Hi folks,
On 10/18/21 11:13 PM, Pariksheet Nanda wrote:
The trouble is, R's installation process will only copy compiled files
from ./libs/ that have exactly the extension ".so" and files ending with
".so.1" are ignored.
--snip--
So is there some mechanism to copy arbitrary files or symlinks to the
final install location? I prefer not to patch upstreams Makefile.am to
remove their -version-info, but currently that's the only option I can
think of.
It turns out removing -version-info or setting it to 0.0.0 will still
try to link against libghmm.so.0 which is still problematic. I don't
see how to disable libtool's versioning.
So after playing around, the only way I can think of doing is is
eliminating the dependency file by compiling it statically and linking
it with the dynamic library, because when I try merging the 2 dynamic
libraries with libtool it gives the same error of not finding
"libghmm.so.1". I have a patch that works on my Debian machines, but
not yet on the Ubuntu CI Image:
https://gitlab.com/coregenomics/tsshmm/-/commit/e9608f01deb7baa13684d2bd65fe11e93f6c2e08
Also pasting the short diff below for search-ability.
Pariksheet
Pariksheet
$ GIT_PAGER=cat git log -1 --patch
commit e9608f01deb7baa13684d2bd65fe11e93f6c2e08 (HEAD -> master,
origin/master, origin/HEAD)
Author: Pariksheet Nanda <pariksheet.na...@uconn.edu>
Date: Tue Oct 19 01:43:09 2021 -0400
BLD: Link bundled dependency statically to workaround load errors
diff --git a/configure.ac b/configure.ac
index 87b4d31..4d0be6e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -135,8 +135,6 @@ AS_IF([test x$with_ghmm_strategy = x],
) # AS_IF
) # AS_IF
-AC_SUBST(GHMM_LIBS, -lghmm)
-
# If GHMM_ROOT was provided, set the header and library paths.
#
# Check for the existance of include/ and lib/ sub-directories and if
both are
@@ -180,7 +178,10 @@ AS_IF(test x$found_ghmm_system != xyes &&
AM_CONDITIONAL(BUNDLED_GHMM, true)
[AX_SUBDIRS_CONFIGURE([src/ghmm-0.9-rc3],
[[CFLAGS=$CFLAGS],
- [--enable-gsl=no],
+ [--enable-static],
+ [--disable-shared],
+ [--with-pic],
+ [--enable-gsl=no],
[--disable-gsltest],
[--with-rng=mt],
[--with-python=no],
@@ -191,8 +192,14 @@ AS_IF(test x$found_ghmm_system != xyes &&
[AS_IF([test -d $GHMM_ROOT], [],
AC_MSG_FAILURE(Directory of bundled GHMM not found.))]
[AC_SUBST(GHMM_CPPFLAGS, ["-I$GHMM_ROOT/.."])]
- # Using -rpath=. prefers the bundled over any system installation.
- [AC_SUBST(GHMM_LDFLAGS, ["-Wl,-rpath=. -L$GHMM_ROOT/.libs"])]
+ # We don't need GMM_LIBS or GHMM_LDFLAGS because we can directly
merge
+ # libraries using tsshmm_la_LIBADD per
+ # https://stackoverflow.com/a/13978856 and
+ #
https://www.gnu.org/software/automake/manual/html_node/Libtool-Convenience-Libraries.html
+ #
+ # However we now need to link against libghmm's libxml2 dependency
+ # because we're merging libraries.
+ [PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6])]
AC_MSG_NOTICE(Applying patches to GHMM to fix errors and
warnings from "R CMD check")
# Patch bug in upstream's configure bug:
#
@@ -239,7 +246,9 @@ AS_IF(test x$found_ghmm_system != xyes &&
#include <ghmm/fbgibbs.h>' src/ghmm-0.9-rc3/tests/mcmc.c
[touch -r src/ghmm-0.9-rc3/tests/mcmc.c{.bak,}]
[diff -u src/ghmm-0.9-rc3/tests/mcmc.c{.bak,}]
- AC_MSG_NOTICE(Finished patching GHMM)
+ AC_MSG_NOTICE(Finished patching GHMM),
+ # Only link if we're not using the static bundled dependency.
+ [AC_SUBST(GHMM_LIBS, -lghmm)]
) # AS_IF
# Variables for Doxygen.
diff --git a/src/Makefile.am b/src/Makefile.am
index 617a4e7..0e38b4a 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -9,18 +9,19 @@ endif
lib_LTLIBRARIES = tsshmm.la
tsshmm_la_CFLAGS = $(PKG_CFLAGS)
tsshmm_la_CPPFLAGS = $(PKG_CPPFLAGS)
+if BUNDLED_GHMM
+tsshmm_la_LIBADD = @GHMM_ROOT@/libghmm.la
+tsshmm_la_LDFLAGS = -module $(PKG_LIBS) @LIBXML2_LIBS@
+else
tsshmm_la_LDFLAGS = -module $(PKG_LIBS)
+endif
tsshmm_la_SOURCES = R_init_tsshmm.c R_wrap_tsshmm.c models.c \
simulate.c train.c tss.c viterbi.c
ACLOCAL_AMFLAGS = -I tools
# Hook that runs after the default "all" rule.
-if BUNDLED_GHMM
-all-local : tsshmm.so libghmm.so
-else
all-local : tsshmm.so
-endif
# One of the limitations with POSIX-compliant `make` is not being able to
# specify multiple outputs from a single rule. Therefore, even though
libtool
@@ -30,14 +31,8 @@ tsshmm.so : tsshmm.la
cp -av .libs/tsshmm.so.0.0.0 $@
chmod -x $@
-if BUNDLED_GHMM
-libghmm.so : @GHMM_ROOT@/libghmm.la
- cp -av @GHMM_ROOT@/.libs/libghmm.so.1.0.0 $@
- chmod -x $@
-endif
-
clean-local :
- rm -f tsshmm.so libghmm.so
+ rm -f tsshmm.so
distclean-local : clean-local
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