R universe build fail

[gregorgorjanc]

Here is build error from https://github.com/r-universe/highlanderlab/actions/runs/21546895920/job/62089596152, which is puzzling as I have not got this on my end or on GitHub Actions running R CMD check.

  Setting r-universe rmarkdown theme...
  * checking for file ‘RcppTskit/RcppTskit/DESCRIPTION’ ... OK
  * preparing ‘RcppTskit’:
  * checking DESCRIPTION meta-information ... OK
  * cleaning src
  * running ‘cleanup’
  Found quarto! Replacing html engine...
  * installing the package to build vignettes
        -----------------------------------
  Setting r-universe rmarkdown theme...
  * installing *source* package ‘RcppTskit’ ...
  ** this is package ‘RcppTskit’ version ‘0.1.0’
  ** using staged installation
  Setting r-universe rmarkdown theme...
  ** libs
  using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
  using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
  gcc -std=gnu2x -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/usr/lib/R/include -DNDEBUG  -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-ePVXIN/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat  -fcf-protection -fdebug-prefix-map=/build/r-base-ePVXIN/r-base-4.5.2=/usr/src/r-base-4.5.2-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -fpic -c tskit/convert.c -o tskit/convert.o
  In file included from ../inst/include/kastore.h:2,
                   from ../inst/include/tskit/tskit/tables.h:41,
                   from ../inst/include/tskit/tables.h:2,
                   from ../inst/include/tskit/tskit/trees.h:37,
                   from ../inst/include/tskit/trees.h:2,
                   from ../inst/include/tskit/tskit/convert.h:33,
                   from ../inst/include/tskit/convert.h:2,
                   from tskit/convert.c:32:
  ../inst/include/tskit/kastore.h:10:10: fatal error: R_ext/Error.h: No such file or directory
     10 | #include <R_ext/Error.h>
        |          ^~~~~~~~~~~~~~~
  compilation terminated.
  make: *** [Makevars:49: tskit/convert.o] Error 1
  ERROR: compilation failed for package ‘RcppTskit’
  * removing ‘/tmp/Rtmp6AGv9h/Rinstbdc6937405a/RcppTskit’
        -----------------------------------
  ERROR: package installation failed
R CMD build (trying without vignettes)
  ---- ERROR: failed to run: R CMD build -----
  Trying to build source package without vignettes....
  * checking for file ‘RcppTskit/RcppTskit/DESCRIPTION’ ... OK
  * preparing ‘RcppTskit’:
  * checking DESCRIPTION meta-information ... OK
  * cleaning src
  * running ‘cleanup’
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘RcppTskit_0.1.0.tar.gz’
  
install package and generate html docs
  * installing to library ‘/github/workspace/pkglib’
  * installing *source* package ‘RcppTskit’ ...
  ** this is package ‘RcppTskit’ version ‘0.1.0’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
  using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
  gcc -std=gnu2x -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/usr/lib/R/include -DNDEBUG  -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-ePVXIN/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat  -fcf-protection -fdebug-prefix-map=/build/r-base-ePVXIN/r-base-4.5.2=/usr/src/r-base-4.5.2-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -fpic -c tskit/convert.c -o tskit/convert.o
  In file included from ../inst/include/kastore.h:2,
                   from ../inst/include/tskit/tskit/tables.h:41,
                   from ../inst/include/tskit/tables.h:2,
                   from ../inst/include/tskit/tskit/trees.h:37,
                   from ../inst/include/tskit/trees.h:2,
                   from ../inst/include/tskit/tskit/convert.h:33,
                   from ../inst/include/tskit/convert.h:2,
                   from tskit/convert.c:32:
  ../inst/include/tskit/kastore.h:10:10: fatal error: R_ext/Error.h: No such file or directory
     10 | #include <R_ext/Error.h>
        |          ^~~~~~~~~~~~~~~
  compilation terminated.
  make: *** [Makevars:49: tskit/convert.o] Error 1
  ERROR: compilation failed for package ‘RcppTskit’
  * removing ‘/github/workspace/pkglib/RcppTskit’
  Error: Failed to install:
  ../inst/include/tskit/kastore.h:10:10: fatal error: R_ext/Error.h: No such file or directory
     10 | #include <R_ext/Error.h>
        |          ^~~~~~~~~~~~~~~
  compilation terminated.
  make: *** [Makevars:49: tskit/convert.o] Error 1
  ERROR: compilation failed for package ‘RcppTskit’
  * removing ‘/github/workspace/pkglib/RcppTskit’

[gregorgorjanc]

Seems that -I$(R_HOME)/include from src/Makevars is not recognised as it should be?

# Preprocessor (PP) include paths and defines
# * A bit complicated include/tskit structure due to how we include tskit headers
# * $(R_HOME)/include is for <R_ext/Error.h>
PKG_CPPFLAGS = \
	-I../inst/include \
	-I../inst/include/tskit \
	-I../inst/include/tskit/tskit \
	-I$(R_HOME)/include

[gregorgorjanc]

Changes in eb2a12f sorted this - see the outcome at https://github.com/r-universe/highlanderlab/actions/runs/21562975671

I assume this means that CRAN build might fail as well with the same error as shown above at #53 (comment)? Let's see ...