Installation fails on Alpine Linux

[bastistician]

The configure script decides to download a pre-built binary, but that is linked against glibc not musl, and loading fails with

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'tiledb' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/runner/R-patched/lib/00LOCK-tiledb/00new/tiledb/libs/tiledb.so':
  Error loading shared library ld-linux-x86-64.so.2: No such file or directory (needed by /home/runner/R-patched/lib/00LOCK-tiledb/00new/tiledb/libs/../tiledb/lib/libtiledb.so.2.26)

So I tried to install the R package with --configure-args=--enable-building, but that fails from TileDB's bootstrap script with "cannot find cplusplus compiler", see the log below (note also how configuration ignores that error and proceeds to no avail). The culprit seems to be

cxx_compiler=`which ${CXX}`

when CXX = g++ -std=gnu++17.

Installation log with '--enable-building'

* installing to library '/tmp/user/lib'
* installing *source* package 'tiledb' ...
** package 'tiledb' successfully unpacked and MD5 sums checked
** 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 default: https://github.com/TileDB-Inc/TileDB/archive/2.26.2.tar.gz  ...
Argument '--force-build-all-deps' has no effect and will be removed in a future version. Vcpkg builds all dependencies by default, please consult the guide in doc/dev/BUILD.md or vcpkg's documentation to see how to provide your own dependencies.
which: unrecognized option: s
BusyBox v1.37.0 (2024-12-13 21:18:49 UTC) multi-call binary.

Usage: which [-a] COMMAND...

Locate COMMAND

	-a	Show all matches
cannot find cplusplus compiler
using inst/tiledb/{lib,include}
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: 'gcc (Alpine 14.2.0) 14.2.0'
using C++ compiler: 'g++ (Alpine 14.2.0) 14.2.0'
using C++17
g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -I. -I../inst/include/  -I../inst/tiledb/include   -DTILEDB_SILENT_BUILD  -I'/home/runner/R-patched/lib/Rcpp/include' -I'/home/runner/R-patched/lib/RcppInt64/include' -I'/home/runner/R-patched/lib/nanoarrow/include' -I/usr/local/include    -fpic  -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__   -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: *** [/home/runner/R-patched/build/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package 'tiledb'
* removing '/tmp/user/lib/tiledb'

[ihnorton]

Hi @bastistician, thanks for opening the issue.

when CXX = g++ -std=gnu++17.

Is there a reason to put the flag in CXX instead of in CXXFLAGS? (I believe that will fail in a number of tools, including some versions of cmake)

that fails from TileDB's bootstrap script with "cannot find cplusplus compiler",

We can probably remove the extraneous calls to which - although it may be some time before such change is available in a release.

---

sc-61921

[bastistician]

I don't know the reason, but CXX is where R's etc/Makeconf includes the configured C++ standard since R 3.4.0. AFAICS, this is also what the vanilla Autoconf macro AC_PROG_CXX would do when "checking for g++ option to enable C++11 features" (nowadays almost surely "none needed"):

If necessary, options are added to CXX to enable support for ISO Standard C++ features with extensions, preferring the newest edition of the C++ standard that is supported.

Addendum: the m4 macro AX_CXX_COMPILE_STDCXX([17]) included in configure.ac (from tools/m4/ax_cxx_compile_stdcxx.m4) does it, too. For example, using g++ 10.2, I get

checking whether g++ supports C++17 features by default... no
checking whether g++ supports C++17 features with -std=gnu++17... yes

and CXX = g++ -std=gnu++17.

[ihnorton]

This should be fixed by TileDB-Inc/TileDB#5426 - we'll have a backport release in February including the change.

[bastistician]

Unfortunately, package installation still fails in both ways with tiledb 0.32.0 as well as the current development version.

You can reproduce my attempts using Alpine's Docker image (docker run --rm -it alpine):

apk add R R-dev R-doc g++
R -s -e 'install.packages("remotes", repos="https://cloud.R-project.org")'

## default installation fails because the downloaded binary is incompatible
R -s -e 'remotes::install_github("TileDB-Inc/TileDB-R")'

## try with --enable-building
apk add cmake curl git
R -s -e 'remotes::install_github("TileDB-Inc/TileDB-R", configure.args = list("tiledb" = "--enable-building"))'
### ./configure: line 6326: tools/buildTileDB.sh: not found
## fails because that requires /bin/bash, which the configure script should check beforehand, so:
apk add bash
R -s -e 'remotes::install_github("TileDB-Inc/TileDB-R", configure.args = list("tiledb" = "--enable-building"))'
## fails with various cmake errors, see below
## (BTW: the configure script should return with an error upon failure so the INSTALL is interrupted)

Relevant outputs:

Default installation: downloads a binary that is incompatible with musl libc

downloading x86_64 TileDB library...
installing TileDB for Alpine Linux:3.22.0...
downloading https://github.com/TileDB-Inc/TileDB/releases/download/2.28.0/tiledb-linux-x86_64-noavx2-2.28.0-4764907.tar.gz 
[...]
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘tiledb’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/lib/R/library/00LOCK-tiledb/00new/tiledb/libs/tiledb.so':
  Error loading shared library ld-linux-x86-64.so.2: No such file or directory (needed by /usr/lib/R/library/00LOCK-tiledb/00new/tiledb/libs/../tiledb/lib/libtiledb.so.2.28)

Configure with `--enable-building`

installing TileDB via building locally...
Downloading default: https://github.com/TileDB-Inc/TileDB/archive/2.28.0.tar.gz  ...
Argument '--force-build-all-deps' has no effect and will be removed in a future version. Vcpkg builds all dependencies by default, please consult the guide in doc/main/BUILD.md or vcpkg's documentation to see how to provide your own dependencies.
TILEDB_DISABLE_AUTO_VCPKG is not defined. Fetch a local copy of vcpkg.
Vcpkg commit string used: ea2a964f9303270322cf3f2d51c265ba146c422d
Using vcpkg features: serialization;s3;tests;webp
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
Hint: The project() command has not yet been called.  It sets up system-specific search paths.
-- Not found clang-tidy
-- Not found clang-format
-- was unable to find clang-format
-- Bootstrapping vcpkg before install
-- Bootstrapping vcpkg before install - done
-- Running vcpkg install
Detecting compiler hash for triplet x64-linux...
error: while detecting compiler information:
The log file content at "/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/buildtrees/detect_compiler/stdout-x64-linux.log" is:
Downloading https://github.com/ninja-build/ninja/releases/download/v1.12.1/ninja-linux.zip -> ninja-linux-1.12.1.zip
Successfully downloaded ninja-linux-1.12.1.zip
-- Configuring x64-linux-rel
CMake Error at scripts/cmake/vcpkg_execute_required_process.cmake:127 (message):
    Command failed: /usr/bin/cmake /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/scripts/detect_compiler -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/packages/detect_compiler_x64-linux -DVCPKG_COMPILER_CACHE_FILE=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/vcpkg_installed/vcpkg/compiler-file-hash-cache.json -DCMAKE_MAKE_PROGRAM=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/downloads/tools/ninja/1.12.1-linux/ninja -DCMAKE_SYSTEM_NAME=Linux -DBUILD_SHARED_LIBS=OFF -DVCPKG_CHAINLOAD_TOOLCHAIN_FILE=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/scripts/toolchains/linux.cmake -DVCPKG_TARGET_TRIPLET=x64-linux -DVCPKG_SET_CHARSET_FLAG=ON -DVCPKG_PLATFORM_TOOLSET=external -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_SKIP=TRUE -DCMAKE_VERBOSE_MAKEFILE=ON -DVCPKG_APPLOCAL_DEPS=OFF -DCMAKE_TOOLCHAIN_FILE=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/scripts/buildsystems/vcpkg.cmake -DCMAKE_ERROR_ON_ABSOLUTE_INSTALL_DESTINATION=ON "-DVCPKG_CXX_FLAGS=-Wno-error=nonnull -Wno-error=deprecated-declarations" -DVCPKG_CXX_FLAGS_RELEASE= -DVCPKG_CXX_FLAGS_DEBUG= "-DVCPKG_C_FLAGS=-Wno-error=nonnull -Wno-error=deprecated-declarations" -DVCPKG_C_FLAGS_RELEASE= -DVCPKG_C_FLAGS_DEBUG= -DVCPKG_CRT_LINKAGE=dynamic -DVCPKG_LINKER_FLAGS= -DVCPKG_LINKER_FLAGS_RELEASE= -DVCPKG_LINKER_FLAGS_DEBUG= -DVCPKG_TARGET_ARCHITECTURE=x64 -DCMAKE_INSTALL_LIBDIR:STRING=lib -DCMAKE_INSTALL_BINDIR:STRING=bin -D_VCPKG_ROOT_DIR=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src -DZ_VCPKG_ROOT_DIR=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src -D_VCPKG_INSTALLED_DIR=/tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/vcpkg_installed -DVCPKG_MANIFEST_INSTALL=OFF
    Working Directory: /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/buildtrees/detect_compiler/x64-linux-rel
    Error code: 1
    See logs for more information:
      /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/buildtrees/detect_compiler/config-x64-linux-rel-CMakeCache.txt.log
      /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/buildtrees/detect_compiler/config-x64-linux-rel-out.log
      /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/buildtrees/detect_compiler/config-x64-linux-rel-err.log

Call Stack (most recent call first):
  scripts/cmake/vcpkg_configure_cmake.cmake:344 (vcpkg_execute_required_process)
  scripts/detect_compiler/portfile.cmake:18 (vcpkg_configure_cmake)
  scripts/ports.cmake:203 (include)


error: vcpkg was unable to detect the active compiler's information. See above for the CMake failure output.
-- Running vcpkg install - failed
CMake Error at /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/_deps/vcpkg-src/scripts/buildsystems/vcpkg.cmake:938 (message):
  vcpkg install failed.  See logs for more information:
  /tmp/RtmpGhkFdJ/R.INSTALL26ad5e6f22b3/tiledb/src/build/vcpkg-manifest-install.log
Call Stack (most recent call first):
  /usr/share/cmake/Modules/CMakeDetermineSystem.cmake:146 (include)
  CMakeLists.txt:121 (project)


CMake Error: CMake was unable to find a build program corresponding to "Unix Makefiles".  CMAKE_MAKE_PROGRAM is not set.  You probably need to select a different build tool.
CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
-- Configuring incomplete, errors occurred!
failed to configure the project

[johnkerl]

Confirmed:

$ git diff
diff --git a/src/libtiledb.cpp b/src/libtiledb.cpp
index 742f501b..b6fce2e3 100644
--- a/src/libtiledb.cpp
+++ b/src/libtiledb.cpp
@@ -1536,6 +1536,8 @@ XPtr<tiledb::Attribute> libtiledb_attribute(XPtr<tiledb::Context> ctx,
       attr_dtype == TILEDB_DATETIME_AS) {
     attr = make_xptr<tiledb::Attribute>(
         new tiledb::Attribute(*ctx.get(), name, attr_dtype));
+
+    Rcpp::Rcout << "NCELLS " << static_cast<uint64_t>(ncells) << "\n";
     attr->set_cell_val_num(static_cast<uint64_t>(ncells));
   } else if (attr_dtype == TILEDB_CHAR || attr_dtype == TILEDB_STRING_ASCII ||
              attr_dtype == TILEDB_STRING_UTF8) {

$ cat ~/Desktop/sba.r
#!/usr/bin/env Rscript
library(tiledb)
tiledb::tiledb_attr(name="a", type="INT32", ncells=NA)

$ Rscript ~/Desktop/sba.r
NCELLS 18446744071562067968