Re: Help requested: r-bioc-rhdf5lib patches need updating for bioc-3.19 upgrade

"Michael R. Crusoe" <[email protected]> Wed, 10 Jul 2024 18:03:26 +0200
Newsgroups	gmane.linux.debian.devel.medical
Message-ID	<[email protected]>

On 10/07/2024 15.58, Nilesh Patra wrote:
> On Wed, Jul 10, 2024 at 12:14:05PM +0200, Michael R. Crusoe wrote:
>> I upgraded r-bioc-rhdf5lib from 1.24.2 to 1.26.0 in the "debian/experimental" branch on salsa.
>>
>> https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/tree/debian/experimental?ref_type=heads
>>
>> However when I try to build other packages using the resulting "r-bioc-rhd5lib" binary package, I get the following build errors:
>>
>> # From r-bioc-alabaster.base https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base
>> g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR
>> /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5_cpp.a: No such file or directory
>> /usr/bin/ld: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/libhdf5.a: No such file or directory
>> collect2: error: ld returned 1 exit status
>>
>> Can I get some help with this?
>>
>> Please push any fixes directly to the "debian/experimental" branch on Salsa and let me know, thank you!
> 
> I don't have the time to write a patch/hack around this right now, but I
> understood what the issue is and it should be relatively easy to fix.
> 
> alabaster.base used Rhdf5lib::pkgconfig("PKG_CXX_LIBS") to get the linker flags
> for Rhdf5 lib as can be see here[1]
> 
> This has been set to an incorrect value as per the debian installed package[2].
> It points to a path that does not exist since we are using hdf5 packaged in
> debian instead of building and using embedded copies.
> 
> Patching the code to point to the correct path should fix the issue for you.

Thank you, Nilesh, that got me further!

With https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/commit/13333ce8837d34d244f60b4a26469ba378babcb0
I get

g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -lz -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o): warning: relocation against `_ZTVN2H518DataTypeIExceptionE' in read-only section `.text'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o): relocation R_X86_64_PC32 against symbol `_ZTVN2H59ExceptionE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[1]: *** [/usr/share/R/share/make/shlib.mk:10: alabaster.base.so] Error 1

> 
>> For building r-bioc-alabaster.base, feel free to use the bioc-3.19 test packages I've been making: https://people.debian.org/~crusoe/bioc/
>>
>> -- 
>> Michael R. Crusoe
> 
> [1]: https://salsa.debian.org/r-pkg-team/r-bioc-alabaster.base/-/blob/master/src/Makevars?ref_type=heads#L1
> [2]: https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5lib/-/blob/debian/experimental/R/zzz.R?ref_type=heads#L73
> 
> Best,
> Nilesh
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