[R-pkg-devel] Problem with vignette compilation

[Duncan Murdoch]

On 16/02/2022 12:08 p.m., EGIDI LEONARDO wrote:
> 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?

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

> 
> 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
> -------------------------------------------------------------------------------------------------------------------------------------
> 
> 	[[alternative HTML version deleted]]
> 
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