The Nightly Dev Build job failed on Monday (2025-01-20)

[github-actions]

The Nightly Dev Build job failed on Monday (2025-01-20) in run 12878606032

---

sc-62563

[johnkerl]

Build log
https://github.com/TileDB-Inc/TileDB-R/actions/runs/12878606032/job/35904810973#step:8:695

CMake Error at CMakeLists.txt:121 (project):
  The CMAKE_CXX_COMPILER:

    g++ -std=gnu++17

  is not a full path and was not found in the PATH.

  Tell CMake where to find the compiler by setting either the environment
  variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
  to the compiler, or to the compiler name if it is in the PATH.

👀

[jdblischak]

Also failed on my fork, and failed after restarting too

[jdblischak]

Given that the error is about being unable to find the compiler when running TileDB's bootstrap script, I assume this was caused by the PR TileDB-Inc/TileDB#5426 to remove detection of the compiler (merged yesterday morning in TileDB-Inc/TileDB@efd3a21).

@dudoslav could you please investigate?

[johnkerl]

@dudoslav FWIW I was able to repro this outside of CI by imitating this repo's .github/workflows/nightly.yaml:

alias dreb='docker run --rm -it --entrypoint=/bin/bash'

dreb dreb rocker/r2u:latest

Rscript -e 'sessionInfo()'
apt update -qq && apt install --yes --no-install-recommends cmake curl git
cd /tmp
git clone https://github.com/TileDB-Inc/TileDB-R
cd TileDB-R
Rscript -e 'remotes::install_deps(".", dependencies=TRUE)'
R CMD build --no-build-vignettes --no-manual .
R CMD INSTALL --configure-args="--with-download=https://github.com/TileDB-Inc/TileDB/archive/refs/heads/main.zip" $(ls -1tr *.tar.gz | tail -1)

[github-actions]

The Nightly Dev Build job failed on Tuesday (2025-01-21) in run 12899570746

[jdblischak]

The nightly builds here and on my fork both failed with the same spurious bzip2 download failure that we also observed in multiple builds last week (#800 (comment)). I restarted it

[github-actions]

The Nightly Dev Build job failed on Wednesday (2025-01-22) in run 12899570746

[jdblischak]

The restarted job is back to failing with the previously identified CMake error of failing to identify the compiler.

[github-actions]

The Nightly Dev Build job failed on Wednesday (2025-01-22) in run 12920658744

[github-actions]

The Nightly Dev Build job failed on Thursday (2025-01-23) in run 12941688221

[jdblischak]

xref: #795

[github-actions]

The Nightly Dev Build job failed on Friday (2025-01-24) in run 12960667404

[github-actions]

The Nightly Dev Build job failed on Saturday (2025-01-25) in run 12970383102

[github-actions]

The Nightly Dev Build job failed on Sunday (2025-01-26) in run 12980600729

[github-actions]

The Nightly Dev Build job failed on Monday (2025-01-27) in run 13002051697

[dudoslav]

@johnkerl I created a branch with modified bootstrap script: https://github.com/dudoslav/TileDB/tree/db/sc-62563/bootstrap

and modified your repro using this branch. Now I don't see compiler not found, but I still see error:

../inst/include/tiledb.h:8:10: fatal error: tiledb/tiledb: No such file or directory
    8 | #include <tiledb/tiledb>

So perhaps this is not only due to bootstrap change. I'll investigate further.

[johnkerl]

@dudoslav thanks!

This is just a symptom, not a cause: fatal error: tiledb/tiledb -- can you please share the entire build output that let to this?

[dudoslav]

@johnkerl Same as you did, but changed the last line, so (inside docker container):

Rscript -e 'sessionInfo()'
apt update -qq && apt install --yes --no-install-recommends cmake curl git
cd /tmp
git clone https://github.com/TileDB-Inc/TileDB-R
cd TileDB-R
Rscript -e 'remotes::install_deps(".", dependencies=TRUE)'
R CMD build --no-build-vignettes --no-manual .
R CMD INSTALL --configure-args="--with-download=https://github.com/dudoslav/TileDB/archive/refs/heads/db/sc-62563/bootstrap.zip" $(ls -1tr *.tar.gz | tail -1)

I suspect that the problem is that the TileDB core library is not being downloaded or is somewhere where it is not supposed to be:

g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -I../inst/include/  -I../inst/tiledb/include   -DTILEDB_SILENT_BUILD  -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/RcppInt64/include' -I'/usr/lib/R/site-library/nanoarrow/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-4sITk6/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-4sITk6/r-base-4.4.2=/usr/src/r-base-4.4.2-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o

There is no special "tiledb" include here ^^, or I mean, I was not able to find it in any of these includes.

[dudoslav]

This might be the issue:

tools/buildTileDB.sh: line 49: ../tiledb-src/bootstrap: No such file or directory

and well... 99% due to incorrect access rights, so the file is not executable.

[johnkerl]

@dudoslav thank you -- and please, please share the entire build output so we can look at it together

[johnkerl]

There is no special "tiledb" include here ^^, or I mean, I was not able to find it in any of these includes.

Yes, this means it can't find core -- and we need to look at the full build output to get an idea of why not

[johnkerl]

(Switching over to Slack)

[dudoslav]

Full build:

root@taco:/tmp/TileDB-R# R CMD INSTALL --configure-args="--with-download=https://github.com/dudoslav/TileDB/archive/refs/heads/db/sc-62563/bootstrap.zip" $(ls -1tr *.tar.gz | tail -1)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘tiledb’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether g++ -std=gnu++17 supports C++17 features by default... yes
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows TileDB... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for filesystem... yes
checking for tiledb/tiledb... no
checking for cmake... yes
checking for curl... yes
checking for git... yes
installing TileDB via building locally...
Downloading https://github.com/dudoslav/TileDB/archive/refs/heads/db/sc-62563/bootstrap.zip: https://github.com/dudoslav/TileDB/archive/refs/heads/db/sc-62563/bootstrap.zip  ...
Converting zip to tar.gz ...
tools/buildTileDB.sh: line 49: ../tiledb-src/bootstrap: No such file or directory
using inst/tiledb/{lib,include}
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++17
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -I../inst/include/  -I../inst/tiledb/include   -DTILEDB_SILENT_BUILD  -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/RcppInt64/include' -I'/usr/lib/R/site-library/nanoarrow/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-4sITk6/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-4sITk6/r-base-4.4.2=/usr/src/r-base-4.4.2-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
../inst/include/tiledb.h:8:10: fatal error: tiledb/tiledb: No such file or directory
    8 | #include <tiledb/tiledb>
      |          ^~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tiledb’
* removing ‘/usr/local/lib/R/site-library/tiledb’

[johnkerl]

Debug info:

docker run -it --rm --entrypoint /bin/bash --net=host rocker/r2u:latest

and within that:

Rscript -e 'sessionInfo()'
apt update -qq && apt install --yes --no-install-recommends cmake curl git
cd /tmp
git clone https://github.com/TileDB-Inc/TileDB-R
cd TileDB-R
Rscript -e 'remotes::install_deps(".", dependencies=TRUE)'
R CMD build --no-build-vignettes --no-manual .
R CMD INSTALL --configure-args="--with-download=https://github.com/dudoslav/TileDB/archive/refs/heads/db/sc-62563/bootstrap.zip" $(ls -1tr *.tar.gz | tail -1)

[dudoslav]

Created a PR that should hopefully fix this: #803

[johnkerl]

Manual nightly run with #803 merged was ☘️

[jdblischak]

Thanks @dudoslav for fixing this!