From jmq2108 @end|ng |rom cumc@co|umb|@@edu Thu Dec 12 16:50:45 2024 From: jmq2108 @end|ng |rom cumc@co|umb|@@edu (Quinones, Jose M.) Date: Thu, 12 Dec 2024 15:50:45 +0000 Subject: [R-sig-Debian] R3.4 on Debian12 Message-ID: Hello, Looking for guidance on compiling R version 3.4 on Debian 12. I?m encountering the following error on compiling: /usr/bin/ld: ../unix/system.o:(.bss+0x0): multiple definition of `R_OutputCon'; CommandLineArgs.o:(.bss+0x0): first defined here /usr/bin/ld: ../unix/sys-unix.o:(.bss+0x0): multiple definition of `R_OutputCon'; CommandLineArgs.o:(.bss+0x0): first defined here /usr/bin/ld: ../unix/sys-unix.o:(.bss+0x8): multiple definition of `ptr_R_ProcessEvents'; ../unix/system.o:(.bss+0xa8): first defined here /usr/bin/ld: ../unix/X11.o:(.bss+0x0): multiple definition of `R_OutputCon'; CommandLineArgs.o:(.bss+0x0): first defined here /usr/bin/ld: connections.o: warning: relocation against `R_OutputCon' in read-only section `.text' /usr/bin/ld: connections.o: relocation R_X86_64_PC32 against symbol `R_OutputCon' 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[3]: *** [Makefile:177: libR.so] Error 1 make[3]: Leaving directory '/mnt/vast/hpc/homes/branch/Software_BUILD/R-3.4.2/src/main' make[2]: *** [Makefile:135: R] Error 2 make[2]: Leaving directory '/mnt/vast/hpc/homes/branch/Software_BUILD/R-3.4.2/src/main' make[1]: *** [Makefile:28: R] Error 1 make[1]: Leaving directory '/mnt/vast/hpc/homes/branch/Software_BUILD/R-3.4.2/src' make: *** [Makefile:61: R] Error 1 Thanks, Jose [[alternative HTML version deleted]] From tom@@@k@||ber@ @end|ng |rom gm@||@com Thu Dec 12 17:10:51 2024 From: tom@@@k@||ber@ @end|ng |rom gm@||@com (Tomas Kalibera) Date: Thu, 12 Dec 2024 17:10:51 +0100 Subject: [R-sig-Debian] R3.4 on Debian12 In-Reply-To: References: Message-ID: On 12/12/24 16:50, Quinones, Jose M. wrote: > Hello, > > Looking for guidance on compiling R version 3.4 on Debian 12. I?m encountering the following error on compiling: > > /usr/bin/ld: ../unix/system.o:(.bss+0x0): multiple definition of `R_OutputCon'; CommandLineArgs.o:(.bss+0x0): first defined here > /usr/bin/ld: ../unix/sys-unix.o:(.bss+0x0): multiple definition of `R_OutputCon'; CommandLineArgs.o:(.bss+0x0): first defined here > /usr/bin/ld: ../unix/sys-unix.o:(.bss+0x8): multiple definition of `ptr_R_ProcessEvents'; ../unix/system.o:(.bss+0xa8): first defined here > /usr/bin/ld: ../unix/X11.o:(.bss+0x0): multiple definition of `R_OutputCon'; CommandLineArgs.o:(.bss+0x0): first defined here Perhaps you can try building with -fcommon. Tomas > /usr/bin/ld: connections.o: warning: relocation against `R_OutputCon' in read-only section `.text' > /usr/bin/ld: connections.o: relocation R_X86_64_PC32 against symbol `R_OutputCon' 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[3]: *** [Makefile:177: libR.so] Error 1 > make[3]: Leaving directory '/mnt/vast/hpc/homes/branch/Software_BUILD/R-3.4.2/src/main' > make[2]: *** [Makefile:135: R] Error 2 > make[2]: Leaving directory '/mnt/vast/hpc/homes/branch/Software_BUILD/R-3.4.2/src/main' > make[1]: *** [Makefile:28: R] Error 1 > make[1]: Leaving directory '/mnt/vast/hpc/homes/branch/Software_BUILD/R-3.4.2/src' > make: *** [Makefile:61: R] Error 1 > > Thanks, > Jose > > [[alternative HTML version deleted]] > > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian From |kry|ov @end|ng |rom d|@root@org Thu Dec 12 17:28:26 2024 From: |kry|ov @end|ng |rom d|@root@org (Ivan Krylov) Date: Thu, 12 Dec 2024 19:28:26 +0300 Subject: [R-sig-Debian] R3.4 on Debian12 In-Reply-To: References: Message-ID: <20241212192826.0f5610f5@arachnoid> You may also need gfortran -fallow-argument-mismatch argument to avoid the problem in src/library/stats/src/lminfl.f, where the same variable, double precision dummy, is used for an array argument and a scalar argument for dqrsl(). Declaring 'dummy' as a length-1 array should also work. -- Best regards, Ivan From edd @end|ng |rom deb|@n@org Thu Dec 12 18:46:10 2024 From: edd @end|ng |rom deb|@n@org (Dirk Eddelbuettel) Date: Thu, 12 Dec 2024 11:46:10 -0600 Subject: [R-sig-Debian] R3.4 on Debian12 In-Reply-To: <20241212192826.0f5610f5@arachnoid> References: <20241212192826.0f5610f5@arachnoid> Message-ID: <26459.8546.100850.723969@rob.eddelbuettel.com> Also, which compiler is this now? Maybe it is more stringent than the one we used when R 3.4.* was current? For Debian, you always have its own version of the wayback machine, namely https://snapshot.debian.org/ (which can be slow to respond because the breadth and depth whatever page you refresh may pull something from fairly cold storage). I am not saying it will be _easy_ to recreate R 3.4.0 under Debian 12 but it is always _possible_. But my money would be on using pre-made (at the time !!) containers: $ docker run --rm -ti r-base:3.4.4 R --version R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/. $ That is running on Ubuntu 24.04 but taking advantage of the official (for Docker) r-base image 3.4.4 (which the volunteers of the docker-library maintain re-using the Dockerfile from our rocker/r-base I look after). Heck, you could even use this container (it's Debian based) and try to peel of the /usr/{lib,share}/R directories and add whatever shared libraries you. That is of course a gross hack and not something I would ever publically recommend ;-) Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org