Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 616/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EBarrays 2.69.0 (landing page) Ming Yuan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the EBarrays package: - 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 Troubleshooting Build Report for more information. - 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: EBarrays |
Version: 2.69.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EBarrays.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings EBarrays_2.69.0.tar.gz |
StartedAt: 2024-08-21 00:28:13 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 00:29:19 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 65.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EBarrays.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EBarrays.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings EBarrays_2.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/EBarrays.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'EBarrays/DESCRIPTION' ... OK * this is package 'EBarrays' version '2.69.0' * 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 * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 code 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 'library' or 'require' call to 'lattice' which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * 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 x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/EBarrays/libs/x64/EBarrays.dll': Found '_exit', possibly from '_exit' (C) 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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/EBarrays.Rcheck/00check.log' for details.
EBarrays.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL EBarrays ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'EBarrays' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ebarrays.c -o ebarrays.o gcc -shared -s -static-libgcc -o EBarrays.dll tmp.def ebarrays.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-EBarrays/00new/EBarrays/libs/x64 ** R ** data ** demo ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (EBarrays)
EBarrays.Rcheck/tests/test.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'BiocGenerics' 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, aperm, 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, 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 0.23 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 1.02 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 1.67 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 2.31 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 3.02 seconds user time > em.out EB model fit Family: LNN ( Lognormal-Normal ) Model parameter estimates: mu_0 sigma.2 tao_0.2 Cluster 1 2.323771 0.10059513 2.010910 Cluster 2 1.331410 0.01006515 1.986308 Estimated mixing proportions: Pattern.1 Pattern.2 Cluster 1 0.4028356 0.09981479 Cluster 2 0.4051748 0.09217483 > post.out <- postprob(em.out, testdata) > table(post.out$pattern[, 2] > .5, c(de.true1,de.true2)) FALSE TRUE FALSE 3188 161 TRUE 33 618 > table((post.out$cluster[, 2] > .5)+1, c(rep("Cluster 1",2000),rep("Cluster 2",2000))) Cluster 1 Cluster 2 1 1878 52 2 122 1948 > 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 1.837787 2.240049 Estimated mixing proportions: Pattern.1 Pattern.2 p.temp 0.7955849 0.2044151 > 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 3143 146 TRUE 78 633 There were 50 or more warnings (use warnings() to see the first 50) > > > > proc.time() user system elapsed 10.70 3.42 14.12
EBarrays.Rcheck/EBarrays-Ex.timings
name | user | system | elapsed | |
crit.fun | 3.77 | 0.56 | 4.34 | |
ebarraysFamily-class | 0 | 0 | 0 | |
emfit | 0.16 | 0.06 | 0.21 | |
gould | 0 | 0 | 0 | |
postprob | 0.20 | 0.03 | 0.23 | |
utilities | 0 | 0 | 0 | |