plw 1.48.0
Magnus Astrand
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/plw |
| Branch: RELEASE_3_11 |
| Last Commit: 097142c |
| Last Changed Date: 2020-04-27 14:16:14 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:plw.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings plw_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/plw.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plw/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plw’ version ‘1.48.0’
* 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 ‘plw’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'plw' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/plw.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘affy’
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.C("qnorm_c", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘plw-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plw
> ### Title: Probe level Locally moderated Weighted median-t.
> ### Aliases: plw
> ### Keywords: htest models design
>
> ### ** Examples
>
>
> # ------------------------------------------
> # Example analyzing the 6 arrays in the
> # AffySpikeU95Subset data set
>
> # Loading the data
> data(AffySpikeU95Subset)
>
> # Defining design and contrast matrix
> group<-factor(rep(1:2,each=3))
> design<-model.matrix(~group-1)
> contrast<-matrix(c(1,-1),1,2)
>
> # Analyzing with an AffyBatch object as input
> model1<-plw(AffySpikeU95Subset,design=design,contrast=contrast,
+ epsilon=0.01)
Background correcting and normalizing.
Init sigma using estimateSigmaMV
Iterating EM-steps
iter sigma m, v
1 6.34e-01 2.90e-01
2 1.38e-01 3.18e-01
3 3.25e-02 2.23e-01
Done!
Summarizing
Init m and spline for v
Iterating EM-steps
iter sigma m, v
1 6.55e-02 1.14e-03
2 8.42e-03 1.38e-02
3 1.35e-03 1.11e-02
4 3.82e-04 9.57e-03
Done!
Summarizing
Iterating EM-steps
iter sigma m, v
1 7.00e-01
2 8.96e-02
3 1.15e-02
4 4.38e-03
Warning in as.vector(fit1$modS2) * varGammaHat :
Recycling array of length 1 in vector-array arithmetic is deprecated.
Use c() or as.vector() instead.
>
> ## Look at fitted vs observed density for log(s2)
> varHistPlot(model1)
>
> ## Look at fitted curve for scale parameter
> scaleParameterPlot(model1)
>
> ## Selecting top genes
> topRankSummary(model1,nGenes=10)
Rank Median t Q1-t Q3-t Med. log2FC
1708_at 1 37.13 31.80 45.24 7.049
36202_at 2 -6.04 -7.04 -5.37 -0.827
1024_at 3 -5.70 -6.83 -5.10 -0.895
36311_at 4 -5.59 -6.87 -3.71 -0.794
36085_at 5 -5.38 -6.06 -4.31 -0.569
546_at 6 -4.75 -5.88 -2.36 -0.695
33818_at 7 -4.71 -4.84 -3.38 -0.512
38734_at 8 -3.94 -4.94 -1.77 -0.666
36889_at 9 -3.65 -4.80 -1.49 -0.650
39058_at 10 -3.14 -4.30 -2.47 -0.562
>
> ## Plotting t-statistics and log2FC for top genes
> par(mfrow=c(1,2))
> plotSummaryT(model1,nGenes=20)
> plotSummaryLog2FC(model1,nGenes=20)
>
>
> ###---------------------------------------
> # Analyzing with BG-adjusted and normalized PM data
> pm1<-pm(bg.correct.rma(AffySpikeU95Subset, bgtype = 2))
> pm2<-matrix(.C("qnorm_c", as.double(as.vector(pm1)),
+ as.integer(nrow(pm1)),
+ as.integer(ncol(pm1)))[[1]],
+ nrow(pm1),ncol(pm1))
> data<-log2(pm2)
>
> probenames<-probeNames(AffySpikeU95Subset)
> model2<-plw(data,design=design,contrast=contrast,
+ probenames=probenames,epsilon=0.01)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
plw
--- call from context ---
plw(data, design = design, contrast = contrast, probenames = probenames,
epsilon = 0.01)
--- call from argument ---
if (class(x) == "AffyBatch") {
pm1 <- pm(x)
if (!plwCheckInput(pm1, design, contrast, checkRegulation = FALSE)) {
cat("plw aborted.", "\n")
return(NULL)
}
if (length(probenames) != nrow(pm1)) {
cat("The vector probenames is not of correct length.",
"\n", "plw aborted.", "\n")
return(NULL)
}
if (verbose) {
cat("Background correcting and normalizing.", "\n")
}
pm1 <- pm(bg.correct.rma(x, bgtype = 2))
rows <- nrow(pm1)
cols <- ncol(pm1)
pm1 <- log2(matrix(.C("qnorm_c", as.double(as.vector(pm1)),
as.integer(rows), as.integer(cols), PACKAGE = "affy")[[1]],
rows, cols))
rownames(pm1) <- probenames
if (!plwCheckInput(pm1, design, contrast, checkRegulation = checkRegulation)) {
cat("plw aborted.", "\n")
return(NULL)
}
} else {
pm1 <- x
if (!plwCheckInput(pm1, design, contrast, checkRegulation = checkRegulation)) {
cat("plw aborted.", "\n")
}
if (length(probenames) != nrow(pm1)) {
cat("The vector probenames is not of correct length.",
"\n", "plw aborted.", "\n")
}
}
--- R stacktrace ---
where 1: plw(data, design = design, contrast = contrast, probenames = probenames,
epsilon = 0.01)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x, design = rep(1, ncol(x)), contrast = matrix(1),
probenames = unlist(ifelse(class(x) == "AffyBatch", list(p = probeNames(x)),
list(p = NULL))), maxIter = 200, epsilon = 1e-06, verbose = TRUE,
nknots = 10, nOut = 2000, nIn = 4000, knots = NULL, checkRegulation = TRUE)
{
cl <- match.call()
if (class(x) == "AffyBatch") {
pm1 <- pm(x)
if (!plwCheckInput(pm1, design, contrast, checkRegulation = FALSE)) {
cat("plw aborted.", "\n")
return(NULL)
}
if (length(probenames) != nrow(pm1)) {
cat("The vector probenames is not of correct length.",
"\n", "plw aborted.", "\n")
return(NULL)
}
if (verbose) {
cat("Background correcting and normalizing.", "\n")
}
pm1 <- pm(bg.correct.rma(x, bgtype = 2))
rows <- nrow(pm1)
cols <- ncol(pm1)
pm1 <- log2(matrix(.C("qnorm_c", as.double(as.vector(pm1)),
as.integer(rows), as.integer(cols), PACKAGE = "affy")[[1]],
rows, cols))
rownames(pm1) <- probenames
if (!plwCheckInput(pm1, design, contrast, checkRegulation = checkRegulation)) {
cat("plw aborted.", "\n")
return(NULL)
}
}
else {
pm1 <- x
if (!plwCheckInput(pm1, design, contrast, checkRegulation = checkRegulation)) {
cat("plw aborted.", "\n")
}
if (length(probenames) != nrow(pm1)) {
cat("The vector probenames is not of correct length.",
"\n", "plw aborted.", "\n")
}
}
ii <- order(as.numeric(factor(probenames)))
probenames <- probenames[ii]
pm1 <- pm1[ii, ]
probeId <- as.numeric(factor(probenames))
geneNames <- levels(factor(probenames))
arrayNames <- colnames(pm1)
if (nrow(contrast) > 1) {
contrast <- contrast[1, ]
}
P <- plwGetTransformationMatrix(design, contrast)
p <- ncol(pm1)
meanX <- pm1 %*% rep(1/p, p)
y <- pm1 %*% P
p <- ncol(y)
fit1 <- estimateSigmaMVbeta(y[, -p], meanX, maxIter = maxIter,
epsilon = epsilon, verbose = verbose, nknots = nknots,
nOut = nOut, nIn = nIn, br = knots)
fit2 <- estimateSigma(y, fit1$m, fit1$v, maxIter = maxIter,
epsilon = epsilon, verbose = verbose)
fit1$Sigma <- fit2$Sigma
fit1$iter <- c(fit1$iter, fit2$iter)
fit1$converged <- all(fit1$iter < maxIter)
D <- matrix((1:p) == p) * 1
gammaHat <- ginv(t(D) %*% ginv(fit2$Sigma) %*% D) %*% t(D) %*%
ginv(fit2$Sigma)
weights <- as.vector(gammaHat %*% t(P))
gammaHat <- as.vector(y %*% t(gammaHat))
varGammaHat <- ginv(t(D) %*% ginv(fit2$Sigma) %*% D)
modT <- as.vector(gammaHat)/sqrt(as.vector(fit1$modS2) *
varGammaHat)
dfT <- fit1$m + ncol(P) - 1
modP <- 2 - pt(abs(modT), dfT) * 2
medianT <- medianByIndex(modT, probeId)
names(fit1$modS2) <- names(gammaHat) <- probenames
names(modP) <- names(modT) <- probenames
names(medianT) <- geneNames
rownames(P) <- names(weights) <- arrayNames
colnames(P) <- c(paste("A", 1:(ncol(P) - 1), sep = ""), "B")
fit1 <- append(fit1, list(call = cl, medianT = medianT, t = modT,
p.value = modP, coefficients = gammaHat, P = P, dfT = dfT,
weights = weights))
class(fit1) <- "plw"
fit1
}
<bytecode: 0x55f787810970>
<environment: namespace:plw>
--- function search by body ---
Function plw in namespace plw has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/plw.Rcheck/00check.log’
for details.