If fetching tarball fails, build should err out at that point and not proceed to fail at linking: ld: library not found for -lsundials_idas

[barracuda156]

This way of building it is fragile:

--->  Extracting sundialr_0.1.6.tar.gz
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/R-sundialr/sundialr_0.1.6.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - 
--->  Configuring R-sundialr
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/sundialr" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes --keep-empty-dirs 
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘sundialr’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘sundialr_0.1.6.tar.gz’

--->  Building R-sundialr
xinstall: mkdir /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/build
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/sundialr" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/build --install-tests 
* installing *source* package ‘sundialr’ ...
** package ‘sundialr’ 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 /opt/local/bin/g++-mp-13 -std=gnu++17 accepts -g... yes
checking for /opt/local/bin/g++-mp-13 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /opt/local/bin/g++-mp-13 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether /opt/local/bin/g++-mp-13 -std=gnu++17 accepts -g... (cached) yes
checking for /opt/local/bin/g++-mp-13 -std=gnu++17 option to enable C++11 features... (cached) none needed
checking for cmake... /opt/local/bin/cmake
set CMAKE_BIN=/opt/local/bin/cmake
trying URL 'https://github.com/LLNL/sundials/releases/download/v7.2.0/sundials-7.2.0.tar.gz'
Content type 'application/octet-stream' length 94348468 bytes (90.0 MB)
======
downloaded 11.2 MB

Error in download.file(url = "https://github.com/LLNL/sundials/releases/download/v7.2.0/sundials-7.2.0.tar.gz",  : 
  download from 'https://github.com/LLNL/sundials/releases/download/v7.2.0/sundials-7.2.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url = "https://github.com/LLNL/sundials/releases/download/v7.2.0/sundials-7.2.0.tar.gz",  :
  downloaded length 11698030 != reported length 94348468
2: In download.file(url = "https://github.com/LLNL/sundials/releases/download/v7.2.0/sundials-7.2.0.tar.gz",  :
  URL 'https://objects.githubusercontent.com/github-production-release-asset-2e65be/105918649/555777cc-d942-4795-ac9b-989816606d53?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=releaseassetproduction%2F20241216%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20241216T134011Z&X-Amz-Expires=300&X-Amz-Signature=280f79491fcd4853c64d0cb2a3e03a062bd3ac49d9fb58d3775fc98ea70d96d6&X-Amz-SignedHeaders=host&response-content-disposition=attachment%3B%20filename%3Dsundials-7.2.0.tar.gz&response-content-type=application%2Foctet-stream': Timeout of 60 seconds was reached
Execution halted

gzip: stdin: unexpected end of file
/opt/local/bin/gtar: Unexpected EOF in archive
/opt/local/bin/gtar: Unexpected EOF in archive
/opt/local/bin/gtar: Error is not recoverable: exiting now
Warning message:
In utils::untar(tarfile = "sundials-7.2.0.tar.gz") :
  '/opt/local/bin/gtar -xf 'sundials-7.2.0.tar.gz'' returned error code 2
set CC=/opt/local/bin/gcc-mp-13
set CFLAGS=-isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc
set CXX=/opt/local/bin/g++-mp-13
set CXXFLAGS=-std=gnu++11 -isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc
set LDFLAGS=-Wl,-headerpad_max_install_names -L/opt/local/lib -lMacportsLegacySupport -Wl,-rpath,/opt/local/lib/libgcc -arch ppc
-- The C compiler identification is GNU 13.3.0
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/local/bin/gcc-mp-13 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
CMake Error at CMakeLists.txt:39 (include):
  include could not find requested file:

    SundialsCMakeMacros


CMake Error at CMakeLists.txt:51 (sundials_git_version):
  Unknown CMake command "sundials_git_version".


-- Configuring incomplete, errors occurred!
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
mv: rename sundials-src/src/* to ./sundials/*: No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.3.0_2+stdlib_flag) 13.3.0’
Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
  running command ''xcrun' --show-sdk-path 2>&1' had status 64
using SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c RcppExports.cpp -o RcppExports.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c check_retval.cpp -o check_retval.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c cvode.cpp -o cvode.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c cvodes.cpp -o cvodes.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c cvsolve.cpp -o cvsolve.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c ida.cpp -o ida.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/RcppArmadillo/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c rhs_func.cpp -o rhs_func.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -L/opt/local/lib -lMacportsLegacySupport -Wl,-rpath,/opt/local/lib/libgcc -arch ppc -o sundialr.so RcppExports.o check_retval.o cvode.o cvodes.o cvsolve.o ida.o rhs_func.o -L/opt/local/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/opt/local/Library/Frameworks/R.framework/Resources/lib -lRblas -lMacportsLegacySupport -lgfortran -lSystemStubs -lef_ppc -L../inst/lib -L../inst/lib -lsundials_idas -lsundials_cvodes -lsundials_nvecserial -lsundials_sunlinsoldense -lsundials_sunmatrixdense -lsundials_core -lm -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory '../inst/lib' following -L not found
ld: warning: directory '../inst/lib' following -L not found
ld: library not found for -lsundials_idas
collect2: error: ld returned 1 exit status
make: *** [sundialr.so] Error 1
ERROR: compilation failed for package ‘sundialr’
* removing ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/build/sundialr’
Command failed:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/sundialr" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-sundialr/R-sundialr/work/build --install-tests 
Exit code: 1
Error: Failed to build R-sundialr: command execution failed

Once fetching a tarball fails, perhaps it should just err out with a clear message, rather than trying to build a package and fail at linking.

[bastistician]

Similarly, if make or make install fail further down in tools/cmake_call.sh, the script should exit with an error, too.

(Problem observed in an exotic setup, where the package tarball is extracted and R CMD INSTALL is run by a different user than the one owning the files; make install tries to replace files in CMAKE_INSTALL_PREFIX=../../inst by downloaded files ...)

[sn248]

Thanks! I have made the following updates

sundialr/src/scripts/sundials_download.sh

Line 8 in 9e5f608

if [ $? -ne 0 ]; then

sundialr/tools/cmake_call.sh

Line 40 in 9e5f608

if [ $? -ne 0 ]; then

sundialr/tools/cmake_call.sh

Line 46 in 9e5f608

if [ $? -ne 0 ]; then

to error out.

[bastistician]

I'm afraid the fix is incomplete. Currently, errors from these scripts are not propagated:

1. cmake_call.sh ignores the exit status from sundials_download.sh.
2. configure[.ac] ignores the exit status from tools/cmake_call.sh.

[sn248]

Thanks!, I will make changes similar to checks used above to the cmake_call.sh and configure.ac file.