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math/R-cran-mvtnorm

Multivariate Normal and t Distributions

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Events

Build Log

===>  Testing for R-cran-mvtnorm-1.3.6
* using log directory '/magus/work/usr/mports/math/R-cran-mvtnorm/work/mvtnorm.Rcheck'
* using R version 4.4.0 (2024-04-24)
* using platform: amd64-portbld-midnightbsd4.0
* R was compiled by
    MidnightBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)
    GNU Fortran (MidnightBSD Ports Collection) 14.2.0
* running under: MidnightBSD m4064 4.0.5 MidnightBSD 4.0.5 stable/4.0-n13794-ebf9c891ff GENERIC amd64
* using session charset: ASCII
* using options '--no-manual --no-build-vignettes'
* checking for file 'mvtnorm/DESCRIPTION' ... OK
* this is package 'mvtnorm' version '1.3-6'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'qrng', 'numDeriv', 'bibtex'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'mvtnorm' can be installed ... OK
* used C compiler: 'MidnightBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)'
* used Fortran compiler: 'GNU Fortran (MidnightBSD Ports Collection) 14.2.0'
* 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 code 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 ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
prepare_Rd: ./man/Mvt.Rd:32: unknown macro '\bibcitet'
prepare_Rd: ./man/Mvt.Rd:33: unknown macro '\bibcitet'
prepare_Rd: ./man/Mvt.Rd:37: unknown macro '\bibcitet'
prepare_Rd: ./man/Mvt.Rd:38: unknown macro '\bibcitep'
prepare_Rd: ./man/Mvt.Rd:69: unknown macro '\bibcitet'
checkRd: (-1) Mvt.Rd:32: Lost braces
    32 |               to formula (1.4) in \bibcitet{mvtnorm::Genz_Bretz_2009}, see also
       |                                            ^
checkRd: (-1) Mvt.Rd:33: Lost braces
    33 |               Chapter 5.1 in \bibcitet{mvtnorm::Kotz+Nadarajah:2004}. This is the
       |                                       ^
checkRd: (-1) Mvt.Rd:37: Lost braces
    37 |                formula right before formula (1.4) in \bibcitet{mvtnorm::Genz_Bretz_2009}
       |                                                               ^
checkRd: (-1) Mvt.Rd:38: Lost braces
    38 |               \bibcitep{see also formula (1.1) in|mvtnorm::Kotz+Nadarajah:2004|}.  It
       |                        ^
checkRd: (-1) Mvt.Rd:69: Lost braces
    69 |   see \bibcitet{mvtnorm::McNeil+Frey+Embrechts:2005}, p. 74.
       |                ^
prepare_Rd: ./man/algorithms.Rd:35: unknown macro '\bibcitet'
prepare_Rd: ./man/algorithms.Rd:36: unknown macro '\bibcitet'
prepare_Rd: ./man/algorithms.Rd:41: unknown macro '\bibcitet'
prepare_Rd: ./man/algorithms.Rd:49: unknown macro '\bibcitet'
checkRd: (-1) algorithms.Rd:35: Lost braces
    35 | by \bibcitet{mvtnorm::numerical-:1992,mvtnorm::comparison:1993} and
       |             ^
checkRd: (-1) algorithms.Rd:36: Lost braces
    36 | \bibcitet{mvtnorm::Genz_Bretz_2002} applicable to
       |          ^
checkRd: (-1) algorithms.Rd:41: Lost braces
    41 | the algorithm by \bibcitet{mvtnorm::Miwa+Hayter+Kuriki:2003} can be used as well. This algorithm can
       |                           ^
checkRd: (-1) algorithms.Rd:49: Lost braces
    49 | by \bibcitet{mvtnorm::Genz:2004}.
       |             ^
prepare_Rd: ./man/lpRR.Rd:45: unknown macro '\bibcitet'
checkRd: (-1) lpRR.Rd:45: Lost braces
    45 |   in \bibcitet{mvtnorm::Genz_Bretz_2009}, Chapter 2.3.1.
       |               ^
prepare_Rd: ./man/lpmvnorm.Rd:55: unknown macro '\bibcitep'
prepare_Rd: ./man/lpmvnorm.Rd:56: unknown macro '\bibcitep'
prepare_Rd: ./man/lpmvnorm.Rd:81: unknown macro '\bibcitep'
prepare_Rd: ./man/lpmvnorm.Rd:82: unknown macro '\bibcitep'
checkRd: (-1) lpmvnorm.Rd:55: Lost braces
    55 | Monte-Carlo procedure \bibcitep{mvtnorm::numerical-:1992} with a quasi-Monte-Carlo approach
       |                                ^
checkRd: (-1) lpmvnorm.Rd:56: Lost braces
    56 | \bibcitep{mvtnorm::Genz_Bretz_2002}. Note that the same weights for evaluating the
       |          ^
checkRd: (-1) lpmvnorm.Rd:81: Lost braces
    81 |   Monte-Carlo \bibcitep{|mvtnorm::numerical-:1992|the default} and quasi-Monte-Carlo 
       |                        ^
checkRd: (-1) lpmvnorm.Rd:82: Lost braces
    82 |   \bibcitep{mvtnorm::Genz_Bretz_2002}
       |            ^
prepare_Rd: ./man/pmvnorm.Rd:45: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvnorm.Rd:46: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvnorm.Rd:47: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvnorm.Rd:70: unknown macro '\bibcitet'
checkRd: (-1) pmvnorm.Rd:45: Lost braces
    45 | \bibcitet{mvtnorm::numerical-:1992} and \bibcitet{mvtnorm::comparison:1993} for algorithm
       |          ^
checkRd: (-1) pmvnorm.Rd:45: Lost braces
    45 | \bibcitet{mvtnorm::numerical-:1992} and \bibcitet{mvtnorm::comparison:1993} for algorithm
       |                                                  ^
checkRd: (-1) pmvnorm.Rd:46: Lost braces
    46 | \code{GenzBretz}, in \bibcitet{mvtnorm::Miwa+Hayter+Kuriki:2003} for algorithm
       |                               ^
checkRd: (-1) pmvnorm.Rd:47: Lost braces
    47 | \code{Miwa}, useful up to dimension 20, and \bibcitet{mvtnorm::Genz:2004}
       |                                                      ^
checkRd: (-1) pmvnorm.Rd:70: Lost braces
    70 | An overview is available from \bibcitet{mvtnorm::Genz_Bretz_2009}.
       |                                        ^
prepare_Rd: ./man/pmvt.Rd:34: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvt.Rd:35: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvt.Rd:39: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvt.Rd:40: unknown macro '\bibcitep'
prepare_Rd: ./man/pmvt.Rd:63: unknown macro '\bibcitet'
prepare_Rd: ./man/pmvt.Rd:69: unknown macro '\bibcitet'
checkRd: (-1) pmvt.Rd:34: Lost braces
    34 |               to formula (1.4) in \bibcitet{mvtnorm::Genz_Bretz_2009}, see also
       |                                            ^
checkRd: (-1) pmvt.Rd:35: Lost braces
    35 |               Chapter 5.1 in \bibcitet{mvtnorm::Kotz+Nadarajah:2004}. This is the
       |                                       ^
checkRd: (-1) pmvt.Rd:39: Lost braces
    39 |                formula right before formula (1.4) in \bibcitet{mvtnorm::Genz_Bretz_2009}
       |                                                               ^
checkRd: (-1) pmvt.Rd:40: Lost braces
    40 |               \bibcitep{see also formula (1.1) in|mvtnorm::Kotz+Nadarajah:2004|}. It
       |                        ^
checkRd: (-1) pmvt.Rd:63: Lost braces
    63 | described in \bibcitet{mvtnorm::numerical-:1999,Genz_Bretz_2002}.
       |                       ^
checkRd: (-1) pmvt.Rd:69: Lost braces
    69 | described by \bibcitet{mvtnorm::Genz:2004}, which only handles semi-infinite integration
       |                       ^
prepare_Rd: ./man/qmvnorm.Rd:57: unknown macro '\bibcitet'
checkRd: (-1) qmvnorm.Rd:57: Lost braces
    57 |   in \bibcitet{mvtnorm::Bornkamp:2018}.
       |               ^
prepare_Rd: ./man/qmvt.Rd:47: unknown macro '\bibcitet'
prepare_Rd: ./man/qmvt.Rd:48: unknown macro '\bibcitet'
prepare_Rd: ./man/qmvt.Rd:52: unknown macro '\bibcitet'
prepare_Rd: ./man/qmvt.Rd:53: unknown macro '\bibcitep'
prepare_Rd: ./man/qmvt.Rd:68: unknown macro '\bibcitet'
checkRd: (-1) qmvt.Rd:47: Lost braces
    47 |               to formula (1.4) in \bibcitet{mvtnorm::Genz_Bretz_2009}, see also
       |                                            ^
checkRd: (-1) qmvt.Rd:48: Lost braces
    48 |               Chapter 5.1 in \bibcitet{mvtnorm::Kotz+Nadarajah:2004}. This is the
       |                                       ^
checkRd: (-1) qmvt.Rd:52: Lost braces
    52 |                formula right before formula (1.4) in \bibcitet{mvtnorm::Genz_Bretz_2009}
       |                                                               ^
checkRd: (-1) qmvt.Rd:53: Lost braces
    53 |               \bibcitep{see also formula (1.1) in|mvtnorm::Kotz+Nadarajah:2004|}.}
       |                        ^
checkRd: (-1) qmvt.Rd:68: Lost braces
    68 |   in \bibcitet{mvtnorm::Bornkamp:2018}.
       |               ^
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking usage of KIND in Fortran files ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'bugfix-tests.R'
  Comparing 'bugfix-tests.Rout' to 'bugfix-tests.Rout.save' ... OK
  Running 'dmvnorm-Ex.R'
  Running 'plmvnorm-Ex.R'
  Comparing 'plmvnorm-Ex.Rout' to 'plmvnorm-Ex.Rout.save' ...166c166
< [1] 0.7734535
---
> [1] 0.7733946
179c179
< [1] 0.08741965
---
> [1] 0.07507118
183c183
< [1] 0.08740329
---
> [1] 0.07507119
195c195
< [1] 0.3499051
---
> [1] 0.3986757
199c199
< [1] 0.3499063
---
> [1] 0.3986758
213c213
< [1] 0.5006143
---
> [1] 0.4565892
220c220
< [1] 0.5006143
---
> [1] 0.4565892
228c228
< [1] 0.5006143
---
> [1] 0.4565892
236c236
< [1] 0.5006143
---
> [1] 0.4565892
248c248
< [1] 0.3494717
---
> [1] 0.320247
252c252
< [1] 0.3494266
---
> [1] 0.320247
264c264
< [1] 0.3501812
---
> [1] 0.4466655
271c271
< [1] 0.3501812
---
> [1] 0.4466655
285c285
< [1] 0.4009144
---
> [1] 0.4499242
292c292
< [1] 0.4009144
---
> [1] 0.4499242
350c350
< [1] 0.9503873
---
> [1] 0.949977
356c356
< [1] 0.9501017
---
> [1] 0.9500024
358c358
< [1] 0.0001557036
---
> [1] 0.0001403885
366c366
< [1] 0.9503882
---
> [1] 0.9500143
372c372
< [1] 0.9500176
---
> [1] 0.9499675
374c374
< [1] 0.0001302458
---
> [1] 0.0001052159
382c382
< [1] 0.9502289
---
> [1] 0.9500265
389c389
< [1] 0.9499176
---
> [1] 0.950041
391c391
< [1] 8.437435e-05
---
> [1] 0.000113758
399c399
< [1] 0.9503619
---
> [1] 0.9499789
422c422
< [1] 0.04204181
---
> [1] 0.04210637
584c584
< [1] 0.2892721
---
> [1] 0.2892618
586c586
< [1] 6.703972e-05
---
> [1] 0.000110303
  Running 'regtest-TVPACK.R'
  Comparing 'regtest-TVPACK.Rout' to 'regtest-TVPACK.Rout.save' ... OK
  Running 'regtest-aperm.R'
 ERROR
Running the tests in 'tests/regtest-aperm.R' failed.
Complete output:
  > 
  > library("mvtnorm")
  > library("numDeriv")
  Error in library("numDeriv") : there is no package called 'numDeriv'
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ...
  'MVT_Rnews.Rnw'... OK
  'lmvnorm_src.Rnw' using 'UTF-8'... failed
 ERROR
Errors in running code in vignettes:
when running code in 'lmvnorm_src.Rnw'
  ...
> nsc <- function(parm) {
+     d <- parm[seq_len(J)]
+     L <- ltMatrices(parm[-seq_len(J)], diag = TRUE)
+     ret <- sldmvnorm(obs = Y, mean = sol .... [TRUNCATED] 

> chk(unname(nsc(start)), grad(nll, start))

  When sourcing 'lmvnorm_src.R':
Error: could not find function "grad"
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  '/magus/work/usr/mports/math/R-cran-mvtnorm/work/mvtnorm.Rcheck/00check.log'
for details.

*** Error code 1

Stop.
make: stopped in /usr/mports/math/R-cran-mvtnorm