sci-biology/ncbi-tools++: set -rpath-link to temp build location

Add more regexps specifying which parts of the test suite should
not be compiled at all.

We have so far problems with say ncbi-tools++-18.0.0 libs installed
in ${EPREFIX}/usr/lib64/ncbi-tools++/ which get picked during linking
of a currently emerged package, like ncbi-tools++-22.0.0. That happens
due to LDPATH being set through

```
  echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
  doenvd "${S}/99${PN}"
```

which results in

```
$ cat /etc/env.d/99ncbi-tools++
LDPATH=/usr/lib64/ncbi-tools++
$
```

and later used during linking of a future version. Some symbols will be
resolved by ${EPREFIX}/usr/lib64/ncbi-tools++/ from older version,
some probably not. It is confusing to debug the errors popping up
during compilation/linking.

Aaron Ucko from NCBI proposed:

To avoid interference from old installations, please try passing
`LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib` to configure, no patches
(likely) needed.

@kiwifb François Bissey commented with:

<quote>
LDPATH is used to generate the ld.so.conf.d files. So it is important
to have it to be able to find the libraries that are not in a standard
path. LDPATH is a Gentoo special. You need to regenerate the cache with
ldconfig after installing such a library and such a path.

...

$ /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -Wl,--verbose
  -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0
  -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-O1
  -Wl,--as-needed -g speedtest.o
  -L/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
    ncbi_cxx--22_0_0_build/lib
  -lprosplign -lxalgoalignutil -ltaxon1 -lxalgoseq -lxcleanup
  -lxobjedit -ltaxon3 -lvalid -lvalerr -lproteinkmer -lxblast
  -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask
  -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr
  -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli
  -lxnetblast -lblastdb -lscoremat -ltables -lxqueryparse -lxregexp
  -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2
  -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect
  -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit
  -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline
  -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -lz -lbz2
  -llzo2 -lz -lnsl -ldl -lpcre -llmdb -lpthread -ldw -ldl -lm
  -lpthread -o speedtest

It cannot find libmlacli.so. Note that there isn’t a `-lmlacli`
anywhere in the above line. It is searched for because you are
compiling an executable and executable cannot have unresolved
symbols. It must in the table of needed libraries for libxobjedit.so
libmlacli.so needed by /scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib/libxobjedit.so

Because there is no path or possibly a final path in libxobjedit.so
that library cannot be found.
Two solutions here:
1) add -lmlacli in the compilation line above
2) Precede the whole line with
LD_LIBRARY_PATH=/scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib

The LDPATH setting probably enabled you to find a previously
installed version of the library.

François

PS: You can pass that analysis upstream because -lmlacli should
probably be added by right.
</quote>

Later François also wrote:

<quote>
rpath are usually the preferred solution but it is not the end all
solution. Looking for LDPATH in your /etc/env.d/ may shock you.
In the case of ncbi, adding path is only one of the solution I
would consider. I don’t see why they need to install in
/usr/lib{,64}/ncbi-tools++ rather than just /usr/lib{,64} in
the first place. It is not even versioned to allow several versions
installed in parallel. It is not plugins or “modules” or other
special kinds of shared objects.

Possibly it is some language runtime - at best. Does it use names
that could collide easily with something else? May be some of them
should be prefixed then.
</quote>

make[3]: Entering directory '/scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/app/speedtest'
Updating dependency information for /scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp.
/usr/bin/x86_64-pc-linux-gnu-g++  -std=gnu++11 -c  -Wall -Wno-format-y2k
  -pthread -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -fPIC
  -g -D_DEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
  -D_MT -D_REENTRANT -D_THREAD_SAFE
  -I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
    ncbi_cxx--22_0_0_build/inc
  -I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
    ncbi_cxx--22_0_0/include
  /scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
    ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp
  -o speedtest.o
/usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11
  -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0
  -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-O1
  -Wl,--as-needed -g speedtest.o
  -L/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
    ncbi_cxx--22_0_0_build/lib
  -lprosplign -lxalgoalignutil -ltaxon1 -lxalgoseq -lxcleanup -lxobjedit
  -ltaxon3 -lvalid -lvalerr -lproteinkmer -lxblast -lxalgoblastdbindex
  -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io
  -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation
  -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat
  -ltables -lxqueryparse -lxregexp -lncbi_xloader_genbank -lncbi_xreader_id1
  -lncbi_xreader_id2 -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader
  -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit
  -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio
  -lgeneral -lxser -lxutil -lxncbi -lxcompress -lz -lbz2 -llzo2 -lz -lnsl
  -ldl -lpcre -llmdb -lpthread -ldw -ldl -lm -lpthread -o speedtest
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/\
   bin/ld: warning: libmlacli.so, needed by /scratch/var/tmp/portage/\
     sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib/\
     libxobjedit.so, not found (try using -rpath or -rpath-link)

The problem here is that the rpath would have to be provided when
you link libxobjedit.so. I checked the log and it wasn’t done.
And you definitely don’t want to do that unless you re-link without
the rpath (or the correct final rpath) at install time. For information
cmake does exactly that.
But in the end adding a path in this case is no substitute to providing
the libraries you need. When building stuff with libtool, libtool produces
test scripts that set LD_LIBRARY_PATH properly for running the tests before
install. So the test executables don’t have to be linked with rpath to
the build folder. Or the objects that you want to ship either.
</quote>

This change will ensure `LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib` is
passed to `bash ./src/build-system/configure` in `src_configure()`
and at least helps to get symbols resolved during linking although it
is probably still far from ideal.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

2 files changed, 12 insertions, 3 deletions

diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
index 8df346f64..fa27aa13b 100644
--- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
+++ b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
@@ -2,3 +2,7 @@
 -.*/test
 -.*/unit_test
 -.*/unit_tests
+-dbapi/driver/ftds.*/freetds/.*/unittests
+-sample
+-.*/demo
+-.*/samples
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 971789fb4..0c0e1b24c 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -289,11 +289,11 @@ src_configure() {
 	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
 	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
 
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
+	einfo "LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
 
 #	ECONF_SOURCE="src/build-system" \
 #		econf \
-	bash \
+	LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash \
 		./src/build-system/configure \
 		--srcdir="${S}" \
 		--prefix="${EPREFIX}/usr" \
@@ -342,7 +342,7 @@ src_compile() {
 	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
 	#
 	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
+	LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib emake -C "${S}"_build/build -f Makefile.flat
 	#
 	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
 	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
@@ -351,6 +351,11 @@ src_compile() {
 src_install() {
 	rm -rvf "${S}"_build/lib/ncbi || die
 	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+	#
+	#if [ ! use static-libs -a ! use static ]; then
+	#	rm -f "${ED}/usr/$(get_libdir)/${PN}"/*.a \
+	#		"${ED}/usr/$(get_libdir)/${PN}"/*-static.a || die
+	#fi
 
 #	dobin "${S}"_build/bin/*
 #	dolib.so "${S}"_build/lib/*so*