• using R version 3.6.3 (2020-02-29)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'Rmpfr/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'Rmpfr' version '0.8-2'
• package encoding: UTF-8
• 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 whether package 'Rmpfr' can be installed ... OK
• 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
• loading checks for arch 'i386'
  • 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 loading without being on the library search path ... OK
  • checking use of S3 registration ... OK
• loading checks for arch 'x64'
  • 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 loading without being on the library search path ... OK
  • checking use of S3 registration ... 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 ... [14s] NOTE
  cbind,Mnumber: no visible global function definition for 'deparse1'
  rbind,Mnumber: no visible global function definition for 'deparse1'
  Undefined global functions or variables:
    deparse1
• 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 line endings in shell scripts ... 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 pragmas in C/C++ headers and code ... OK
• checking compiled code ... OK
• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ...
  • running examples for arch 'i386' ... ERROR
    Running examples in 'Rmpfr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: log1mexp
    > ### Title: Compute f(a) = log(1 +/- exp(-a)) Numerically Optimally
    > ### Aliases: log1pexp log1mexp
    > ### Keywords: math
    >
    > ### ** Examples
    >
    > fExpr <- expression(
    + DEF = log(1 - exp(-a)),
    + expm1 = log(-expm1(-a)),
    + log1p = log1p(-exp(-a)),
    + F = log1mexp(a))
    > a. <- 2^seq(-58, 10, length = 256)
    > a <- a. ; str(fa <- do.call(cbind, as.list(fExpr)))
     num [1:256, 1:4] -Inf -Inf -Inf -Inf -Inf ...
     - attr(*, "dimnames")=List of 2
      ..$ : NULL
      ..$ : chr [1:4] "DEF" "expm1" "log1p" "F"
    > head(fa)# expm1() works here
          DEF expm1 log1p F
    [1,] -Inf -40.20254 -Inf -40.20254
    [2,] -Inf -40.01770 -Inf -40.01770
    [3,] -Inf -39.83286 -Inf -39.83286
    [4,] -Inf -39.64802 -Inf -39.64802
    [5,] -Inf -39.46318 -Inf -39.46318
    [6,] -Inf -39.27834 -Inf -39.27834
    > tail(fa)# log1p() works here
           DEF expm1 log1p F
    [251,] 0 0 -3.263800e-177 -3.263800e-177
    [252,] 0 0 -4.814940e-213 -4.814940e-213
    [253,] 0 0 -3.774342e-256 -3.774342e-256
    [254,] 0 0 -5.242582e-308 -5.242582e-308
    [255,] 0 0 0.000000e+00 0.000000e+00
    [256,] 0 0 0.000000e+00 0.000000e+00
    >
    > ## graphically:
    > lwd <- 1.5*(5:2); col <- adjustcolor(1:4, 0.4)
    > op <- par(mfcol=c(1,2), mgp = c(1.25, .6, 0), mar = .1+c(3,2,1,1))
    > matplot(a, fa, type = "l", log = "x", col=col, lwd=lwd)
    > legend("topleft", fExpr, col=col, lwd=lwd, lty=1:4, bty="n")
    > # expm1() & log1mexp() work here
    >
    > matplot(a, -fa, type = "l", log = "xy", col=col, lwd=lwd)
    Warning in xy.coords(x, y, xlabel, ylabel, log = log) :
      40 y values <= 0 omitted from logarithmic plot
    Warning in xy.coords(x, y, xlabel, ylabel, log) :
      18 y values <= 0 omitted from logarithmic plot
    > legend("left", paste("-",fExpr), col=col, lwd=lwd, lty=1:4, bty="n")
    > # log1p() & log1mexp() work here
    > par(op)
    >
    > aM <- 2^seqMpfr(-58, 10, length=length(a.)) # => default prec = 128
    > a <- aM; dim(faM <- do.call(cbind, as.list(fExpr))) # 256 x 4, "same" as 'fa'
    [1] 256 4
    > ## Here, for small 'a' log1p() and even 'DEF' is still good enough
    > l_f <- asNumeric(log(-faM))
    > all.equal(l_f[,"F"], l_f[,"log1p"], tol=0) # see TRUE (Lnx 64-bit)
    [1] TRUE
    > io <- a. < 80 # for these, the differences are small
    > all.equal(l_f[io,"F"], l_f[io,"expm1"], tol=0) # see 6.662e-9
    [1] "Mean relative difference: 6.622392e-09"
    > all.equal(l_f[io,"F"], l_f[io, "DEF" ], tol=0)
    [1] "Mean relative difference: 6.622392e-09"
    > stopifnot(exprs = {
    + all.equal(l_f[,"F"], l_f[,"log1p"], tol= 1e-15)
    + all.equal(l_f[io,"F"], l_f[io,"expm1"], tol= 1e-7)
    + all.equal(l_f[io,"F"], l_f[io, "DEF" ], tol= 1e-7)
    + })
    > ## For 128-bit prec, if we go down to 2^-130, "log1p" is no longer ok:
    > aM2 <- 2^seqMpfr(-130, 10, by = 1/2)
    > a <- aM2; fa2 <- do.call(cbind, as.list(fExpr))
    > head(asNumeric(fa2), 12)
                DEF expm1 log1p F
     [1,] -Inf -90.10913 -Inf -90.10913
     [2,] -Inf -89.76256 -Inf -89.76256
     [3,] -Inf -89.41599 -Inf -89.41599
     [4,] -88.72284 -89.06941 -88.72284 -89.06941
     [5,] -88.72284 -88.72284 -88.72284 -88.72284
     [6,] -88.72284 -88.37627 -88.72284 -88.37627
     [7,] -88.02969 -88.02969 -88.02969 -88.02969
     [8,] -87.62423 -87.68312 -87.62423 -87.68312
     [9,] -87.33654 -87.33654 -87.33654 -87.33654
    [10,] -86.93108 -86.98997 -86.93108 -86.98997
    [11,] -86.64340 -86.64340 -86.64340 -86.64340
    [12,] -86.32494 -86.29682 -86.32494 -86.29682
    > tail(asNumeric(fa2), 12)
                     DEF expm1 log1p F
    [270,] -1.489490e-10 -1.489490e-10 -1.489490e-10 -1.489490e-10
    [271,] -1.266417e-14 -1.266417e-14 -1.266417e-14 -1.266417e-14
    [272,] -2.218581e-20 -2.218581e-20 -2.218581e-20 -2.218581e-20
    [273,] -1.603811e-28 -1.603811e-28 -1.603811e-28 -1.603811e-28
    [274,] 0.000000e+00 0.000000e+00 -4.922102e-40 -4.922102e-40
    [275,] 0.000000e+00 0.000000e+00 -2.572209e-56 -2.572209e-56
    [276,] 0.000000e+00 0.000000e+00 -2.422709e-79 -2.422709e-79
    [277,] 0.000000e+00 0.000000e+00 -6.616261e-112 -6.616261e-112
    [278,] 0.000000e+00 0.000000e+00 -5.869519e-158 -5.869519e-158
    [279,] 0.000000e+00 0.000000e+00 -4.377491e-223 -4.377491e-223
    [280,] 0.000000e+00 0.000000e+00 -3.445126e-315 -3.445126e-315
    [281,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
    >
    > matplot(a, log(-fa2[,1:3]) -log(-fa2[,"F"]), type="l", log="x",
    + lty=1:3, lwd=2*(3:1)-1, col=adjustcolor(2:4, 1/3))
    Error in xy.coords(x, y, xlabel, ylabel, log = log) :
      'list' object cannot be coerced to type 'double'
    Calls: matplot -> xy.coords
    Execution halted
  • running examples for arch 'x64' ... ERROR
    Running examples in 'Rmpfr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: log1mexp
    > ### Title: Compute f(a) = log(1 +/- exp(-a)) Numerically Optimally
    > ### Aliases: log1pexp log1mexp
    > ### Keywords: math
    >
    > ### ** Examples
    >
    > fExpr <- expression(
    + DEF = log(1 - exp(-a)),
    + expm1 = log(-expm1(-a)),
    + log1p = log1p(-exp(-a)),
    + F = log1mexp(a))
    > a. <- 2^seq(-58, 10, length = 256)
    > a <- a. ; str(fa <- do.call(cbind, as.list(fExpr)))
     num [1:256, 1:4] -Inf -Inf -Inf -Inf -Inf ...
     - attr(*, "dimnames")=List of 2
      ..$ : NULL
      ..$ : chr [1:4] "DEF" "expm1" "log1p" "F"
    > head(fa)# expm1() works here
          DEF expm1 log1p F
    [1,] -Inf -40.20254 -Inf -40.20254
    [2,] -Inf -40.01770 -Inf -40.01770
    [3,] -Inf -39.83286 -Inf -39.83286
    [4,] -Inf -39.64802 -Inf -39.64802
    [5,] -Inf -39.46318 -Inf -39.46318
    [6,] -Inf -39.27834 -Inf -39.27834
    > tail(fa)# log1p() works here
           DEF expm1 log1p F
    [251,] 0 0 -3.263800e-177 -3.263800e-177
    [252,] 0 0 -4.814940e-213 -4.814940e-213
    [253,] 0 0 -3.774342e-256 -3.774342e-256
    [254,] 0 0 -5.242582e-308 -5.242582e-308
    [255,] 0 0 0.000000e+00 0.000000e+00
    [256,] 0 0 0.000000e+00 0.000000e+00
    >
    > ## graphically:
    > lwd <- 1.5*(5:2); col <- adjustcolor(1:4, 0.4)
    > op <- par(mfcol=c(1,2), mgp = c(1.25, .6, 0), mar = .1+c(3,2,1,1))
    > matplot(a, fa, type = "l", log = "x", col=col, lwd=lwd)
    > legend("topleft", fExpr, col=col, lwd=lwd, lty=1:4, bty="n")
    > # expm1() & log1mexp() work here
    >
    > matplot(a, -fa, type = "l", log = "xy", col=col, lwd=lwd)
    Warning in xy.coords(x, y, xlabel, ylabel, log = log) :
      40 y values <= 0 omitted from logarithmic plot
    Warning in xy.coords(x, y, xlabel, ylabel, log) :
      18 y values <= 0 omitted from logarithmic plot
    > legend("left", paste("-",fExpr), col=col, lwd=lwd, lty=1:4, bty="n")
    > # log1p() & log1mexp() work here
    > par(op)
    >
    > aM <- 2^seqMpfr(-58, 10, length=length(a.)) # => default prec = 128
    > a <- aM; dim(faM <- do.call(cbind, as.list(fExpr))) # 256 x 4, "same" as 'fa'
    [1] 256 4
    > ## Here, for small 'a' log1p() and even 'DEF' is still good enough
    > l_f <- asNumeric(log(-faM))
    > all.equal(l_f[,"F"], l_f[,"log1p"], tol=0) # see TRUE (Lnx 64-bit)
    [1] TRUE
    > io <- a. < 80 # for these, the differences are small
    > all.equal(l_f[io,"F"], l_f[io,"expm1"], tol=0) # see 6.662e-9
    [1] "Mean relative difference: 6.622392e-09"
    > all.equal(l_f[io,"F"], l_f[io, "DEF" ], tol=0)
    [1] "Mean relative difference: 6.622392e-09"
    > stopifnot(exprs = {
    + all.equal(l_f[,"F"], l_f[,"log1p"], tol= 1e-15)
    + all.equal(l_f[io,"F"], l_f[io,"expm1"], tol= 1e-7)
    + all.equal(l_f[io,"F"], l_f[io, "DEF" ], tol= 1e-7)
    + })
    > ## For 128-bit prec, if we go down to 2^-130, "log1p" is no longer ok:
    > aM2 <- 2^seqMpfr(-130, 10, by = 1/2)
    > a <- aM2; fa2 <- do.call(cbind, as.list(fExpr))
    > head(asNumeric(fa2), 12)
                DEF expm1 log1p F
     [1,] -Inf -90.10913 -Inf -90.10913
     [2,] -Inf -89.76256 -Inf -89.76256
     [3,] -Inf -89.41599 -Inf -89.41599
     [4,] -88.72284 -89.06941 -88.72284 -89.06941
     [5,] -88.72284 -88.72284 -88.72284 -88.72284
     [6,] -88.72284 -88.37627 -88.72284 -88.37627
     [7,] -88.02969 -88.02969 -88.02969 -88.02969
     [8,] -87.62423 -87.68312 -87.62423 -87.68312
     [9,] -87.33654 -87.33654 -87.33654 -87.33654
    [10,] -86.93108 -86.98997 -86.93108 -86.98997
    [11,] -86.64340 -86.64340 -86.64340 -86.64340
    [12,] -86.32494 -86.29682 -86.32494 -86.29682
    > tail(asNumeric(fa2), 12)
                     DEF expm1 log1p F
    [270,] -1.489490e-10 -1.489490e-10 -1.489490e-10 -1.489490e-10
    [271,] -1.266417e-14 -1.266417e-14 -1.266417e-14 -1.266417e-14
    [272,] -2.218581e-20 -2.218581e-20 -2.218581e-20 -2.218581e-20
    [273,] -1.603811e-28 -1.603811e-28 -1.603811e-28 -1.603811e-28
    [274,] 0.000000e+00 0.000000e+00 -4.922102e-40 -4.922102e-40
    [275,] 0.000000e+00 0.000000e+00 -2.572209e-56 -2.572209e-56
    [276,] 0.000000e+00 0.000000e+00 -2.422709e-79 -2.422709e-79
    [277,] 0.000000e+00 0.000000e+00 -6.616261e-112 -6.616261e-112
    [278,] 0.000000e+00 0.000000e+00 -5.869519e-158 -5.869519e-158
    [279,] 0.000000e+00 0.000000e+00 -4.377491e-223 -4.377491e-223
    [280,] 0.000000e+00 0.000000e+00 -3.445126e-315 -3.445126e-315
    [281,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
    >
    > matplot(a, log(-fa2[,1:3]) -log(-fa2[,"F"]), type="l", log="x",
    + lty=1:3, lwd=2*(3:1)-1, col=adjustcolor(2:4, 1/3))
    Error in xy.coords(x, y, xlabel, ylabel, log = log) :
      'list' object cannot be coerced to type 'double'
    Calls: matplot -> xy.coords
    Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ...
  • running tests for arch 'i386' ... [44s] OK
      Running 'arith-ex.R' [6s]
      Running 'binomial-etc.R' [1s]
      Running 'bit-repr.R' [1s]
      Comparing 'bit-repr.Rout' to 'bit-repr.Rout.save' ... OK
      Running 'create.R' [2s]
      Running 'functionals.R' [17s]
      Running 'lowlevel.R' [1s]
      Running 'matrix-ex.R' [3s]
      Running 'special-fun-ex.R' [12s]
      Running 'tstHexBin.R' [1s]
  • running tests for arch 'x64' ... [46s] OK
      Running 'arith-ex.R' [6s]
      Running 'binomial-etc.R' [1s]
      Running 'bit-repr.R' [2s]
      Comparing 'bit-repr.Rout' to 'bit-repr.Rout.save' ... OK
      Running 'create.R' [2s]
      Running 'functionals.R' [18s]
      Running 'lowlevel.R' [2s]
      Running 'matrix-ex.R' [3s]
      Running 'special-fun-ex.R' [10s]
      Running 'tstHexBin.R' [1s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking re-building of vignette outputs ... [26s] WARNING
  Error(s) in re-building vignettes:
  --- re-building 'Maechler_useR_2011-abstr.Rnw' using Sweave
  Loading required package: Rmpfr
  Loading required package: gmp
  
  Attaching package: 'gmp'
  
  The following objects are masked from 'package:base':
  
      %*%, apply, crossprod, matrix, tcrossprod
  
  C code of R package 'Rmpfr': GMP using 64 bits per limb
  
  
  Attaching package: 'Rmpfr'
  
  The following object is masked from 'package:gmp':
  
      outer
  
  The following objects are masked from 'package:stats':
  
      dbinom, dgamma, dnbinom, dnorm, dpois, pnorm
  
  The following objects are masked from 'package:base':
  
      cbind, pmax, pmin, rbind
  
  --- finished re-building 'Maechler_useR_2011-abstr.Rnw'
  
  --- re-building 'Rmpfr-pkg.Rnw' using Sweave
  Loading required package: sfsmisc
  Loading required package: Rmpfr
  Loading required package: gmp
  
  Attaching package: 'gmp'
  
  The following objects are masked from 'package:sfsmisc':
  
      factorize, is.whole
  
  The following objects are masked from 'package:base':
  
      %*%, apply, crossprod, matrix, tcrossprod
  
  C code of R package 'Rmpfr': GMP using 64 bits per limb
  
  
  Attaching package: 'Rmpfr'
  
  The following object is masked from 'package:gmp':
  
      outer
  
  The following objects are masked from 'package:stats':
  
      dbinom, dgamma, dnbinom, dnorm, dpois, pnorm
  
  The following objects are masked from 'package:base':
  
      cbind, pmax, pmin, rbind
  
  
  Error: processing vignette 'Rmpfr-pkg.Rnw' failed with diagnostics:
   chunk 23 (label = format-lrg)
  Error in deparse1(a) : could not find function "deparse1"
  
  --- failed re-building 'Rmpfr-pkg.Rnw'
  
  --- re-building 'log1mexp-note.Rnw' using Sweave
  Loading required package: gmp
  
  Attaching package: `gmp'
  
  The following objects are masked from `package:sfsmisc':
  
      factorize, is.whole
  
  The following objects are masked from `package:base':
  
      %*%, apply, crossprod, matrix, tcrossprod
  
  C code of R package 'Rmpfr': GMP using 64 bits per limb
  
  
  Attaching package: `Rmpfr'
  
  The following object is masked from `package:gmp':
  
      outer
  
  The following objects are masked from `package:stats':
  
      dbinom, dgamma, dnbinom, dnorm, dpois, pnorm
  
  The following objects are masked from `package:base':
  
      cbind, pmax, pmin, rbind
  
  !!! Error: Too many files!
  PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
  !!! Error: Too many files!
  PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
  !!! Error: Too many files!
  PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
  !!! Error: Too many files!
  PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
  --- finished re-building 'log1mexp-note.Rnw'
  
  SUMMARY: processing the following file failed:
    'Rmpfr-pkg.Rnw'
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE