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CHECK report for plw on machv2

This page was generated on 2020-10-17 11:59:13 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE plw PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1326/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 

Summary

Package: plw
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:plw.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings plw_1.48.0.tar.gz
StartedAt: 2020-10-17 04:00:03 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:01:03 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 59.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: plw.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:plw.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings plw_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/plw.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘/Users/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 sizes of PDF files under ‘inst/doc’ ... OK
* 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: 0x7fca71faec38>
<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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/plw.Rcheck/00check.log’
for details.


Installation output

plw.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL plw
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘plw’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c SpecialFunctions.c -o SpecialFunctions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c SpecialOptim.c -o SpecialOptim.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o plw.so SpecialFunctions.o SpecialOptim.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-plw/00new/plw/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
Warning: Package 'plw' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'plw' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (plw)

Tests output


Example timings

plw.Rcheck/plw-Ex.timings

nameusersystemelapsed
HowToPLW0.0010.0010.002
lmw0.8910.0360.930
logitT0.7960.0250.823