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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 966/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Icens 1.72.0 (landing page) Bioconductor Package Maintainer
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the Icens package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Icens |
| Version: 1.72.0 |
| 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_1.72.0.tar.gz |
| StartedAt: 2023-10-18 01:20:02 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 01:21:40 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 98.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Icens.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.72.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Icens.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Icens/DESCRIPTION’ ... OK
* this is package ‘Icens’ version ‘1.72.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ISDM 22.407 0.291 34.81
* 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 -2.753681e-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-3.17-bioc-mac-arm64/meat/Icens.Rcheck/00check.log’
for details.
Icens.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Icens ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)
Icens.Rcheck/tests/testbv.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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$values
[1] 9.019594e+00 4.947594e+00 2.889820e+00 2.000000e+00 2.000000e+00
[6] 1.461001e+00 1.207129e+00 1.000000e+00 4.748624e-01 -2.753681e-16
> # one zero eigenvalue
>
> ev1 <- b$vectors[,10]
>
> #but the estimator is unique since we cannot move in the direction of
> #recesion
>
> proc.time()
user system elapsed
1.553 0.150 2.661
Icens.Rcheck/tests/testbv.Rout.save
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
>
Icens.Rcheck/Icens-Ex.timings
| name | user | system | elapsed | |
| BVcliques | 0.053 | 0.010 | 0.097 | |
| BVclmat | 0.445 | 0.017 | 0.710 | |
| BVsupport | 0.449 | 0.007 | 0.693 | |
| EM | 0.041 | 0.005 | 0.070 | |
| EMICM | 0.054 | 0.005 | 0.092 | |
| ISDM | 22.407 | 0.291 | 34.810 | |
| MLEintvl | 0.015 | 0.002 | 0.029 | |
| Maclist | 0.008 | 0.002 | 0.009 | |
| Macmat | 0.008 | 0.001 | 0.012 | |
| PGM | 0.071 | 0.007 | 0.133 | |
| Plotboxes | 0.025 | 0.002 | 0.040 | |
| VEM | 0.061 | 0.003 | 0.099 | |
| cmv | 0.002 | 0.001 | 0.006 | |
| cosmesis | 0.001 | 0.001 | 0.003 | |
| hiv | 0.005 | 0.002 | 0.009 | |
| plot.icsurv | 0.163 | 0.007 | 0.257 | |
| pruitt | 0.001 | 0.001 | 0.002 | |