Leo Lahti
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/netresponse |
| git_branch: RELEASE_3_17 |
| git_last_commit: ef556d6 |
| git_last_commit_date: 2023-04-25 10:18:03 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1379/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netresponse 1.60.0 (landing page) Leo Lahti
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the netresponse package: - 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: netresponse |
| Version: 1.60.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netresponse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netresponse_1.60.0.tar.gz |
| StartedAt: 2023-10-18 11:20:56 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 11:23:20 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 144.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netresponse.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netresponse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netresponse_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/netresponse.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netresponse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netresponse’ version ‘1.60.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocStyle', 'Rgraphviz', 'rmarkdown', 'minet', 'mclust', 'reshape2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘netresponse’ 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 ... 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
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘bicmixture.R’
Running ‘mixture.model.test.R’
Running ‘mixture.model.test.multimodal.R’
Running ‘mixture.model.test.singlemode.R’
Running ‘timing.R’
Running ‘toydata2.R’
Running ‘validate.netresponse.R’
Running ‘vdpmixture.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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/netresponse.Rcheck/00check.log’
for details.
netresponse.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netresponse
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘netresponse’ ...
** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c netresponse.c -o netresponse.o
netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable]
const char *prior_fields[]={"Mumu","S2mu",
^
netresponse.c:686:6: warning: variable 'Mumu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:21: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:15: note: initialize the variable 'Mumu' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'S2mu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:27: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:22: note: initialize the variable 'S2mu' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'Mubar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:33: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:30: note: initialize the variable 'Mubar' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'Mutilde' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:40: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:40: note: initialize the variable 'Mutilde' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'AlphaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:7: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:14: note: initialize the variable 'AlphaKsi' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:686:6: warning: variable 'BetaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:17: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:24: note: initialize the variable 'BetaKsi' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:686:6: warning: variable 'KsiAlpha' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:26: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:35: note: initialize the variable 'KsiAlpha' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:686:6: warning: variable 'KsiBeta' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:36: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:45: note: initialize the variable 'KsiBeta' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:696:6: warning: variable 'U_p' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim2) {
^~~~
netresponse.c:716:7: note: uninitialized use occurs here
U_p, U_hat,
^~~
netresponse.c:696:3: note: remove the 'if' if its condition is always true
if(dim2) {
^~~~~~~~~
netresponse.c:656:51: note: initialize the variable 'U_p' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:696:6: warning: variable 'U_hat' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim2) {
^~~~
netresponse.c:716:12: note: uninitialized use occurs here
U_p, U_hat,
^~~~~
netresponse.c:696:3: note: remove the 'if' if its condition is always true
if(dim2) {
^~~~~~~~~
netresponse.c:661:14: note: initialize the variable 'U_hat' to silence this warning
SEXP* U_hat;
^
= NULL
11 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o netresponse.so netresponse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-netresponse/00new/netresponse/libs
** R
** data
** inst
** 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 (netresponse)
netresponse.Rcheck/tests/bicmixture.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
> # 1. vdp.mixt: moodien loytyminen eri dimensiolla, naytemaarilla ja komponenteilla
> # -> ainakin nopea check
>
> #######################################################################
>
> # Generate random data from five Gaussians.
> # Detect modes with vdp-gm.
> # Plot data points and detected clusters with variance ellipses
>
> #######################################################################
>
> library(netresponse)
Loading required package: BiocStyle
Loading required package: Rgraphviz
Loading required package: graph
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
Loading required package: grid
Loading required package: rmarkdown
Attaching package: 'rmarkdown'
The following objects are masked from 'package:BiocStyle':
html_document, md_document, pdf_document
Loading required package: minet
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2
netresponse (C) 2008-2023 Leo Lahti et al.
https://github.com/antagomir/netresponse
> #source("~/Rpackages/netresponse/netresponse/R/detect.responses.R")
> #source("~/Rpackages/netresponse/netresponse/R/internals.R")
> #source("~/Rpackages/netresponse/netresponse/R/vdp.mixt.R")
> #dyn.load("/home/tuli/Rpackages/netresponse/netresponse/src/netresponse.so")
>
> ######### Generate DATA #############################################
>
> # Generate Nc components from normal-inverseGamma prior
>
> set.seed(12346)
>
> dd <- 3 # Dimensionality of data
> Nc <- 5 # Number of components
> Ns <- 200 # Number of data points
> sd0 <- 3 # component spread
> rgam.shape = 2 # parameters for Gamma distribution
> rgam.scale = 2 # parameters for Gamma distribution to define precisions
>
>
> # Generate means and variances (covariance diagonals) for the components
> component.means <- matrix(rnorm(Nc*dd, mean = 0, sd = sd0), nrow = Nc, ncol = dd)
> component.vars <- matrix(1/rgamma(Nc*dd, shape = rgam.shape, scale = rgam.scale),
+ nrow = Nc, ncol = dd)
> component.sds <- sqrt(component.vars)
>
>
> # Size for each component -> sample randomly for each data point from uniform distr.
> # i.e. cluster assignments
> sample2comp <- sample.int(Nc, Ns, replace = TRUE)
>
> D <- array(NA, dim = c(Ns, dd))
> for (i in 1:Ns) {
+ # component identity of this sample
+ ci <- sample2comp[[i]]
+ cm <- component.means[ci,]
+ csd <- component.sds[ci,]
+ D[i,] <- rnorm(dd, mean = cm, sd = csd)
+ }
>
>
> ######################################################################
>
> # Fit mixture model
> out <- mixture.model(D, mixture.method = "bic")
>
> # FIXME rowmeans(qofz) is constant but not 1
> #qofz <- P.r.s(t(D), list(mu = out$mu, sd = out$sd, w = out$w), log = FALSE)
>
> ############################################################
>
> # Compare input data and results
>
> ord.out <- order(out$mu[,1])
> ord.in <- order(component.means[,1])
>
> means.out <- out$mu[ord.out,]
> means.in <- component.means[ord.in,]
>
> # Cluster stds and variances
> sds.out <- out$sd[ord.out,]
> sds.in <- sqrt(component.vars[ord.in,])
>
> # -----------------------------------------------------------
>
> vars.out <- sds.out^2
> vars.in <- sds.in^2
>
> # Check correspondence between input and output
> if (length(means.in) == length(means.out)) {
+ cm <- cor(as.vector(means.in), as.vector(means.out))
+ csd <- cor(as.vector(sds.in), as.vector(sds.out))
+ }
>
> # Plot results (assuming 2D)
>
> ran <- range(c(as.vector(means.in - 2*vars.in),
+ as.vector(means.in + 2*vars.in),
+ as.vector(means.out + 2*vars.out),
+ as.vector(means.out - 2*vars.out)))
>
> plot(D, pch = 20, main = paste("Cor.means:", round(cm,3), "/ Cor.sds:", round(csd,3)), xlim = ran, ylim = ran)
> #for (ci in 1:nrow(means.out)) { add.ellipse(centroid = means.out[ci,], covmat = diag(vars.out[ci,]), col = "red") }
> #for (ci in 1:nrow(means.in)) { add.ellipse(centroid = means.in[ci,], covmat = diag(vars.in[ci,]), col = "blue") }
>
> ######################################################
>
> #for (ci in 1:nrow(means.out)) {
> # points(means.out[ci,1], means.out[ci,2], col = "red", pch = 19)
> # el <- ellipse(matrix(c(vars.out[ci,1],0,0,vars.out[ci,2]),2), centre = means.out[ci,])
> # lines(el, col = "red")
> #}
>
> #for (ci in 1:nrow(means.in)) {
> # points(means.in[ci,1], means.in[ci,2], col = "blue", pch = 19)
> # el <- ellipse(matrix(c(vars.in[ci,1],0,0,vars.in[ci,2]),2), centre = means.in[ci,])
> # lines(el, col = "blue")
> #}
>
>
>
>
>
>
> proc.time()
user system elapsed
2.429 0.203 4.241
netresponse.Rcheck/tests/mixture.model.test.multimodal.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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(netresponse)
Loading required package: BiocStyle
Loading required package: Rgraphviz
Loading required package: graph
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
Loading required package: grid
Loading required package: rmarkdown
Attaching package: 'rmarkdown'
The following objects are masked from 'package:BiocStyle':
html_document, md_document, pdf_document
Loading required package: minet
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2
netresponse (C) 2008-2023 Leo Lahti et al.
https://github.com/antagomir/netresponse
>
> # Three MODES
>
> # set.seed(34884)
> set.seed(3488400)
>
> Ns <- 200
> Nd <- 2
>
> D3 <- rbind(matrix(rnorm(Ns*Nd, mean = 0), ncol = Nd),
+ matrix(rnorm(Ns*Nd, mean = 3), ncol = Nd),
+ cbind(rnorm(Ns, mean = -3), rnorm(Ns, mean = 3))
+ )
>
> #X11()
> par(mfrow = c(2,2))
> for (mm in c("vdp", "bic")) {
+ for (pp in c(FALSE, TRUE)) {
+
+ # Fit nonparametric Gaussian mixture model
+ out <- mixture.model(D3, mixture.method = mm, pca.basis = pp)
+ plot(D3, col = apply(out$qofz, 1, which.max), main = paste(mm, "/ pca:", pp))
+
+ }
+ }
>
> # VDP is less sensitive than BIC in detecting Gaussian modes (more
> # separation between the clusters needed)
>
> # pca.basis option is less important for sensitive detection but
> # it will help to avoid overfitting to unimodal features that
> # are not parallel to the axes (unimodal distribution often becomes
> # splitted in two or more clusters in these cases)
>
>
> proc.time()
user system elapsed
3.887 0.247 5.737
netresponse.Rcheck/tests/mixture.model.test.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
> # Validate mixture models
>
> # Generate random data from five Gaussians.
> # Detect modes
> # Plot data points and detected clusters
>
> library(netresponse)
Loading required package: BiocStyle
Loading required package: Rgraphviz
Loading required package: graph
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
Loading required package: grid
Loading required package: rmarkdown
Attaching package: 'rmarkdown'
The following objects are masked from 'package:BiocStyle':
html_document, md_document, pdf_document
Loading required package: minet
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2
netresponse (C) 2008-2023 Leo Lahti et al.
https://github.com/antagomir/netresponse
>
> #fs <- list.files("~/Rpackages/netresponse/netresponse/R/", full.names = TRUE); for (f in fs) {source(f)}; dyn.load("/home/tuli/Rpackages/netresponse/netresponse/src/netresponse.so")
>
> ######### Generate DATA #######################
>
> res <- generate.toydata()
> D <- res$data
> component.means <- res$means
> component.sds <- res$sds
> sample2comp <- res$sample2comp
>
> ######################################################################
>
> par(mfrow = c(2,1))
>
> for (mm in c("vdp", "bic")) {
+
+ # Fit nonparametric Gaussian mixture model
+ #source("~/Rpackages/netresponse/netresponse/R/vdp.mixt.R")
+ out <- mixture.model(D, mixture.method = mm, max.responses = 10, pca.basis = FALSE)
+
+ ############################################################
+
+ # Compare input data and results
+
+ ord.out <- order(out$mu[,1])
+ ord.in <- order(component.means[,1])
+
+ means.out <- out$mu[ord.out,]
+ means.in <- component.means[ord.in,]
+
+ # Cluster stds and variances
+ sds.out <- out$sd[ord.out,]
+ vars.out <- sds.out^2
+
+ sds.in <- component.sds[ord.in,]
+ vars.in <- sds.in^2
+
+ # Check correspondence between input and output
+ if (length(means.in) == length(means.out)) {
+ cm <- cor(as.vector(means.in), as.vector(means.out))
+ csd <- cor(as.vector(sds.in), as.vector(sds.out))
+ }
+
+ # Plot results (assuming 2D)
+ ran <- range(c(as.vector(means.in - 2*vars.in),
+ as.vector(means.in + 2*vars.in),
+ as.vector(means.out + 2*vars.out),
+ as.vector(means.out - 2*vars.out)))
+
+ real.modes <- sample2comp
+ obs.modes <- apply(out$qofz, 1, which.max)
+
+ # plot(D, pch = 20, main = paste(mm, "/ cor.means:", round(cm,6), "/ Cor.sds:", round(csd,6)), xlim = ran, ylim = ran)
+
+ # plot(D, pch = real.modes, col = obs.modes, main = paste(mm, "/ cor.means:", round(cm,6), "/ Cor.sds:", round(csd,6)), xlim = ran, ylim = ran)
+
+ # for (ci in 1:nrow(means.out)) { add.ellipse(centroid = means.out[ci,], covmat = diag(vars.out[ci,]), col = "red") }
+ # for (ci in 1:nrow(means.in)) { add.ellipse(centroid = means.in[ci,], covmat = diag(vars.in[ci,]), col = "blue") }
+
+ }
>
>
> proc.time()
user system elapsed
2.433 0.212 4.346
netresponse.Rcheck/tests/mixture.model.test.singlemode.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
>
> skip <- FALSE
>
> if (!skip) {
+
+ library(netresponse)
+
+ # SINGLE MODE
+
+ # Produce test data that has full covariance
+ # It is expected that
+ # pca.basis = FALSE splits Gaussian with full covariance into two modes
+ # pca.basis = TRUE should detect just a single mode
+
+ Ns <- 200
+ Nd <- 2
+ k <- 1.5
+
+ D2 <- matrix(rnorm(Ns*Nd), ncol = Nd) %*% rbind(c(1,k), c(k,1))
+
+ par(mfrow = c(2,2))
+ for (mm in c("vdp", "bic")) {
+ for (pp in c(FALSE, TRUE)) {
+
+ # Fit nonparametric Gaussian mixture model
+ out <- mixture.model(D2, mixture.method = mm, pca.basis = pp)
+ plot(D2, col = apply(out$qofz, 1, which.max), main = paste("mm:" , mm, "/ pp:", pp))
+
+ }
+ }
+
+ }
Loading required package: BiocStyle
Loading required package: Rgraphviz
Loading required package: graph
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
Loading required package: grid
Loading required package: rmarkdown
Attaching package: 'rmarkdown'
The following objects are masked from 'package:BiocStyle':
html_document, md_document, pdf_document
Loading required package: minet
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2
netresponse (C) 2008-2023 Leo Lahti et al.
https://github.com/antagomir/netresponse
>
> proc.time()
user system elapsed
2.371 0.221 3.962
netresponse.Rcheck/tests/timing.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
>
> # Play with different options and check their effect on running times for bic and vdp
>
> skip <- TRUE
>
> if (!skip) {
+
+ Ns <- 100
+ Nd <- 2
+
+ set.seed(3488400)
+
+ D <- cbind(
+
+ rbind(matrix(rnorm(Ns*Nd, mean = 0), ncol = Nd),
+ matrix(rnorm(Ns*Nd, mean = 2), ncol = Nd),
+ cbind(rnorm(Ns, mean = -1), rnorm(Ns, mean = 3))
+ ),
+
+ rbind(matrix(rnorm(Ns*Nd, mean = 0), ncol = Nd),
+ matrix(rnorm(Ns*Nd, mean = 2), ncol = Nd),
+ cbind(rnorm(Ns, mean = -1), rnorm(Ns, mean = 3))
+ )
+ )
+
+ rownames(D) <- paste("R", 1:nrow(D), sep = "-")
+ colnames(D) <- paste("C", 1:ncol(D), sep = "-")
+
+ ts <- c()
+ for (mm in c("bic", "vdp")) {
+
+
+ # NOTE: no PCA basis needed with mixture.method = "bic"
+ tt <- system.time(detect.responses(D, verbose = TRUE, max.responses = 5,
+ mixture.method = mm, information.criterion = "BIC",
+ merging.threshold = 0, bic.threshold = 0, pca.basis = TRUE))
+
+ print(paste(mm, ":", round(tt[["elapsed"]], 3)))
+ ts[[mm]] <- tt[["elapsed"]]
+ }
+
+ print(paste(names(ts)[[1]], "/", names(ts)[[2]], ": ", round(ts[[1]]/ts[[2]], 3)))
+
+ }
>
> # -> VDP is much faster when sample sizes increase
> # 1000 samples -> 25-fold speedup with VDP
>
>
>
> proc.time()
user system elapsed
0.212 0.068 0.444
netresponse.Rcheck/tests/toydata2.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
> # Generate Nc components from normal-inverseGamma prior
>
> set.seed(12346)
>
> Ns <- 300
> Nd <- 2
>
> # Isotropic cloud
> D1 <- matrix(rnorm(Ns*Nd), ncol = Nd)
>
> # Single diagonal mode
> D2 <- matrix(rnorm(Ns*Nd), ncol = Nd) %*% rbind(c(1,2), c(2,1))
>
> # Two isotropic modes
> D3 <- rbind(matrix(rnorm(Ns/2*Nd), ncol = Nd), matrix(rnorm(Ns/2*Nd, mean = 3), ncol = Nd))
> D <- cbind(D1, D2, D3)
>
> colnames(D) <- paste("Feature-", 1:ncol(D), sep = "")
> rownames(D) <- paste("Sample-", 1:nrow(D), sep = "")
>
>
> proc.time()
user system elapsed
0.212 0.065 0.435
netresponse.Rcheck/tests/validate.netresponse.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
>
> skip <- TRUE
>
> if (!skip) {
+
+ # 2. netresponse test
+ # test later with varying parameters
+
+ # Load the package
+ library(netresponse)
+ #load("../data/toydata.rda")
+ fs <- list.files("../R/", full.names = TRUE); for (f in fs) {source(f)};
+
+ data(toydata)
+
+ D <- toydata$emat
+ netw <- toydata$netw
+
+ # The toy data is random data with 10 features (genes).
+ # The features
+ rf <- c(4, 5, 6)
+ #form a subnetwork with coherent responses
+ # with means
+ r1 <- c(0, 3, 0)
+ r2 <- c(-5, 0, 2)
+ r3 <- c(5, -3, -3)
+ mu.real <- rbind(r1, r2, r3)
+ # real weights
+ w.real <- c(70, 70, 60)/200
+ # and unit variances
+ rv <- 1
+
+ # Fit the model
+ #res <- detect.responses(D, netw, verbose = TRUE, mc.cores = 2)
+ #res <- detect.responses(D, netw, verbose = TRUE, max.responses = 4)
+
+ res <- detect.responses(D, netw, verbose = TRUE, max.responses = 3, mixture.method = "bic", information.criterion = "BIC", merging.threshold = 1, bic.threshold = 10, pca.basis = FALSE)
+
+ print("OK")
+
+ # Subnets (each is a list of nodes)
+ subnets <- get.subnets(res)
+
+ # the correct subnet is retrieved in subnet number 2:
+ #> subnet[[2]]
+ #[1] "feat4" "feat5" "feat6"
+
+ # how about responses
+ # Retrieve model for the subnetwork with lowest cost function value
+ # means, standard devations and weights for the components
+ if (!is.null(subnets)) {
+ m <- get.model.parameters(res, subnet.id = "Subnet-2")
+
+ # order retrieved and real response means by the first feature
+ # (to ensure responses are listed in the same order)
+ # and compare deviation from correct solution
+ ord.obs <- order(m$mu[,1])
+ ord.real <- order(mu.real[,1])
+
+ print(paste("Correlation between real and observed responses:", cor(as.vector(m$mu[ord.obs,]), as.vector(mu.real[ord.real,]))))
+
+ # all real variances are 1, compare to observed ones
+ print(paste("Maximum deviation from real variances: ", max(abs(rv - range(m$sd))/rv)))
+
+ # weights deviate somewhat, this is likely due to relatively small sample size
+ #print("Maximum deviation from real weights: ")
+ #print( (w.real[ord.real] - m$w[ord.obs])/w.real[ord.real])
+
+ print("estimated and real mean matrices")
+ print(m$mu[ord.obs,])
+ print(mu.real[ord.real,])
+
+ }
+
+ }
>
> proc.time()
user system elapsed
0.214 0.065 0.456
netresponse.Rcheck/tests/vdpmixture.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
>
> # 1. vdp.mixt: moodien loytyminen eri dimensiolla, naytemaarilla ja komponenteilla
> # -> ainakin nopea check
>
> #######################################################################
>
> # Generate random data from five Gaussians.
> # Detect modes with vdp-gm.
> # Plot data points and detected clusters with variance ellipses
>
> #######################################################################
>
> library(netresponse)
Loading required package: BiocStyle
Loading required package: Rgraphviz
Loading required package: graph
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
Loading required package: grid
Loading required package: rmarkdown
Attaching package: 'rmarkdown'
The following objects are masked from 'package:BiocStyle':
html_document, md_document, pdf_document
Loading required package: minet
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2
netresponse (C) 2008-2023 Leo Lahti et al.
https://github.com/antagomir/netresponse
> #source("~/Rpackages/netresponse/netresponse/R/detect.responses.R")
> #source("~/Rpackages/netresponse/netresponse/R/internals.R")
> #source("~/Rpackages/netresponse/netresponse/R/vdp.mixt.R")
> #dyn.load("/home/tuli/Rpackages/netresponse/netresponse/src/netresponse.so")
>
>
> ######### Generate DATA #############################################
>
> res <- generate.toydata()
> D <- res$data
> component.means <- res$means
> component.sds <- res$sds
> sample2comp <- res$sample2comp
>
> ######################################################################
>
> # Fit nonparametric Gaussian mixture model
> out <- vdp.mixt(D)
> # out <- vdp.mixt(D, c.max = 3) # try with limited number of components -> OK
>
> ############################################################
>
> # Compare input data and results
>
> ord.out <- order(out$posterior$centroids[,1])
> ord.in <- order(component.means[,1])
>
> means.out <- out$posterior$centroids[ord.out,]
> means.in <- component.means[ord.in,]
>
> # Cluster stds and variances
> sds.out <- out$posterior$sds[ord.out,]
> sds.in <- component.sds[ord.in,]
> vars.out <- sds.out^2
> vars.in <- sds.in^2
>
> # Check correspondence between input and output
> if (length(means.in) == length(means.out)) {
+ cm <- cor(as.vector(means.in), as.vector(means.out))
+ csd <- cor(as.vector(sds.in), as.vector(sds.out))
+ }
>
> # Plot results (assuming 2D)
>
> ran <- range(c(as.vector(means.in - 2*vars.in),
+ as.vector(means.in + 2*vars.in),
+ as.vector(means.out + 2*vars.out),
+ as.vector(means.out - 2*vars.out)))
>
> #plot(D, pch = 20, main = paste("Cor.means:", round(cm,3), "/ Cor.sds:", round(csd,3)), xlim = ran, ylim = ran)
> #for (ci in 1:nrow(means.out)) { add.ellipse(centroid = means.out[ci,], covmat = diag(vars.out[ci,]), col = "red") }
> #for (ci in 1:nrow(means.in)) { add.ellipse(centroid = means.in[ci,], covmat = diag(vars.in[ci,]), col = "blue") }
>
>
>
> proc.time()
user system elapsed
2.153 0.205 3.630
netresponse.Rcheck/netresponse-Ex.timings
| name | user | system | elapsed | |
| NetResponseModel-class | 0.001 | 0.001 | 0.002 | |
| PlotMixture | 0.001 | 0.000 | 0.000 | |
| PlotMixtureBivariate | 0.001 | 0.001 | 0.000 | |
| PlotMixtureMultivariate | 0 | 0 | 0 | |
| PlotMixtureUnivariate | 0 | 0 | 0 | |
| centerData | 0.001 | 0.001 | 0.001 | |
| check.matrix | 0 | 0 | 0 | |
| check.network | 0.000 | 0.000 | 0.001 | |
| continuous.responses | 0.000 | 0.000 | 0.001 | |
| detect.responses | 0.000 | 0.000 | 0.001 | |
| dna | 0.022 | 0.003 | 0.040 | |
| enrichment.list.factor | 0 | 0 | 0 | |
| enrichment.list.factor.minimal | 0.001 | 0.000 | 0.002 | |
| factor.responses | 0 | 0 | 0 | |
| factor.responses.minimal | 0.000 | 0.001 | 0.001 | |
| filter.network | 0 | 0 | 0 | |
| find.similar.features | 0.002 | 0.002 | 0.006 | |
| generate.toydata | 0.002 | 0.000 | 0.004 | |
| get.dat-NetResponseModel-method | 0.000 | 0.000 | 0.001 | |
| get.model.parameters | 0.003 | 0.004 | 0.011 | |
| get.subnets-NetResponseModel-method | 0 | 0 | 0 | |
| getqofz-NetResponseModel-method | 0 | 0 | 0 | |
| independent.models | 0.001 | 0.001 | 0.000 | |
| list.responses.continuous.multi | 0.001 | 0.000 | 0.000 | |
| list.responses.continuous.single | 0.001 | 0.000 | 0.000 | |
| list.significant.responses | 0.000 | 0.001 | 0.001 | |
| listify.groupings | 0 | 0 | 0 | |
| mixture.model | 0 | 0 | 0 | |
| model.stats | 0.002 | 0.002 | 0.009 | |
| netresponse-package | 0.000 | 0.001 | 0.001 | |
| order.responses | 0 | 0 | 0 | |
| osmo | 0.042 | 0.004 | 0.069 | |
| pick.model.pairs | 0.000 | 0.001 | 0.000 | |
| pick.model.parameters | 0.000 | 0.000 | 0.001 | |
| plotPCA | 0 | 0 | 0 | |
| plot_associations | 0.001 | 0.000 | 0.000 | |
| plot_data | 0 | 0 | 0 | |
| plot_expression | 0 | 0 | 0 | |
| plot_matrix | 0.012 | 0.002 | 0.023 | |
| plot_response | 0 | 0 | 0 | |
| plot_responses | 0.000 | 0.000 | 0.001 | |
| plot_scale | 0.000 | 0.000 | 0.002 | |
| plot_subnet | 0 | 0 | 0 | |
| read.sif | 0.000 | 0.000 | 0.001 | |
| remove.negative.edges | 0.000 | 0.000 | 0.001 | |
| response.enrichment | 0 | 0 | 0 | |
| response2sample | 0.004 | 0.003 | 0.011 | |
| sample2response | 0.002 | 0.001 | 0.005 | |
| set.breaks | 0.000 | 0.000 | 0.003 | |
| toydata | 0.002 | 0.002 | 0.006 | |
| update.model.pair | 0.001 | 0.000 | 0.000 | |
| vdp.mixt | 0.044 | 0.009 | 0.082 | |
| vectorize.groupings | 0 | 0 | 0 | |