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This page was generated on 2018-04-12 13:17:28 -0400 (Thu, 12 Apr 2018).
Package 674/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Icens 1.50.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: Icens |
Version: 1.50.0 |
Command: rm -rf Icens.buildbin-libdir Icens.Rcheck && mkdir Icens.buildbin-libdir Icens.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Icens.buildbin-libdir Icens_1.50.0.tar.gz >Icens.Rcheck\00install.out 2>&1 && cp Icens.Rcheck\00install.out Icens-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Icens.buildbin-libdir --install="check:Icens-install.out" --force-multiarch --no-vignettes --timings Icens_1.50.0.tar.gz |
StartedAt: 2018-04-12 00:47:01 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:48:13 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 72.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Icens.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Icens.buildbin-libdir Icens.Rcheck && mkdir Icens.buildbin-libdir Icens.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Icens.buildbin-libdir Icens_1.50.0.tar.gz >Icens.Rcheck\00install.out 2>&1 && cp Icens.Rcheck\00install.out Icens-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Icens.buildbin-libdir --install="check:Icens-install.out" --force-multiarch --no-vignettes --timings Icens_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Icens.Rcheck' * using R version 3.4.4 (2018-03-15) * 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 '1.50.0' * 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 * 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 4.639536e-17 --- > [6] 1.461001e+00 1.207129e+00 1.000000e+00 4.748624e-01 -2.480201e-16 Warning message: running command '"diff" -bw "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\Rtmpikhwjy\Rdiffa20f05bdc74a" "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\Rtmpikhwjy\Rdiffb20f03166e37"' had status 1 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 Warning message: running command '"diff" -bw "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpkvxLqO\Rdiffa29d427bf3eac" "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpkvxLqO\Rdiffb29d428784567"' had status 1 OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Icens.Rcheck/00check.log' for details.
Icens.Rcheck/00install.out
install for i386 * installing *source* package 'Icens' ... ** R ** data ** inst ** preparing 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 In R CMD INSTALL install for x64 * installing *source* package 'Icens' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'Icens' as Icens_1.50.0.zip * DONE (Icens) In R CMD INSTALL In R CMD INSTALL
Icens.Rcheck/tests_i386/testbv.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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$values [1] 9.019594e+00 4.947594e+00 2.889820e+00 2.000000e+00 2.000000e+00 [6] 1.461001e+00 1.207129e+00 1.000000e+00 4.748624e-01 4.639536e-17 > # one zero eigenvalue > > ev1 <- b$vectors[,10] > > #but the estimator is unique since we cannot move in the direction of > #recesion > > proc.time() user system elapsed 1.37 0.06 1.42 |
Icens.Rcheck/tests_x64/testbv.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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 1.53 0.07 1.59 |
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 > |
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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 > |
Icens.Rcheck/examples_i386/Icens-Ex.timings
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Icens.Rcheck/examples_x64/Icens-Ex.timings
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