Bioconductor Package Maintainer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/Icens |
| Branch: RELEASE_3_12 |
| Last Commit: 134c530 |
| Last Changed Date: 2020-10-27 10:23:36 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:48 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the Icens package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 864/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Icens 1.62.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Icens |
| Version: 1.62.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Icens.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Icens_1.62.0.tar.gz |
| StartedAt: 2021-05-06 03:44:22 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:45:50 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 87.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Icens.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Icens.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Icens_1.62.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Icens.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Icens/DESCRIPTION' ... OK
* this is package 'Icens' version '1.62.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ISDM 5.25 0.02 5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
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
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/Icens.Rcheck/00check.log'
for details.
Icens.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Icens_1.62.0.tar.gz && rm -rf Icens.buildbin-libdir && mkdir Icens.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Icens.buildbin-libdir Icens_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Icens_1.62.0.zip && rm Icens_1.62.0.tar.gz Icens_1.62.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 21196 100 21196 0 0 744k 0 --:--:-- --:--:-- --:--:-- 766k
install for i386
* installing *source* package 'Icens' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Icens'
finding HTML links ... done
BVcliques html
BVclmat html
BVsupport html
Bisect html
EM html
EMICM html
ISDM html
Icens-internal html
MLEintvl html
Maclist html
Macmat html
PGM html
PMGA html
Plotboxes html
VEM html
cmv html
cosmesis html
hiv html
icsurv html
plot.icsurv html
pruitt html
** 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
install for x64
* installing *source* package 'Icens' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Icens' as Icens_1.62.0.zip
* DONE (Icens)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Icens' successfully unpacked and MD5 sums checked
|
Icens.Rcheck/tests_i386/testbv.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
1.65 0.15 1.96
|
Icens.Rcheck/tests_x64/testbv.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
1.57 0.09 1.65
|
|
Icens.Rcheck/tests_i386/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/tests_x64/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
>
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Icens.Rcheck/examples_i386/Icens-Ex.timings
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Icens.Rcheck/examples_x64/Icens-Ex.timings
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