Re: [Rd] r-base: FTBFS: Add "${boot_path}/zero" for OpenJDK zero build
Dandan,
thanks! Dirk reported it as
https://bugs.r-project.org/show_bug.cgi?id=18884
and it should be fixed in R-devel r88154 - please confirm if it works for you
and if it does, I'll port it to R 4.5.0 Patched.
Cheers,
Simon
> On Apr 17, 2025, at 3:40 PM, zhangdandan wrote:
>
> Source: r-base
> Version: 4.5.0-1
> Severity: normal
> Tags: FTBFS patch
> User: debian-loonga...@lists.debian.org
> Usertags: loong64
>
> Hi maintainers,
>
> Compiling the rjava 1.0-11-1 failed for loong64 in the Debian Package
> Auto-Building environment.
> The build error log(build error on 10 architectures) is as follows,
> ```
> checking whether sigsetjmp is declared... yes
> checking whether siglongjmp is declared... yes
> checking Java support in R... present:
> interpreter : '/usr/lib/jvm/default-java/bin/java'
> archiver: '/usr/lib/jvm/default-java/bin/jar'
> compiler: '/usr/lib/jvm/default-java/bin/javac'
> header prep.: ''
> cpp flags : ''
> java libs : ''
> configure: error: One or more Java configuration variables are not set.
> ```
> The full log of rjava can be found at
> https://buildd.debian.org/status/package.php?p=rjava&suite=sid
> https://buildd.debian.org/status/fetch.php?pkg=rjava&arch=loong64&ver=1.0-11-2&stamp=1744704288&raw=0
>
> After analysis, the reason is that libjvm.so is not found when compiling
> rjava(depend r-base).
> For loong64 or other architectures(build zero in openjdk-21), libjvm.so was
> supported in /usr/lib/jvm/default-java/lib/zero/ [1][2], not
> /usr/lib/jvm/default-java/lib/server/.
> So we need to add "${boot_path}/zero" for OpenJDK zero build in r-base source
> package.
>
> Please consider the patch I attached for r-base.
> I have built r-base successfully in my local ENV.
> The result of my local test command `R CMD javareconf`, JNI linker flags can
> be found normally for OpenJDK zero build:
> ```
> # R CMD javareconf
> Java interpreter : /usr/lib/jvm/default-java/bin/java
> Java version : 21.0.6
> Java home path : /usr/lib/jvm/default-java
> Java compiler: /usr/lib/jvm/default-java/bin/javac
> Java headers gen.:
> Java archive tool: /usr/lib/jvm/default-java/bin/jar
>
> trying to compile and link a JNI program
> detected JNI cpp flags: -I$(JAVA_HOME)/include
> -I$(JAVA_HOME)/include/linux
> detected JNI linker flags : -L$(JAVA_HOME)/lib/zero -ljvm
> ..
> JAVA_HOME: /usr/lib/jvm/default-java
> Java library path: $(JAVA_HOME)/lib/zero
> JNI cpp flags: -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
> JNI linker flags : -L$(JAVA_HOME)/lib/zero -ljvm
> Updating Java configuration in /usr/lib/R
> Done.
> ```
>
> Based on my local r-base (r-base-core_4.5.0-1+loong64.1_loong64.deb), rjava
> is built successfully.
> ```
> checking whether siglongjmp is declared... yes
> checking Java support in R... present:
> interpreter : '/usr/lib/jvm/default-java/bin/java'
> archiver: '/usr/lib/jvm/default-java/bin/jar'
> compiler: '/usr/lib/jvm/default-java/bin/javac'
> header prep.: ''
> cpp flags : '-I/usr/lib/jvm/default-java/include
> -I/usr/lib/jvm/default-java/include/linux'
> java libs : '-L/usr/lib/jvm/default-java/lib/zero -ljvm'
> checking whether Java run-time works... yes
> ..
>dh_builddeb -O--buildsystem=R
> dpkg-deb: building package 'r-cran-rjava' in
> '../r-cran-rjava_1.0-11-1_loong64.deb'.
> dpkg-deb: building package 'r-cran-rjava-dbgsym' in
> '../r-cran-rjava-dbgsym_1.0-11-1_loong64.deb'.
> dpkg-genbuildinfo -O../rjava_1.0-11-1_loong64.buildinfo
> dpkg-genchanges -O../rjava_1.0-11-1_loong64.changes
> ```
>
> BTW, I do not find the link how to contribute patch(submit pull request) via
> GITHUB to R source code upstream(https://contributor.r-project.org/).
> So I submitted this patch to debian r-base source package first and Cc
> upstream's r-devel@r-project.org..
> Could you add the patch "Add "${boot_path}/zero" for OpenJDK zero build" in
> the next upload?
> Your opinions are welcome.
>
> [1]: https://github.com/openjdk/jdk/pull/5440
> [2]: https://github.com/openjdk/jdk/pull/4787
>
> Thanks,
> Dandan Zhang
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] r-base: FTBFS: Add "${boot_path}/zero" for OpenJDK zero build
On 17 April 2025 at 11:40, zhangdandan wrote:
| Source: r-base
| Version: 4.5.0-1
| Severity: normal
| Tags: FTBFS patch
| User: debian-loonga...@lists.debian.org
| Usertags: loong64
|
| Hi maintainers,
|
| Compiling the rjava 1.0-11-1 failed for loong64 in the Debian Package
| Auto-Building environment.
| The build error log(build error on 10 architectures) is as follows,
| ```
| checking whether sigsetjmp is declared... yes
| checking whether siglongjmp is declared... yes
| checking Java support in R... present:
| interpreter : '/usr/lib/jvm/default-java/bin/java'
| archiver : '/usr/lib/jvm/default-java/bin/jar'
| compiler : '/usr/lib/jvm/default-java/bin/javac'
| header prep.: ''
| cpp flags : ''
| java libs : ''
| configure: error: One or more Java configuration variables are not set.
| ```
| The full log of rjava can be found at
| https://buildd.debian.org/status/package.php?p=rjava&suite=sid
|
https://buildd.debian.org/status/fetch.php?pkg=rjava&arch=loong64&ver=1.0-11-2&stamp=1744704288&raw=0
|
| After analysis, the reason is that libjvm.so is not found when compiling
| rjava(depend r-base).
| For loong64 or other architectures(build zero in openjdk-21), libjvm.so
| was supported in /usr/lib/jvm/default-java/lib/zero/ [1][2], not
| /usr/lib/jvm/default-java/lib/server/.
| So we need to add "${boot_path}/zero" for OpenJDK zero build in r-base
| source package.
Superb. Thank you so much. I will fold this in, and report it upstream.
| Please consider the patch I attached for r-base.
| I have built r-base successfully in my local ENV.
| The result of my local test command `R CMD javareconf`, JNI linker flags
| can be found normally for OpenJDK zero build:
| ```
| # R CMD javareconf
| Java interpreter : /usr/lib/jvm/default-java/bin/java
| Java version : 21.0.6
| Java home path : /usr/lib/jvm/default-java
| Java compiler : /usr/lib/jvm/default-java/bin/javac
| Java headers gen.:
| Java archive tool: /usr/lib/jvm/default-java/bin/jar
|
| trying to compile and link a JNI program
| detected JNI cpp flags : -I$(JAVA_HOME)/include
| -I$(JAVA_HOME)/include/linux
| detected JNI linker flags : -L$(JAVA_HOME)/lib/zero -ljvm
| ..
| JAVA_HOME : /usr/lib/jvm/default-java
| Java library path: $(JAVA_HOME)/lib/zero
| JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
| JNI linker flags : -L$(JAVA_HOME)/lib/zero -ljvm
| Updating Java configuration in /usr/lib/R
| Done.
| ```
|
| Based on my local r-base (r-base-core_4.5.0-1+loong64.1_loong64.deb),
| rjava is built successfully.
| ```
| checking whether siglongjmp is declared... yes
| checking Java support in R... present:
| interpreter : '/usr/lib/jvm/default-java/bin/java'
| archiver : '/usr/lib/jvm/default-java/bin/jar'
| compiler : '/usr/lib/jvm/default-java/bin/javac'
| header prep.: ''
| cpp flags : '-I/usr/lib/jvm/default-java/include
| -I/usr/lib/jvm/default-java/include/linux'
| java libs : '-L/usr/lib/jvm/default-java/lib/zero -ljvm'
| checking whether Java run-time works... yes
| ..
| dh_builddeb -O--buildsystem=R
| dpkg-deb: building package 'r-cran-rjava' in
| '../r-cran-rjava_1.0-11-1_loong64.deb'.
| dpkg-deb: building package 'r-cran-rjava-dbgsym' in
| '../r-cran-rjava-dbgsym_1.0-11-1_loong64.deb'.
| dpkg-genbuildinfo -O../rjava_1.0-11-1_loong64.buildinfo
| dpkg-genchanges -O../rjava_1.0-11-1_loong64.changes
| ```
|
| BTW, I do not find the link how to contribute patch(submit pull request)
| via GITHUB to R source code upstream(https://contributor.r-project.org/).
| So I submitted this patch to debian r-base source package first and Cc
| upstream's r-devel@r-project.org..
Upstream uses svn and a bugzille instance at https://bugs.r-project.org/ for
which one needs an account (spam :-/ ) -- I have one and will file it there
and of course give you credit for it.
Best, Dirk
| Could you add the patch "Add "${boot_path}/zero" for OpenJDK zero build"
| in the next upload?
| Your opinions are welcome.
|
| [1]: https://github.com/openjdk/jdk/pull/5440
| [2]: https://github.com/openjdk/jdk/pull/4787
|
| Thanks,
| Dandan Zhang
|
| x[DELETED ATTACHMENT r-base-add-the-path-of-libjvm.so-for-zero-build.patch,
text/x-patch]
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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[Rd] r-base: FTBFS: Add "${boot_path}/zero" for OpenJDK zero build
Source: r-base
Version: 4.5.0-1
Severity: normal
Tags: FTBFS patch
User: debian-loonga...@lists.debian.org
Usertags: loong64
Hi maintainers,
Compiling the rjava 1.0-11-1 failed for loong64 in the Debian Package
Auto-Building environment.
The build error log(build error on 10 architectures) is as follows,
```
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/lib/jvm/default-java/bin/java'
archiver : '/usr/lib/jvm/default-java/bin/jar'
compiler : '/usr/lib/jvm/default-java/bin/javac'
header prep.: ''
cpp flags : ''
java libs : ''
configure: error: One or more Java configuration variables are not set.
```
The full log of rjava can be found at
https://buildd.debian.org/status/package.php?p=rjava&suite=sid
https://buildd.debian.org/status/fetch.php?pkg=rjava&arch=loong64&ver=1.0-11-2&stamp=1744704288&raw=0
After analysis, the reason is that libjvm.so is not found when compiling
rjava(depend r-base).
For loong64 or other architectures(build zero in openjdk-21), libjvm.so
was supported in /usr/lib/jvm/default-java/lib/zero/ [1][2], not
/usr/lib/jvm/default-java/lib/server/.
So we need to add "${boot_path}/zero" for OpenJDK zero build in r-base
source package.
Please consider the patch I attached for r-base.
I have built r-base successfully in my local ENV.
The result of my local test command `R CMD javareconf`, JNI linker flags
can be found normally for OpenJDK zero build:
```
# R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version : 21.0.6
Java home path : /usr/lib/jvm/default-java
Java compiler : /usr/lib/jvm/default-java/bin/javac
Java headers gen.:
Java archive tool: /usr/lib/jvm/default-java/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include
-I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/zero -ljvm
..
JAVA_HOME : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/zero
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/zero -ljvm
Updating Java configuration in /usr/lib/R
Done.
```
Based on my local r-base (r-base-core_4.5.0-1+loong64.1_loong64.deb),
rjava is built successfully.
```
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/lib/jvm/default-java/bin/java'
archiver : '/usr/lib/jvm/default-java/bin/jar'
compiler : '/usr/lib/jvm/default-java/bin/javac'
header prep.: ''
cpp flags : '-I/usr/lib/jvm/default-java/include
-I/usr/lib/jvm/default-java/include/linux'
java libs : '-L/usr/lib/jvm/default-java/lib/zero -ljvm'
checking whether Java run-time works... yes
..
dh_builddeb -O--buildsystem=R
dpkg-deb: building package 'r-cran-rjava' in
'../r-cran-rjava_1.0-11-1_loong64.deb'.
dpkg-deb: building package 'r-cran-rjava-dbgsym' in
'../r-cran-rjava-dbgsym_1.0-11-1_loong64.deb'.
dpkg-genbuildinfo -O../rjava_1.0-11-1_loong64.buildinfo
dpkg-genchanges -O../rjava_1.0-11-1_loong64.changes
```
BTW, I do not find the link how to contribute patch(submit pull request)
via GITHUB to R source code upstream(https://contributor.r-project.org/).
So I submitted this patch to debian r-base source package first and Cc
upstream's r-devel@r-project.org..
Could you add the patch "Add "${boot_path}/zero" for OpenJDK zero build"
in the next upload?
Your opinions are welcome.
[1]: https://github.com/openjdk/jdk/pull/5440
[2]: https://github.com/openjdk/jdk/pull/4787
Thanks,
Dandan Zhang
Description: Add "${boot_path}/zero" for OpenJDK zero build.
.
r-base (4.5.0-1+loong64.1) unstable; urgency=medium
.
* src/scripts/javareconf.in: Add "${boot_path}/zero" for OpenJDK zero build.
Author: Dandan Zhang
---
Last-Update: 2025-04-17
--- r-base-4.5.0.orig/src/scripts/javareconf.in
+++ r-base-4.5.0/src/scripts/javareconf.in
@@ -226,7 +226,7 @@ if test "${JAVA_LIBS}" = '~autodetect~';
if test ${has_libjvm} = no; then
boot_path=`"$JAVA" -classpath "${tools_classpath}" getsp sun.boot.library.path| ${SED-sed} -e 's/:$//' -e 's/^://'`
if test -n "${boot_path}"; then
- for dir in "${boot_path}" "${boot_path}/client" "${boot_path}/server"; do
+ for dir in "${boot_path}" "${boot_path}/client" "${boot_path}/server" "${boot_path}/zero"; do
if test -f "$dir/libjvm${DYLIB_EXT}"; then
has_libjvm=yes
java_library_path="${dir}"
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