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[R-pkg-devel] Problem with vignette compilation

2 messages · EGIDI LEONARDO, Duncan Murdoch

Original
EGIDI LEONARDO
# 
Hi all,

I am ready to submit the ?footBayes? package for football models fitting.
However, even though my vignette knits correctly on my local machine and my package reports zero errors/warnings,
I am repeatedly getting this warning/error below when I check on Win builder through devtools::check_win_devel().
I did so many attempts, it is frustrating! I report the error below. The quitting line of the chunk regard a ?rstan? fit.
My VignetteBuilder in the description is ?knitr?
Any suggestion?

Thanks a lot.

Leonardo


-------------------------------------------------------------------------------------------------------------------------------------
* checking re-building of vignette outputs ... [76s] ERROR
Error(s) in re-building vignettes:
--- re-building 'footBayes_a_rapid_guide.Rmd' using knitr
This is bayesplot version 1.8.1
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
This is loo version 2.4.1
- Online documentation and vignettes at mc-stan.org/loo
- As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
- Windows 10 users: loo may be very slow if 'mc.cores' is set in your .Rprofile file (see https://github.com/stan-dev/loo/issues/94).

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

?????? Attaching packages ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? tidyverse 1.3.1 ??????
??? tibble  3.1.6     ??? purrr   0.3.4
??? tidyr   1.2.0     ??? stringr 1.4.0
??? readr   2.1.2     ??? forcats 0.5.1
?????? Conflicts ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? tidyverse_conflicts() ??????
??? dplyr::filter() masks stats::filter()
??? dplyr::lag()    masks stats::lag()
make cmd is
  make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file26368298720af.dll" WIN=64 TCLBIN= OBJECTS="file26368298720af.o"

make would use
make[1]: Entering directory '/d/temp/RtmpALbt6R/working_dir/Rtmpe0dyI1'
if test "zfile26368298720af.o" != "z"; then \
  if test -e "file26368298720af-win.def"; then \
    echo g++  -shared -s -static-libgcc -o file26368298720af.dll file26368298720af-win.def file26368298720af.o  -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib"  -L"D:/RCompile/recent/R/bin/x64" -lR ; \
    g++  -shared -s -static-libgcc -o file26368298720af.dll file26368298720af-win.def file26368298720af.o  -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib"  -L"D:/RCompile/recent/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    nm file26368298720af.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo g++  -shared -s -static-libgcc -o file26368298720af.dll tmp.def file26368298720af.o  -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib"  -L"D:/RCompile/recent/R/bin/x64" -lR ; \
    g++  -shared -s -static-libgcc -o file26368298720af.dll tmp.def file26368298720af.o  -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools42/x86_64-w64-mingw32.static.posix/lib"  -L"D:/RCompile/recent/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
make[1]: Leaving directory '/d/temp/RtmpALbt6R/working_dir/Rtmpe0dyI1'
Quitting from lines 271-307 (footBayes_a_rapid_guide.Rmd)
Quitting from lines 271-307 (footBayes_a_rapid_guide.Rmd)
Error: processing vignette 'footBayes_a_rapid_guide.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'footBayes_a_rapid_guide.Rmd'

SUMMARY: processing the following file failed:
  'footBayes_a_rapid_guide.Rmd'

Error: Vignette re-building failed.
Execution halted
-------------------------------------------------------------------------------------------------------------------------------------
Duncan Murdoch
#
On 16/02/2022 12:08 p.m., EGIDI LEONARDO wrote:
I don't know rstan, but those who do could probably help more if they 
had access to your source.  Is it online anywhere?

Duncan Murdoch