Last updated on 2020-08-07 01:50:35 CEST.
| Package | NOTE | OK |
|---|---|---|
| AIM | 12 | |
| glasso | 12 | |
| GSA | 12 |
Current CRAN status: NOTE: 12
Version: 1.01
Check: package namespace information
Result: NOTE
Namespace with empty importFrom: 'survival'
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.01
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'survival'
A package should be listed in only one of these fields.
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.01
Check: R code for possible problems
Result: NOTE
backfit.cox.interaction: no visible global function definition for
'coxph'
backfit.lm.interaction: no visible global function definition for 'lm'
backfit.logistic.interaction: no visible global function definition for
'glm'
backfit.logistic.main: no visible global function definition for 'glm'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
cv.lm.interaction: no visible global function definition for 'lm'
cv.lm.main: no visible global function definition for 'lm'
cv.logistic.interaction: no visible global function definition for
'glm'
cv.logistic.main: no visible global function definition for 'glm'
lm.interaction: no visible global function definition for 'lm'
logistic.interaction: no visible global function definition for 'glm'
logistic.main: no visible global function definition for 'glm'
Undefined global functions or variables:
coxph glm lm
Consider adding
importFrom("stats", "glm", "lm")
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.01
Check: Rd line widths
Result: NOTE
Rd file 'cox.interaction.Rd':
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
Rd file 'cox.main.Rd':
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
Rd file 'cv.cox.interaction.Rd':
\usage lines wider than 90 characters:
cv.cox.interaction(x, trt, y, status, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0)
Rd file 'cv.cox.main.Rd':
\usage lines wider than 90 characters:
cv.cox.main(x, y, status, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0)
Rd file 'cv.lm.interaction.Rd':
\usage lines wider than 90 characters:
cv.lm.interaction(x, trt, y, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0)
Rd file 'cv.lm.main.Rd':
\usage lines wider than 90 characters:
cv.lm.main(x, y, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0)
Rd file 'cv.logistic.interaction.Rd':
\usage lines wider than 90 characters:
cv.logistic.interaction(x, trt, y, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0, weight=1)
Rd file 'cv.logistic.main.Rd':
\usage lines wider than 90 characters:
cv.logistic.main(x, y, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0, weight=1)
Rd file 'index.prediction.Rd':
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
Rd file 'lm.interaction.Rd':
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
Rd file 'lm.main.Rd':
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
Rd file 'logistic.interaction.Rd':
\usage lines wider than 90 characters:
logistic.interaction(x, trt, y, nsteps=8, mincut=.1, backfit=F, maxnumcut=1, dirp=0, weight=1)
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
Rd file 'logistic.main.Rd':
\examples lines wider than 100 characters:
## compute the index based on the 2nd model of the sequence using new data xx, and compare the result with the true index
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
Current CRAN status: OK: 12
Current CRAN status: NOTE: 12
Version: 1.03.1
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.03.1
Check: R code for possible problems
Result: NOTE
GSA: no visible global function definition for 'impute.knn'
Undefined global functions or variables:
impute.knn
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.03.1
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: 1.03.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘impute’
Flavor: r-oldrel-macos-x86_64