.obj$genesets, resp.type="Two class unpaired", nperms=100)
Rd file 'GSA.func.Rd':
\usage lines wider than 90 characters:
s0 = NULL, s0.perc = NULL, minsize = 15, maxsize= 500, restand = TRUE, restand.basis=c("catalog","data"))
\examples lines wider than 100 characters:
# GSA.func.obj<-GSA.func(x,y, genenames=genenames, genesets=geneset.obj$genesets, resp.type="Two class unpaired")
Rd file 'GSA.genescores.Rd':
\examples lines wider than 100 characters:
GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets, resp.type="Two class unpaired", nperms=100)
Rd file 'GSA.listsets.Rd':
\examples lines wider than 100 characters:
GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets, resp.type="Two class unpaired", nperms=100)
Rd file 'GSA.plot.Rd':
\examples lines wider than 100 characters:
GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets, resp.type="Two class unpaired", nperms=100)
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: 1.03
Check: Rd \usage sections
Result: NOTE
S3 methods shown with full name in documentation object 'GSA-internal':
‘print.GSA.func’ ‘print.GSA’ ‘summary.GSA.genesets’
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.
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: 1.03
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘impute’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64