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

On Wed, Jul 10, 2024 at 06:03:26PM +0200, Michael R. Crusoe wrote:
> 
> 
> 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

Probably some hdf5 hackery at play here. On re-looking at it, I wonder if itmakes sense to pass in
the paths to libhdf5.a -- maybe not from debian pov? We could likely just rely on -lhdf5.

This patch gets alabaster.base building for me:

--- a/src/Makevars
+++ b/src/Makevars
@@ -1,3 +1,3 @@
-RHDF5_LIBS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")') 
-PKG_CPPFLAGS=-I../inst/include
-PKG_LIBS=$(RHDF5_LIBS) -lz
+RHDF5_LIBS=/usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so -L/usr/lib/$(shell dpkg-architecture -qDEB_HOST_MULTIARCH)/hdf5/serial -lhdf5 -lhdf5_cpp -lcrypto -lcurl -lpthread -lsz
+PKG_CPPFLAGS=-I../inst/include -I/usr/include/hdf5/serial/
+PKG_LIBS=-fPIC $(RHDF5_LIBS) -lz

Best,
Nilesh

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