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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Icens.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Icens_1.79.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Icens.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Icens/DESCRIPTION’ ... OK
* this is package ‘Icens’ version ‘1.79.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Icens’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
VEMICMmac: no visible binding for global variable ‘EMstep’
Undefined global functions or variables:
  EMstep
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testbv.R’
  Comparing ‘testbv.Rout’ to ‘testbv.Rout.save’ ...117c117
<  [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -1.624956e-16
---
>  [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -2.480201e-16
 NOTE
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Icens.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Icens
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Icens’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Icens)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #some random data
> library(Icens)
Loading required package: survival
> 
> intvlx <- matrix(c(
+ 0.8820387, 10.666764,
+ 15.2923703, 18.390665,
+ 10.0710104,
+ 18.9,
+ 7.9796946, 10.964210,
+ 5.2703924, 11.267734,
+ 18.7,
+ 19.875977,
+ 5.9667531, 19.886629,
+ 9.7729062, 13.055671,
+ 3.1947369,
+ 7.482414,
+ 4.2636605,  7.216566,
+ 5.3197158, 15.686208,
+ 0.2885009,
+ 11.463272,
+ 0.2885009,
+ 11.463272),ncol=2,byrow=TRUE)
> 
> intvly <- matrix(c(
+ 8.431484, 11.324923,
+ 9.6,
+ 18.739108,
+ 1.438516,  3.232738,
+ 10.6, 11.711857,
+ 14.298833,
+ 16.752745,
+ 9.431221, 16.958045,
+ 2.396955,  7.541405,
+ 12.334413,
+ 21.932913,
+ 7.0, 19.268005,
+ 9.342461, 13.843589,
+ 14.717762,
+ 22.361883,
+ 16.983453, 20.541734,
+ 7.918273, 10.),ncol=2,byrow=TRUE)
> 
> #find the cliques
> BVcliques(intvlx,intvly)
[[1]]
[1] 7 9

[[2]]
[1] 10  9  1 13

[[3]]
[1] 11  5  9

[[4]]
[1] 11  9 12

[[5]]
[1] 3 7

[[6]]
[1] 4 1

[[7]]
[1]  8 11  5

[[8]]
[1]  8 11 12

[[9]]
[1]  2 11

[[10]]
[1] 6

> 
> #find the support
> BVsupport(intvlx,intvly)
         xlo       xhi       ylo       yhi
1   5.966753  7.482414  7.000000  7.541405
2   4.263661  7.216566  9.342461 10.000000
3   5.319716  7.482414 14.717762 16.752745
4   5.319716  7.482414 16.983453 19.268005
5  10.071010 18.900000  2.396955  3.232738
6   7.979695 10.666764 10.600000 11.324923
7   9.772906 11.267734 14.717762 16.752745
8   9.772906 11.463272 16.983453 20.541734
9  15.292370 15.686208 14.717762 18.739108
10 18.700000 19.875977  9.431221 16.958045
> 
> #find the clique matrix
> clmat <- BVclmat(BVcliques(intvlx,intvly))
> 
> #the matrix is rank deficient
>  clmat[4,]+clmat[7,]-clmat[3,]-clmat[8,]
 [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
> 
> #should be the zero vector
> 
> #now for some estimation
> 
>  p1 <- VEM(clmat)
> 
>  p2 <- PGM(clmat)
> 
>  #p3 seems to be different from p1 and p2!
>  p3 <- EMICM(clmat)
> 
>  # so is the est unique?
> 
>   w<-clmat%*%t(clmat)
>   b<-eigen(w)
> 
>    b$values
 [1]  9.019594e+00  4.947594e+00  2.889820e+00  2.000000e+00  2.000000e+00
 [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -1.624956e-16
>    # one zero eigenvalue
> 
>    ev1 <- b$vectors[,10]
> 
>    #but the estimator is unique since we cannot move in the direction of
>    #recesion
> 
> proc.time()
   user  system elapsed 
  0.826   0.096   0.923 

R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.0 Under development (unstable) (2004-03-04), ISBN 3-900051-00-3

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> #some random data
> library(Icens)
> 
> intvlx <- matrix(c(
+ 0.8820387, 10.666764,
+ 15.2923703, 18.390665,
+ 10.0710104,
+ 18.9,
+ 7.9796946, 10.964210,
+ 5.2703924, 11.267734,
+ 18.7,
+ 19.875977,
+ 5.9667531, 19.886629,
+ 9.7729062, 13.055671,
+ 3.1947369,
+ 7.482414,
+ 4.2636605,  7.216566,
+ 5.3197158, 15.686208,
+ 0.2885009,
+ 11.463272,
+ 0.2885009,
+ 11.463272),ncol=2,byrow=TRUE)
> 
> intvly <- matrix(c(
+ 8.431484, 11.324923,
+ 9.6,
+ 18.739108,
+ 1.438516,  3.232738,
+ 10.6, 11.711857,
+ 14.298833,
+ 16.752745,
+ 9.431221, 16.958045,
+ 2.396955,  7.541405,
+ 12.334413,
+ 21.932913,
+ 7.0, 19.268005,
+ 9.342461, 13.843589,
+ 14.717762,
+ 22.361883,
+ 16.983453, 20.541734,
+ 7.918273, 10.),ncol=2,byrow=TRUE)
> 
> #find the cliques
> BVcliques(intvlx,intvly)
[[1]]
[1] 7 9

[[2]]
[1] 10  9  1 13

[[3]]
[1] 11  5  9

[[4]]
[1] 11  9 12

[[5]]
[1] 3 7

[[6]]
[1] 4 1

[[7]]
[1]  8 11  5

[[8]]
[1]  8 11 12

[[9]]
[1]  2 11

[[10]]
[1] 6

> 
> #find the support
> BVsupport(intvlx,intvly)
         xlo       xhi       ylo       yhi
1   5.966753  7.482414  7.000000  7.541405
2   4.263661  7.216566  9.342461 10.000000
3   5.319716  7.482414 14.717762 16.752745
4   5.319716  7.482414 16.983453 19.268005
5  10.071010 18.900000  2.396955  3.232738
6   7.979695 10.666764 10.600000 11.324923
7   9.772906 11.267734 14.717762 16.752745
8   9.772906 11.463272 16.983453 20.541734
9  15.292370 15.686208 14.717762 18.739108
10 18.700000 19.875977  9.431221 16.958045
> 
> #find the clique matrix
> clmat <- BVclmat(BVcliques(intvlx,intvly))
> 
> #the matrix is rank deficient
>  clmat[4,]+clmat[7,]-clmat[3,]-clmat[8,]
 [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
> 
> #should be the zero vector
> 
> #now for some estimation
> 
>  p1 <- VEM(clmat)
> 
>  p2 <- PGM(clmat)
> 
>  #p3 seems to be different from p1 and p2!
>  p3 <- EMICM(clmat)
> 
>  # so is the est unique?
> 
>   w<-clmat%*%t(clmat)
>   b<-eigen(w)
> 
>    b$values
 [1]  9.019594e+00  4.947594e+00  2.889820e+00  2.000000e+00  2.000000e+00
 [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -2.480201e-16
>    # one zero eigenvalue
> 
>    ev1 <- b$vectors[,10]
> 
>    #but the estimator is unique since we cannot move in the direction of
>    #recesion
>