Ming Yuan
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/EBarrays |
| git_branch: RELEASE_3_18 |
| git_last_commit: 8f2e6be |
| git_last_commit_date: 2023-10-24 09:33:06 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:18 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 616/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EBarrays 2.66.0 (landing page) Ming Yuan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.66.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBarrays.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBarrays_2.66.0.tar.gz |
| StartedAt: 2024-03-03 20:21:51 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:22:47 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 56.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBarrays.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBarrays.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBarrays_2.66.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBarrays.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBarrays/DESCRIPTION’ ... OK
* this is package ‘EBarrays’ version ‘2.66.0’
* 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 ‘EBarrays’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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
* 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 is not available
* 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 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/EBarrays.Rcheck/00check.log’
for details.
EBarrays.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EBarrays ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘EBarrays’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ebarrays.c -o ebarrays.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o EBarrays.so ebarrays.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-EBarrays/00new/EBarrays/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
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, 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 0.30 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 0.81 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 1.06 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 1.56 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 1.83 seconds user time
> em.out
EB model fit
Family: LNN ( Lognormal-Normal )
Model parameter estimates:
mu_0 sigma.2 tao_0.2
Cluster 1 1.319743 0.0102703 1.918182
Cluster 2 2.389876 0.1010164 1.949290
Estimated mixing proportions:
Pattern.1 Pattern.2
Cluster 1 0.4038177 0.10264463
Cluster 2 0.4009228 0.09261484
> post.out <- postprob(em.out, testdata)
> table(post.out$pattern[, 2] > .5, c(de.true1,de.true2))
FALSE TRUE
FALSE 3181 155
TRUE 31 633
> table((post.out$cluster[, 2] > .5)+1, c(rep("Cluster 1",2000),rep("Cluster 2",2000)))
Cluster 1 Cluster 2
1 160 1934
2 1840 66
> 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 0.33 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 1.850527 2.211393
Estimated mixing proportions:
Pattern.1 Pattern.2
p.temp 0.7912758 0.2087242
> 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 3130 151
TRUE 82 637
There were 50 or more warnings (use warnings() to see the first 50)
>
>
>
> proc.time()
user system elapsed
7.589 0.920 8.637
EBarrays.Rcheck/EBarrays-Ex.timings
| name | user | system | elapsed | |
| crit.fun | 2.098 | 0.650 | 2.819 | |
| ebarraysFamily-class | 0.006 | 0.001 | 0.007 | |
| emfit | 0.142 | 0.025 | 0.170 | |
| gould | 0.006 | 0.002 | 0.008 | |
| postprob | 0.132 | 0.018 | 0.151 | |
| utilities | 0.002 | 0.000 | 0.002 | |