Last updated on 2024-08-31 23:49:42 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| base.rms | 9 | 4 | |
| cutoff | 9 | 4 | |
| do | 9 | 4 | |
| ggrisk | 9 | 4 | |
| msig | 9 | 4 | |
| nomogramFormula | 9 | 4 |
Current CRAN status: ERROR: 9, NOTE: 4
Version: 1.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘do’
See section ‘The DESCRIPTION file’ 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: 1.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0
Check: examples
Result: ERROR
Running examples in 'base.rms-Ex.R' failed
The error most likely occurred in:
> ### Name: coxph2cph
> ### Title: Convert results of cox regression from coxph() to cph()
> ### Aliases: coxph2cph
>
> ### ** Examples
>
> library(survival)
> fit <- coxph(Surv(mpg,vs)~am+gear+carb,data=mtcars)
> coxph2cph(fit)
Error: object '.__T__[:base' is not exported by 'namespace:data.table'
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown
Quitting from lines 47-49 [unnamed-chunk-6] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
object '.__T__[:base' is not exported by 'namespace:data.table'
--- failed re-building 'tutorial.Rmd'
--- re-building 'version.Rmd' using rmarkdown
--- finished re-building 'version.Rmd'
SUMMARY: processing the following file failed:
'tutorial.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 9, NOTE: 4
Version: 1.3
Check: package dependencies
Result: ERROR
Packages required but not available: 'set', 'do'
See section ‘The DESCRIPTION file’ 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: 1.3
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.3
Check: examples
Result: ERROR
Running examples in 'cutoff-Ex.R' failed
The error most likely occurred in:
> ### Name: cox
> ### Title: Significant Cutoff Value for Cox Regression
> ### Aliases: cox
>
> ### ** Examples
>
> cox(data=mtcars,
+ time = 'disp', y='am', x='wt',
+ cut.numb=2,
+ n.per=0.25,
+ y.per=0.10)
1: all combination: 406
2: filter by n.per
----
Error: object '.__T__[:base' is not exported by 'namespace:data.table'
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 9, OK: 4
Version: 2.0.0.0
Check: whether package can be installed
Result: ERROR
Installation failed.
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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 9, OK: 4
Version: 1.3
Check: package dependencies
Result: ERROR
Packages required but not available:
'do', 'set', 'cutoff', 'nomogramFormula'
See section ‘The DESCRIPTION file’ 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: 1.3
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 9, OK: 4
Version: 1.0
Check: package dependencies
Result: ERROR
Packages required but not available: 'do', 'set'
See section ‘The DESCRIPTION file’ 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: 1.0
Check: examples
Result: ERROR
Running examples in 'msig-Ex.R' failed
The error most likely occurred in:
> ### Name: local_msig
> ### Title: Query gene set names from local data
> ### Aliases: local_msig
>
> ### ** Examples
>
> x <- local_msig('IMMUNE_RESPONSE')
Error: object '.__T__[:base' is not exported by 'namespace:data.table'
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 9, NOTE: 4
Version: 1.2.0.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘do’
See section ‘The DESCRIPTION file’ 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: 1.2.0.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2.0.0
Check: examples
Result: ERROR
Running examples in 'nomogramFormula-Ex.R' failed
The error most likely occurred in:
> ### Name: TotalPoints.rms
> ### Title: Caculate Total Points for nomogram Picture
> ### Aliases: TotalPoints.rms
>
> ### ** Examples
>
> library(rms)
Loading required package: Hmisc
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
> n <- 1000
> set.seed(17)
> d <- data.frame(age = rnorm(n, 50, 10),
+ blood.pressure = rnorm(n, 120, 15),
+ cholesterol = rnorm(n, 200, 25),
+ sex = factor(sample(c('female','male'), n,TRUE)))
>
> d <- upData(d,
+ L = .4*(sex=='male') + .045*(age-50) +
+ (log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')),
+ y = ifelse(runif(n) < plogis(L), 1, 0))
Input object size: 29616 bytes; 4 variables 1000 observations
Added variable L
Added variable y
New object size: 41856 bytes; 6 variables 1000 observations
>
> ddist <- datadist(d); options(datadist='ddist')
>
> f <- lrm(y ~ lsp(age,50) + sex * rcs(cholesterol, 4) + blood.pressure,
+ data=d)
> nom <- nomogram(f)
> TotalPoints.rms(rd = d,fit = f,nom = nom)
Error: object '.__T__[:base' is not exported by 'namespace:data.table'
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64