Last updated on 2018-06-17 19:49:32 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2-1 | 2.65 | 20.68 | 23.33 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2-1 | 2.35 | 16.24 | 18.59 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2-1 | 34.53 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2-1 | 31.88 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 0.2-1 | 12.00 | 49.00 | 61.00 | NOTE | |
| r-patched-linux-x86_64 | 0.2-1 | 2.36 | 19.49 | 21.85 | ERROR | |
| r-patched-solaris-x86 | 0.2-1 | 51.60 | NOTE | |||
| r-release-linux-x86_64 | 0.2-1 | 2.54 | 19.61 | 22.15 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.2-1 | 14.00 | 54.00 | 68.00 | NOTE | |
| r-release-osx-x86_64 | 0.2-1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2-1 | 8.00 | 42.00 | 50.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.2-1 | NOTE |
Version: 0.2-1
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Title field: should not end in a period.
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: 0.2-1
Check: S3 generic/method consistency
Result: NOTE
Found the following apparent S3 methods exported but not registered:
plot.cghFLasso print.summary.cghFLasso summary.cghFLasso
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: 0.2-1
Check: R code for possible problems
Result: NOTE
CGH.fused.lasso.one.fast: no visible global function definition for
‘lowess’
L2L1ExpandFit: no visible global function definition for
‘L2L1PathExtract’
consensusFDR: no visible global function definition for ‘pbinom’
my.mad: no visible global function definition for ‘median’
output.cghFLasso: no visible global function definition for
‘write.table’
plot.CGH.FL.All: no visible global function definition for ‘plot’
plot.CGH.FL.All: no visible global function definition for ‘segments’
plot.CGH.FL.All: no visible global function definition for ‘text’
plot.CGH.FL.Consensus: no visible global function definition for
‘rainbow’
plot.CGH.FL.Consensus: no visible global function definition for ‘plot’
plot.CGH.FL.Consensus: no visible global function definition for
‘segments’
plot.CGH.FL.Consensus: no visible global function definition for ‘gray’
plot.CGH.FL.Consensus: no visible global function definition for ‘text’
plot.CGH.FL.Single: no visible global function definition for ‘plot’
plot.CGH.FL.Single: no visible global function definition for ‘gray’
plot.CGH.FL.Single: no visible global function definition for
‘segments’
plot.CGH.FL.Single: no visible global function definition for ‘text’
plot.cghFLasso: no visible global function definition for ‘plot’
plot.cghFLasso: no visible global function definition for ‘gray’
plot.cghFLasso: no visible global function definition for ‘abline’
plot.cghFLasso: no visible global function definition for ‘points’
segment.score: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
L2L1PathExtract abline gray lowess median pbinom plot pnorm points
rainbow segments text write.table
Consider adding
importFrom("grDevices", "gray", "rainbow")
importFrom("graphics", "abline", "plot", "points", "segments", "text")
importFrom("stats", "lowess", "median", "pbinom", "pnorm")
importFrom("utils", "write.table")
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: 0.2-1
Check: Rd line widths
Result: NOTE
Rd file 'cghFLasso.Rd':
\usage lines wider than 90 characters:
cghFLasso(CGH.Array, chromosome=NULL, nucleotide.position=NULL, FL.norm=NULL, FDR=NULL, filter=NULL, missing.PlugIn=TRUE, smooth.size=5 ... [TRUNCATED]
\examples lines wider than 100 characters:
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
Rd file 'cghFLasso.ref.Rd':
\examples lines wider than 100 characters:
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
Rd file 'output.cghFLasso.Rd':
\examples lines wider than 100 characters:
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
Rd file 'plot.cghFLasso.Rd':
\examples lines wider than 100 characters:
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
Rd file 'summary.cghFLasso.Rd':
\examples lines wider than 100 characters:
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
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: 0.2-1
Check: Rd \usage sections
Result: NOTE
S3 methods shown with full name in documentation object 'plot.cghFLasso':
‘plot.cghFLasso’
S3 methods shown with full name in documentation object 'summary.cghFLasso':
‘summary.cghFLasso’ ‘print.summary.cghFLasso’
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: 0.2-1
Check: compiled code
Result: NOTE
File ‘cghFLasso/libs/cghFLasso.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable 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-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2-1
Check: examples
Result: ERROR
Running examples in ‘cghFLasso-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cghFLasso
> ### Title: A function to call alteration for CGH arrays using the fused
> ### lasso regression
> ### Aliases: cghFLasso
> ### Keywords: methods
>
> ### ** Examples
>
>
> library(cghFLasso)
> data(CGH)
>
> #############
> ### Example 1: Process one chromosome vector without using normal references.
>
> CGH.FL.obj1<-cghFLasso(CGH$GBM.y)
[1] 1
> plot(CGH.FL.obj1, index=1, type="Lines")
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64