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This page was generated on 2023-04-12 10:55:37 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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CHECK results for Icens on nebbiolo2


To the developers/maintainers of the Icens package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Icens.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 958/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Icens 1.71.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/Icens
git_branch: devel
git_last_commit: d2b330d
git_last_commit_date: 2022-11-01 10:36:46 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: Icens
Version: 1.71.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Icens.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Icens_1.71.0.tar.gz
StartedAt: 2023-04-12 06:52:45 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 06:53:29 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 44.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Icens.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Icens.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Icens_1.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Icens.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘Icens/DESCRIPTION’ ... OK
* this is package ‘Icens’ version ‘1.71.0’
* 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 loading without being on the library search path ... 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
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Icens.Rcheck/00check.log’
for details.



Installation output

Icens.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Icens
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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

Icens.Rcheck/tests/testbv.Rout


R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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$values
 [1]  9.019594e+00  4.947594e+00  2.889820e+00  2.000000e+00  2.000000e+00
 [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -1.624956e-16
>    # one zero eigenvalue
> 
>    ev1 <- b$vectors[,10]
> 
>    #but the estimator is unique since we cannot move in the direction of
>    #recesion
> 
> proc.time()
   user  system elapsed 
  1.369   0.087   1.440 

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
> 

Example timings

Icens.Rcheck/Icens-Ex.timings

nameusersystemelapsed
BVcliques0.0390.0160.055
BVclmat0.3960.0040.400
BVsupport0.3920.0000.392
EM0.0350.0000.035
EMICM0.0470.0000.047
ISDM3.3630.1473.511
MLEintvl0.0110.0040.014
Maclist0.0080.0010.008
Macmat0.0080.0000.008
PGM0.0520.0070.061
Plotboxes0.0220.0070.030
VEM0.0520.0050.057
cmv0.0020.0000.002
cosmesis0.0020.0000.001
hiv0.0050.0000.005
plot.icsurv0.1530.0120.165
pruitt0.0010.0000.001