CRAN Package Check Results for Package chipPCR

Last updated on 2015-04-18 21:48:56.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.8-10 3.32 92.41 95.72 OK
r-devel-linux-x86_64-debian-gcc 0.0.8-10 3.17 87.27 90.44 OK
r-devel-linux-x86_64-fedora-clang 0.0.8-10 192.11 OK
r-devel-linux-x86_64-fedora-gcc 0.0.8-10 181.49 OK
r-devel-osx-x86_64-clang 0.0.8-10 160.65 OK
r-patched-linux-x86_64 0.0.8-10 3.18 88.33 91.50 OK
r-patched-solaris-sparc 0.0.8-10 1021.00 OK
r-patched-solaris-x86 0.0.8-10 230.70 OK
r-release-linux-x86_64 0.0.8-10 3.19 89.45 92.64 OK
r-release-osx-x86_64-mavericks 0.0.8-10 ERROR
r-release-osx-x86_64-snowleopard 0.0.8-10 ERROR
r-release-windows-ix86+x86_64 0.0.8-10 9.00 176.00 185.00 OK
r-oldrel-windows-ix86+x86_64 0.0.8-10 18.00 179.00 197.00 OK

Check Details

Version: 0.0.8-10
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘drc’ ‘MBmca’
Flavor: r-release-osx-x86_64-mavericks

Version: 0.0.8-10
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘MBmca’
Flavor: r-release-osx-x86_64-mavericks

Version: 0.0.8-10
Check: examples
Result: ERROR
    Running examples in ‘chipPCR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: effcalc
    > ### Title: Analysis of the amplification efficiency
    > ### Aliases: effcalc effcalc.numeric effcalc.matrix effcalc.data.frame
    > ### effcalc,numeric,numeric-method effcalc,matrix,missing-method
    > ### effcalc,data.frame,missing-method
    > ### Keywords: efficiency methods
    >
    > ### ** Examples
    >
    > ## Not run:
    > # First Example
    > # Amplification efficiency plot
    >
    > require(MBmca)
    Loading required package: MBmca
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘MBmca’
    > par(mfrow = c(1,2), las = 0, bty = "n", cex.axis = 1.2, cex.lab = 1.2,
    + font = 2, cex.main = 1, oma = c(0.1, 0.1, 0.5, 0.1))
    >
    > # Simulate a qPCR reaction with AmpSim for 45 cycles and some noise.
    > # Define number of cycles
    > cyc.no <- 45
    >
    > # Create an empty plot
    > plot(NA, NA, xlim = c(1,cyc.no), ylim = c(0.01,1.1), xlab = "Cycles",
    + ylab = "Fluorescence", main = "")
    > mtext("A", cex = 2, side = 3, adj = 0, font = 2)
    >
    > # Create a sequence of "whised" Cq value for the simulation
    > cycle <- rep(seq(15, 34, 3.5), 3)
    >
    > # Define the levels for the decadic dilution with concentrations
    > # from 100 to 0.001 (six steps).
    > # The in-slico experiment is designed to have three replicates at
    > # six dilution steps.
    > dilution <-rep(c(100, 10, 1, 0.1, 0.01, 0.001), 3)
    >
    > # Create an empty matrix for the results of the concentration
    > # dependent Cq values
    > ma.out <- matrix(data = NA, nrow = cyc.no,
    + ncol = length(cycle))
    >
    > # Use AmpSim to simulate amplification curves at different
    > # concentrations. The simulation is performed with the addition
    > # of some noise. This will do a generation of unique amplification
    > # curves, even under idential paramter settings. Calculate the
    > # pseudo Second Derivative Maximum (SDM) (Cq) by using the the
    > # diffQ2 function from the MBmca package.
    >
    > Cq.out <- vector()
    >
    > for (i in 1:18) {
    + ma.out[1:cyc.no, i] <- AmpSim(cyc = c(1:cyc.no), b.eff = -50, bl = 0.001,
    + ampl = 1, Cq = cycle[i], noise = TRUE,
    + nnl = 0.02)[, 2]
    + lines(1:cyc.no, ma.out[, i])
    + tmpP <- mcaSmoother(1:cyc.no, ma.out[, i])
    + #TURNED OFF INDER - NEW COMPATIBILITY TO MBmca STILL PENDING
    + Cq.tmp <- diffQ2(tmpP, inder = FALSE)$xTm1.2.D2[1]
    + abline(v = Cq.tmp)
    + Cq.out <- c(Cq.out, Cq.tmp)
    + }
    Error: could not find function "mcaSmoother"
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 0.0.8-10
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in ‘chipPCR.Rnw’
     ...
    > plot(NA, NA, xlim = c(1, 40), ylim = c(0, 10), xlab = "Cycle",
    + ylab = "Fluorescence", main = "EvaGreen")
    
    > mtext("A", cex = 1.1, side = 3, adj = 0, font = 2)
    
    > EG <- amp.liner(range = 3:34, input = C127EGHP)
    
     When sourcing ‘chipPCR.R’:
    Error: could not find function "mcaSmoother"
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 0.0.8-10
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Warning in smoother(x, y, trans = FALSE, bg.outliers = FALSE, method = list(method.smooth), :
     x is not uniform/equidistant (different inter cycle or time intervals.
     This may cause artifacts during the pre-processing.
    NA values introduced by smoothing method mova. fixNA() used.
    Warning in fixNA(x, y, spline = TRUE) :
     NA values constitutes more than 0.3 of the input data.
    Approximation may not be correct.
    Warning in fixNA(x, y, spline = TRUE) :
     More than 2 missing values in last 6 elements.
    Approximation may not be correct.
    Warning in supsmu(x, y, span = "cv") :
     250 observations with NAs, NaNs and/or Infs deleted
    Warning in smoother(x, y, trans = FALSE, bg.outliers = FALSE, method = list(method.smooth), :
     x is not uniform/equidistant (different inter cycle or time intervals.
     This may cause artifacts during the pre-processing.
    NA values introduced by smoothing method mova. fixNA() used.
    Warning in smoother(x, y, trans = FALSE, bg.outliers = FALSE, method = list(method.smooth), :
     x is not uniform/equidistant (different inter cycle or time intervals.
     This may cause artifacts during the pre-processing.
    NA values introduced by smoothing method mova. fixNA() used.
    Loading required package: MBmca
    Quitting from lines 1929-1984 (chipPCR.Rnw)
    Error: processing vignette 'chipPCR.Rnw' failed with diagnostics:
    could not find function "mcaSmoother"
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 0.0.8-10
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘lmtest’ ‘quantreg’ ‘Rfit’
    
    Packages suggested but not available for checking: ‘drc’ ‘knitr’ ‘RDML’
    
    VignetteBuilder package required for checking but installed: ‘knitr’
    
    Files named as vignettes but with no recognized vignette engine:
     ‘inst/doc/chipPCR.Rnw’
    (Is a VignetteBuilder field missing?)
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64-snowleopard