Package: MANOR

Version: 1.59.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MANOR

StartedAt: 2020-01-15 19:55:14 -0500 (Wed, 15 Jan 2020)

EndedAt: 2020-01-15 19:55:25 -0500 (Wed, 15 Jan 2020)

EllapsedTime: 10.8 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MANOR
###
##############################################################################
##############################################################################


* checking for file ‘MANOR/DESCRIPTION’ ... OK
* preparing ‘MANOR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MANOR.Rnw’ using Sweave
Loading required package: MANOR
Loading required package: GLAD

######################################################################################

Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

######################################################################################

New options are available in daglad: see help for details.

Warning: Package 'MANOR' is deprecated and will be removed from Bioconductor
  version 3.12

Attaching package: ‘MANOR’

The following object is masked from ‘package:base’:

    norm


Error: processing vignette 'MANOR.Rnw' failed with diagnostics:
 chunk 16 
Error in UseMethod("genome.plot") : 
  no applicable method for 'genome.plot' applied to an object of class "arrayCGH"

--- failed re-building ‘MANOR.Rnw’

SUMMARY: processing the following file failed:
  ‘MANOR.Rnw’

Error: Vignette re-building failed.
Execution halted