[R-pkg-devel] Segmentation Fault cause 'memory not mapped' on Debian only
Hi all, I wanted to publish my RITCH package (https://github.com/DavZim/RITCH) to CRAN, which has Rcpp code. It has, in it�s CICD Pipeline, Tests for Macos, Windows, and Ubuntu (devel, release,, and oldrel-1), which all succeed on Github Actions. When I submitted the package to CRAN, I was notified, that I got the following error on Debian (the tests on Windows throw no such bug, neither do the Github Actions tests): *** caught segfault *** address 0x55939b7ca000, cause 'memory not mapped' Segmentation fault The full Report is currently available here: https://win-builder.r-project.org/incoming_pretest/RITCH_0.1.14_20230420_223157/Debian/00check.log (note the error happens in the test_filter_itch.R unit tests). I looked for the error online but couldn�t find anything useful, and as I am not able to reproduce the segfault locally, cannot debug it. Do you have any ideas or hunches what might cause this and how to resolve it? Thank you, David [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Segmentation Fault cause 'memory not mapped' on Debian only
Hi David, On 21 April 2023 at 19:17, D Z wrote: | Hi all, | I wanted to publish my RITCH package (https://github.com/DavZim/RITCH) to CRAN, which has Rcpp code. That would be great! | It has, in it�s CICD Pipeline, Tests for Macos, Windows, and Ubuntu (devel, release,, and oldrel-1), which all succeed on Github Actions. | When I submitted the package to CRAN, I was notified, that I got the following error on Debian (the tests on Windows throw no such bug, neither do the Github Actions tests): | | |*** caught segfault *** | | address 0x55939b7ca000, cause 'memory not mapped' | | Segmentation fault | | The full Report is currently available here: https://win-builder.r-project.org/incoming_pretest/RITCH_0.1.14_20230420_223157/Debian/00check.log (note the error happens in the test_filter_itch.R unit tests). | | I looked for the error online but couldn�t find anything useful, and as I am not able to reproduce the segfault locally, cannot debug it. | Do you have any ideas or hunches what might cause this and how to resolve it? "Absence of error" on one platform does proove correctness on all, the hint from the segfault should be taken seriously. I just updated my older checkout of your repo, built a current tarball and simply invoked R CMD check --use-valgrind RITCH_0.1.14.tar.gz which you could do on CI too (I can help as needed, I would also pull the CI runners forward from Ubuntu 20.04 to 22.04). When we do the above, the examples output file RITCH-Ex.Rout ends in ==2269271== LEAK SUMMARY: ==2269271==definitely lost: 1,363,969 bytes in 5,473 blocks ==2269271==indirectly lost: 177,235 bytes in 1,281 blocks ==2269271== possibly lost: 101,924,267 bytes in 148 blocks ==2269271==still reachable: 89,572,890 bytes in 17,950 blocks ==2269271== suppressed: 0 bytes in 0 blocks ==2269271== Reachable blocks (those to which a pointer was found) are not shown. ==2269271== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2269271== ==2269271== ERROR SUMMARY: 30 errors from 30 contexts (suppressed: 0 from 0) and the tests end in ==2273761== LEAK SUMMARY: ==2273761==definitely lost: 5,223,981 bytes in 141,151 blocks ==2273761==indirectly lost: 2,241,700 bytes in 2,767 blocks ==2273761== possibly lost: 1,201,493,644 bytes in 270 blocks ==2273761==still reachable: 133,909,136 bytes in 19,110 blocks ==2273761== suppressed: 0 bytes in 0 blocks ==2273761== Reachable blocks (those to which a pointer was found) are not shown. ==2273761== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2273761== ==2273761== ERROR SUMMARY: 43 errors from 39 contexts (suppressed: 0 from 0) That probably warrants a few more close looks. Hth, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Segmentation Fault cause 'memory not mapped' on Debian only
Hi David, In addition to running under valgrind as Dirk suggests below, you should also run under UBSAN and ASAN. You can do all 3 (and more) using Winston Cheng's docker images: https://github.com/wch/r-debug/ That should help you narrow down the problematic code. Best, Josh On Fri, Apr 21, 2023 at 2:33 PM Dirk Eddelbuettel wrote: > > > Hi David, > > On 21 April 2023 at 19:17, D Z wrote: > | Hi all, > | I wanted to publish my RITCH package (https://github.com/DavZim/RITCH) to > CRAN, which has Rcpp code. > > That would be great! > > | It has, in it’s CICD Pipeline, Tests for Macos, Windows, and Ubuntu (devel, > release,, and oldrel-1), which all succeed on Github Actions. > | When I submitted the package to CRAN, I was notified, that I got the > following error on Debian (the tests on Windows throw no such bug, neither do > the Github Actions tests): > | > | > |*** caught segfault *** > | > | address 0x55939b7ca000, cause 'memory not mapped' > | > | Segmentation fault > | > | The full Report is currently available here: > https://win-builder.r-project.org/incoming_pretest/RITCH_0.1.14_20230420_223157/Debian/00check.log > (note the error happens in the test_filter_itch.R unit tests). > | > | I looked for the error online but couldn’t find anything useful, and as I > am not able to reproduce the segfault locally, cannot debug it. > | Do you have any ideas or hunches what might cause this and how to resolve > it? > > "Absence of error" on one platform does proove correctness on all, the hint > from the segfault should be taken seriously. I just updated my older > checkout of your repo, built a current tarball and simply invoked > >R CMD check --use-valgrind RITCH_0.1.14.tar.gz > > which you could do on CI too (I can help as needed, I would also pull the CI > runners forward from Ubuntu 20.04 to 22.04). When we do the above, the > examples output file RITCH-Ex.Rout ends in > > ==2269271== LEAK SUMMARY: > ==2269271==definitely lost: 1,363,969 bytes in 5,473 blocks > ==2269271==indirectly lost: 177,235 bytes in 1,281 blocks > ==2269271== possibly lost: 101,924,267 bytes in 148 blocks > ==2269271==still reachable: 89,572,890 bytes in 17,950 blocks > ==2269271== suppressed: 0 bytes in 0 blocks > ==2269271== Reachable blocks (those to which a pointer was found) are not > shown. > ==2269271== To see them, rerun with: --leak-check=full --show-leak-kinds=all > ==2269271== > ==2269271== ERROR SUMMARY: 30 errors from 30 contexts (suppressed: 0 from 0) > > and the tests end in > > ==2273761== LEAK SUMMARY: > ==2273761==definitely lost: 5,223,981 bytes in 141,151 blocks > ==2273761==indirectly lost: 2,241,700 bytes in 2,767 blocks > ==2273761== possibly lost: 1,201,493,644 bytes in 270 blocks > ==2273761==still reachable: 133,909,136 bytes in 19,110 blocks > ==2273761== suppressed: 0 bytes in 0 blocks > ==2273761== Reachable blocks (those to which a pointer was found) are not > shown. > ==2273761== To see them, rerun with: --leak-check=full --show-leak-kinds=all > ==2273761== > ==2273761== ERROR SUMMARY: 43 errors from 39 contexts (suppressed: 0 from 0) > > That probably warrants a few more close looks. > > Hth, Dirk > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
