Source: r-base Version: 4.5.0-1 Severity: normal Tags: FTBFS patch User: debian-loongarch at 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 at r-project.org.. Could you add the patch "Add "${boot_path}/zero" for OpenJDK zero build" in the next upload? Your opinions are welcome. [1]: https://github.com/openjdk/jdk/pull/5440 [2]: https://github.com/openjdk/jdk/pull/4787 Thanks, Dandan Zhang -------------- next part -------------- A non-text attachment was scrubbed... Name: r-base-add-the-path-of-libjvm.so-for-zero-build.patch Type: text/x-patch Size: 899 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-devel/attachments/20250417/a2e467f2/attachment.bin>
r-base: FTBFS: Add "${boot_path}/zero" for OpenJDK zero build
3 messages · zhangdandan, Dirk Eddelbuettel, Simon Urbanek
On 17 April 2025 at 11:40, zhangdandan wrote:
| Source: r-base | Version: 4.5.0-1 | Severity: normal | Tags: FTBFS patch | User: debian-loongarch at 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 at 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 "${boot_path}/zero" for OpenJDK zero build" | in the next upload? | Your opinions are welcome. | | [1]: https://github.com/openjdk/jdk/pull/5440 | [2]: https://github.com/openjdk/jdk/pull/4787 | | Thanks, | Dandan Zhang | | x[DELETED ATTACHMENT r-base-add-the-path-of-libjvm.so-for-zero-build.patch, text/x-patch]
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dandan, thanks! Dirk reported it as https://bugs.r-project.org/show_bug.cgi?id=18884 and it should be fixed in R-devel r88154 - please confirm if it works for you and if it does, I'll port it to R 4.5.0 Patched. Cheers, Simon
On Apr 17, 2025, at 3:40 PM, zhangdandan <zhangdandan at loongson.cn> wrote: Source: r-base Version: 4.5.0-1 Severity: normal Tags: FTBFS patch User: debian-loongarch at lists.debian.org Usertags: loong64 Hi maintainers, Compiling the rjava 1.0-11-1 failed for loong64 in the Debian Package Auto-Building environment. The build error log(build error on 10 architectures) is as follows, ``` checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking Java support in R... present: interpreter : '/usr/lib/jvm/default-java/bin/java' archiver : '/usr/lib/jvm/default-java/bin/jar' compiler : '/usr/lib/jvm/default-java/bin/javac' header prep.: '' cpp flags : '' java libs : '' configure: error: One or more Java configuration variables are not set. ``` The full log of rjava can be found at https://buildd.debian.org/status/package.php?p=rjava&suite=sid https://buildd.debian.org/status/fetch.php?pkg=rjava&arch=loong64&ver=1.0-11-2&stamp=1744704288&raw=0 After analysis, the reason is that libjvm.so is not found when compiling rjava(depend r-base). For loong64 or other architectures(build zero in openjdk-21), libjvm.so was supported in /usr/lib/jvm/default-java/lib/zero/ [1][2], not /usr/lib/jvm/default-java/lib/server/. So we need to add "${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 at 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-base-add-the-path-of-libjvm.so-for-zero-build.patch>______________________________________________ R-devel at r-project.org mailing list