Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the EBarrays package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBarrays.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 547/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EBarrays 2.56.0 (landing page) Ming Yuan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: EBarrays |
Version: 2.56.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBarrays.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EBarrays_2.56.0.tar.gz |
StartedAt: 2021-10-14 22:36:58 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:38:23 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 85.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EBarrays.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBarrays.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EBarrays_2.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'EBarrays/DESCRIPTION' ... OK * this is package 'EBarrays' version '2.56.0' * 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 'EBarrays' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'Biobase' 'lattice' 'methods' A package should be listed in only one of these fields. * 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 'library' or 'require' call to 'lattice' which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.ebarraysEMfit See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE prepare_Rd: crit.fun.Rd:51: Dropping empty section \keyword prepare_Rd: ebplots.Rd:116-117: Dropping empty section \examples * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/EBarrays/libs/i386/EBarrays.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/EBarrays/libs/x64/EBarrays.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... 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 'test.R' OK ** running tests for arch 'x64' ... Running 'test.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.Rcheck/00check.log' for details.
EBarrays.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/EBarrays_2.56.0.tar.gz && rm -rf EBarrays.buildbin-libdir && mkdir EBarrays.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBarrays.buildbin-libdir EBarrays_2.56.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL EBarrays_2.56.0.zip && rm EBarrays_2.56.0.tar.gz EBarrays_2.56.0.zip ### ############################################################################## ############################################################################## % 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 243k 100 243k 0 0 847k 0 --:--:-- --:--:-- --:--:-- 850k install for i386 * installing *source* package 'EBarrays' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ebarrays.c -o ebarrays.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o EBarrays.dll tmp.def ebarrays.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.buildbin-libdir/00LOCK-EBarrays/00new/EBarrays/libs/i386 ** R ** data ** demo ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'EBarrays' finding HTML links ... done EBarrays-Internal html crit.fun html ebarraysFamily-class html ebplots html emfit html gould html postprob html utilities html ** building package indices ** installing vignettes ** 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 'EBarrays' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ebarrays.c -o ebarrays.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o EBarrays.dll tmp.def ebarrays.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.buildbin-libdir/EBarrays/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'EBarrays' as EBarrays_2.56.0.zip * DONE (EBarrays) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'EBarrays' successfully unpacked and MD5 sums checked
EBarrays.Rcheck/tests_i386/test.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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. > library(EBarrays) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: lattice > demo(ebarrays) demo(ebarrays) ---- ~~~~~~~~ > library(EBarrays) > ## EM algorithm > ## Lognormal-Normal Demo > > ## mu10,sigma2,tau are parameters in the LNNB model; pde is the > ## proportion of differentially expressed genes; n is the > ## total number of genes; nr1 and nr2 are the number of replicate > ## arrays in each group. > > lnnb.sim <- function(mu10, sigmasq, tausq, pde, n, nr1, nr2) + { + de <- sample(c(TRUE, FALSE), size = n, replace = TRUE, prob = c(pde, 1 - pde)) + x <- matrix(NA, n, nr1) + y <- matrix(NA, n, nr2) + mu1 <- rnorm(n, mu10, sqrt(tausq)) + mu2.de <- rnorm(n, mu10, sqrt(tausq)) + mu2 <- mu1 + mu2[de] <- mu2.de[de] + for(j in 1:nr1) { + x[, j] <- rnorm(n, mu1, sqrt(sigmasq)) + } + for(j in 1:nr2) { + y[, j] <- rnorm(n, mu2, sqrt(sigmasq)) + } + outmat <- exp(cbind(x, y)) + list(mu1 = mu1, mu2 = mu2, outmat = outmat, de = de) + } > ## simulating data with > ## mu_0 = 2.33, sigma^2 = 0.1, tau^2 = 2 > ## P(DE) = 0.2 > > sim.data1 <- lnnb.sim(2.33, 0.1, 2, 0.2, 2000, nr1 = 3, nr2 = 3) > de.true1 <- sim.data1$de ## true indicators of differential expression > sim.data2 <- lnnb.sim(1.33, 0.01, 2, 0.2, 2000, nr1 = 3, nr2 = 3) > de.true2 <- sim.data2$de ## true indicators of differential expression > testdata <- rbind(sim.data1$outmat,sim.data2$outmat) > hypotheses <- ebPatterns(c("1 1 1 1 1 1", "1 1 1 2 2 2")) > em.out <- emfit(testdata, family = "LNN", hypotheses, + cluster = 1:5, + type = 2, + verbose = TRUE, + num.iter = 10) Checking for negative entries... Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 0.28 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 1.04 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 1.20 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 1.76 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 2.19 seconds user time > em.out EB model fit Family: LNN ( Lognormal-Normal ) Model parameter estimates: mu_0 sigma.2 tao_0.2 Cluster 1 2.370598 0.1003321 2.041651 Cluster 2 1.323206 0.0103339 1.943924 Estimated mixing proportions: Pattern.1 Pattern.2 Cluster 1 0.4017568 0.09948277 Cluster 2 0.3940671 0.10469325 > post.out <- postprob(em.out, testdata) > table(post.out$pattern[, 2] > .5, c(de.true1,de.true2)) FALSE TRUE FALSE 3168 141 TRUE 24 667 > table((post.out$cluster[, 2] > .5)+1, c(rep("Cluster 1",2000),rep("Cluster 2",2000))) Cluster 1 Cluster 2 1 1869 63 2 131 1937 > plotMarginal(em.out,testdata) > par(ask=TRUE) > plotCluster(em.out,testdata) > par(ask=FALSE) > lnnmv.em.out <- emfit(testdata, family = "LNNMV", hypotheses, groupid=c(1,1,1,2,2,2), + verbose = TRUE, + num.iter = 10, + p.init = c(0.95, 0.05)) Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 0.72 seconds user time > lnnmv.em.out EB model fit Family: LNNMV ( Lognormal-Normal with modified variances ) Model parameter estimates: mu_0 tao_0.2 1 1.85046 2.259741 Estimated mixing proportions: Pattern.1 Pattern.2 p.temp 0.7825764 0.2174236 > post.out <- postprob(lnnmv.em.out, testdata, groupid=c(1,1,1,2,2,2)) > table(post.out$pattern[, 2] > .5, c(de.true1,de.true2)) FALSE TRUE FALSE 3118 135 TRUE 74 673 There were 50 or more warnings (use warnings() to see the first 50) > > > > proc.time() user system elapsed 9.04 0.25 9.29 |
EBarrays.Rcheck/tests_x64/test.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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. > library(EBarrays) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: lattice > demo(ebarrays) demo(ebarrays) ---- ~~~~~~~~ > library(EBarrays) > ## EM algorithm > ## Lognormal-Normal Demo > > ## mu10,sigma2,tau are parameters in the LNNB model; pde is the > ## proportion of differentially expressed genes; n is the > ## total number of genes; nr1 and nr2 are the number of replicate > ## arrays in each group. > > lnnb.sim <- function(mu10, sigmasq, tausq, pde, n, nr1, nr2) + { + de <- sample(c(TRUE, FALSE), size = n, replace = TRUE, prob = c(pde, 1 - pde)) + x <- matrix(NA, n, nr1) + y <- matrix(NA, n, nr2) + mu1 <- rnorm(n, mu10, sqrt(tausq)) + mu2.de <- rnorm(n, mu10, sqrt(tausq)) + mu2 <- mu1 + mu2[de] <- mu2.de[de] + for(j in 1:nr1) { + x[, j] <- rnorm(n, mu1, sqrt(sigmasq)) + } + for(j in 1:nr2) { + y[, j] <- rnorm(n, mu2, sqrt(sigmasq)) + } + outmat <- exp(cbind(x, y)) + list(mu1 = mu1, mu2 = mu2, outmat = outmat, de = de) + } > ## simulating data with > ## mu_0 = 2.33, sigma^2 = 0.1, tau^2 = 2 > ## P(DE) = 0.2 > > sim.data1 <- lnnb.sim(2.33, 0.1, 2, 0.2, 2000, nr1 = 3, nr2 = 3) > de.true1 <- sim.data1$de ## true indicators of differential expression > sim.data2 <- lnnb.sim(1.33, 0.01, 2, 0.2, 2000, nr1 = 3, nr2 = 3) > de.true2 <- sim.data2$de ## true indicators of differential expression > testdata <- rbind(sim.data1$outmat,sim.data2$outmat) > hypotheses <- ebPatterns(c("1 1 1 1 1 1", "1 1 1 2 2 2")) > em.out <- emfit(testdata, family = "LNN", hypotheses, + cluster = 1:5, + type = 2, + verbose = TRUE, + num.iter = 10) Checking for negative entries... Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 0.31 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 0.85 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 1.49 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 1.90 seconds user time Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 2.36 seconds user time > em.out EB model fit Family: LNN ( Lognormal-Normal ) Model parameter estimates: mu_0 sigma.2 tao_0.2 Cluster 1 1.373798 0.01013525 1.979309 Cluster 2 2.357468 0.10015473 2.016061 Estimated mixing proportions: Pattern.1 Pattern.2 Cluster 1 0.3997553 0.1021728 Cluster 2 0.3972669 0.1008051 > post.out <- postprob(em.out, testdata) > table(post.out$pattern[, 2] > .5, c(de.true1,de.true2)) FALSE TRUE FALSE 3169 155 TRUE 27 649 > table((post.out$cluster[, 2] > .5)+1, c(rep("Cluster 1",2000),rep("Cluster 2",2000))) Cluster 1 Cluster 2 1 138 1945 2 1862 55 > plotMarginal(em.out,testdata) > par(ask=TRUE) > plotCluster(em.out,testdata) > par(ask=FALSE) > lnnmv.em.out <- emfit(testdata, family = "LNNMV", hypotheses, groupid=c(1,1,1,2,2,2), + verbose = TRUE, + num.iter = 10, + p.init = c(0.95, 0.05)) Checking for negative entries... Generating summary statistics for patterns. This may take a few seconds... Starting EM iterations (total 10 ). This may take a while Starting iteration 1 ... Starting iteration 2 ... Starting iteration 3 ... Starting iteration 4 ... Starting iteration 5 ... Starting iteration 6 ... Starting iteration 7 ... Starting iteration 8 ... Starting iteration 9 ... Starting iteration 10 ... Fit used 0.58 seconds user time > lnnmv.em.out EB model fit Family: LNNMV ( Lognormal-Normal with modified variances ) Model parameter estimates: mu_0 tao_0.2 1 1.870027 2.23832 Estimated mixing proportions: Pattern.1 Pattern.2 p.temp 0.7815595 0.2184405 > post.out <- postprob(lnnmv.em.out, testdata, groupid=c(1,1,1,2,2,2)) > table(post.out$pattern[, 2] > .5, c(de.true1,de.true2)) FALSE TRUE FALSE 3114 142 TRUE 82 662 There were 50 or more warnings (use warnings() to see the first 50) > > > > proc.time() user system elapsed 9.45 0.07 9.53 |
EBarrays.Rcheck/examples_i386/EBarrays-Ex.timings
|
EBarrays.Rcheck/examples_x64/EBarrays-Ex.timings
|