Multiple platform build/check report for BioC 3.14 - CHECK results for Icens on machv2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /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_1.66.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Icens.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Icens/DESCRIPTION’ ... OK
* this is package ‘Icens’ version ‘1.66.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 R 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 -2.640501e-16
---
>  [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -2.480201e-16
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/Icens.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Icens
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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$values
 [1]  9.019594e+00  4.947594e+00  2.889820e+00  2.000000e+00  2.000000e+00
 [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -2.640501e-16
>    # one zero eigenvalue
> 
>    ev1 <- b$vectors[,10]
> 
>    #but the estimator is unique since we cannot move in the direction of
>    #recesion
> 
> proc.time()
   user  system elapsed 
  2.128   0.179   2.285


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
>

name	user	system	elapsed
BVcliques	0.094	0.017	0.110
BVclmat	0.805	0.026	0.831
BVsupport	0.777	0.010	0.788
EM	0.085	0.008	0.093
EMICM	0.099	0.006	0.106
ISDM	3.670	0.022	3.697
MLEintvl	0.032	0.002	0.034
Maclist	0.009	0.001	0.010
Macmat	0.013	0.002	0.015
PGM	0.151	0.011	0.162
Plotboxes	0.048	0.003	0.050
VEM	0.147	0.005	0.151
cmv	0.002	0.002	0.004
cosmesis	0.002	0.001	0.002
hiv	0.007	0.002	0.009
plot.icsurv	0.329	0.009	0.337
pruitt	0.001	0.001	0.002

CHECK results for Icens on machv2

Summary

Command output

Installation output

Tests output

Example timings