bug#47428: Problems building the up-to-date "devel" manual for the website
Hi! help-debb...@gnu.org (GNU bug Tracking System) skribis: > Leo Famulari writes: > >> On Fri, Apr 02, 2021 at 11:33:57AM +0200, Mathieu Othacehe wrote: >>> >>> > ). Please consider running po4a-updatepo to refresh it. >>> > Your input po file ./guix-manual.de.po seems outdated (The amount of >>> > entries differ between files: 10012 is not 325 >>> > ). Please consider running po4a-updatepo to refresh it. >>> > mmap(PROT_NONE) failed >>> > builder for >>> > `/gnu/store/86gnwxxw7lfkifaal6fhflmkn3fczyhf-guix-translated-texinfo.drv' >>> > failed due to signal 11 (Segmentation fault) >>> >>> I worked around it by building this derivation on one core. Looks like >>> the cookbook, website, manual and devel manual are now building fine. >>> >>> Closing this one, >> >> Awesome, thanks for your work! > > I've pushed this with commit af2d6ec092 to master: > > modified guix/self.scm > @@ -410,7 +410,10 @@ a list of extra files, such as '(\"contributing\")." > ;; Limit thread creation by 'n-par-for-each'. Going beyond can > ;; lead libgc 8.0.4 to abort with: > ;; mmap(PROT_NONE) failed > -(min (parallel-job-count) 4)) > +;; > +;; FIXME: The above error would still happen when using only 4 > +;; build jobs, so disable parallelism entirely for the time > being. > +(min (parallel-job-count) 1)) > >(mkdir #$output) >(copy-recursively #$documentation "." > > To guard about the occasional failures we were still hitting building > the latest manuals for the website. FWIW, the map(PROT_NONE) issue was (I think) fixed by 0aef94e7bcbd272720f14c5343f74da5201ef90a (in May), itself a followup to 47d48f0c43c13c0b43bc3e37b6239efd4bf2f74c, so I think the comment is stale. Now, berlin’s mcron jobs are supposedly running a newer Guix: --8<---cut here---start->8--- ludo@berlin ~$ sudo herd schedule mcron |grep update-guix-manual-devel |sort -u /gnu/store/xsmjh2k3pjx6cv0rvkkqw8jsj8a574n4-update-guix-manual-devel ludo@berlin ~$ guix gc -R /gnu/store/xsmjh2k3pjx6cv0rvkkqw8jsj8a574n4-update-guix-manual-devel |grep guix /gnu/store/p9di786py35m4kxszf466wcla6jvq96h-guix-1.3.0-3.50dfbbf /gnu/store/xsmjh2k3pjx6cv0rvkkqw8jsj8a574n4-update-guix-manual-devel --8<---cut here---end--->8--- Am I right that the error that we see now is not “mmap(PROT_NONE)” but something else? Thanks, Ludo’.
bug#49463: [core-updates] libdatrie occasionally fails test
On ‘core-updates’ commit 7a9f4822c0c431c25071977b68ab79d152887ec3, libdatrie occasionally has one test failure (on x86_64-linux): --8<---cut here---start->8--- make[3]: Entering directory '/tmp/guix-build-libdatrie-0.2.13.drv-0/libdatrie-0.2.13/tests' PASS: test_walk PASS: test_iterator PASS: test_store-retrieve PASS: test_term_state PASS: test_nonalpha PASS: test_file PASS: test_byte_list FAIL: test_serialization PASS: test_byte_alpha PASS: test_null_trie Testsuite summary for libdatrie 0.2.13 # TOTAL: 10 # PASS: 9 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 See tests/test-suite.log Please report to https://github.com/tlwg/libdatrie/issues make[3]: *** [Makefile:829: test-suite.log] Error 1 make[3]: Leaving directory '/tmp/guix-build-libdatrie-0.2.13.drv-0/libdatrie-0.2.13/tests' make[2]: *** [Makefile:937: check-TESTS] Error 2 make[2]: Leaving directory '/tmp/guix-build-libdatrie-0.2.13.drv-0/libdatrie-0.2.13/tests' make[1]: *** [Makefile:1074: check-am] Error 2 make[1]: Leaving directory '/tmp/guix-build-libdatrie-0.2.13.drv-0/libdatrie-0.2.13/tests' make: *** [Makefile:471: check-recursive] Error 1 Test suite failed, dumping logs. --- ./tests/test-suite.log -- libdatrie 0.2.13: tests/test-suite.log # TOTAL: 10 # PASS: 9 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: test_serialization => Preparing trie... => Saving trie to file... => Getting serialized trie size... serialized trie size 1376 => Allocating... allocated 0x40ba70 => Serializing... => Serialized... Failed to reopen trie file test.tri. FAIL test_serialization (exit status: 1) --8<---cut here---end--->8--- It’s problematic because it’s a dependency of Guix on that branch: --8<---cut here---start->8--- $ ./pre-inst-env guix graph --path guix libdatrie guix@1.3.0-4.4985a42 graphviz@2.47.1 pango@1.48.4 libthai@0.1.28 libdatrie@0.2.13 --8<---cut here---end--->8--- Ludo’.
bug#49463: [core-updates] libdatrie occasionally fails test
Ludovic Courtès skribis: > FAIL: test_serialization > > > => Preparing trie... > => Saving trie to file... > => Getting serialized trie size... > serialized trie size 1376 > => Allocating... > allocated 0x40ba70 > => Serializing... > => Serialized... > Failed to reopen trie file test.tri. > FAIL test_serialization (exit status: 1) This is a classical problem of having several tests fiddling with the same file: --8<---cut here---start->8--- $ grep --color -nH --null -e 'test\.tri' *.c test_file.c32:#define TRIE_FILENAME "test.tri" test_serialization.c34:#define TRIE_FILENAME "test.tri" --8<---cut here---end--->8--- Fixed by running tests sequentially in commit 5f919605e94b12d7f56656a30f66f205c24cde98. Ludo’.
bug#47428: Problems building the up-to-date "devel" manual for the website
Hello, Ludovic Courtès writes: [...] >> modified guix/self.scm >> @@ -410,7 +410,10 @@ a list of extra files, such as '(\"contributing\")." >> ;; Limit thread creation by 'n-par-for-each'. Going beyond can >> ;; lead libgc 8.0.4 to abort with: >> ;; mmap(PROT_NONE) failed >> -(min (parallel-job-count) 4)) >> +;; >> +;; FIXME: The above error would still happen when using only 4 >> +;; build jobs, so disable parallelism entirely for the time >> being. >> +(min (parallel-job-count) 1)) >> >>(mkdir #$output) >>(copy-recursively #$documentation "." >> >> To guard about the occasional failures we were still hitting building >> the latest manuals for the website. > > FWIW, the map(PROT_NONE) issue was (I think) fixed by > 0aef94e7bcbd272720f14c5343f74da5201ef90a (in May), itself a followup to > 47d48f0c43c13c0b43bc3e37b6239efd4bf2f74c, so I think the comment is > stale. > > Now, berlin’s mcron jobs are supposedly running a newer Guix: > > ludo@berlin ~$ sudo herd schedule mcron |grep update-guix-manual-devel |sort > -u > /gnu/store/xsmjh2k3pjx6cv0rvkkqw8jsj8a574n4-update-guix-manual-devel > ludo@berlin ~$ guix gc -R > /gnu/store/xsmjh2k3pjx6cv0rvkkqw8jsj8a574n4-update-guix-manual-devel |grep > guix > /gnu/store/p9di786py35m4kxszf466wcla6jvq96h-guix-1.3.0-3.50dfbbf > /gnu/store/xsmjh2k3pjx6cv0rvkkqw8jsj8a574n4-update-guix-manual-devel > > Am I right that the error that we see now is not “mmap(PROT_NONE)” but > something else? Sadly, the error is still the same, even using guix in my tree (master): --8<---cut here---start->8--- mmap(PROT_NONE) failed builder for `/gnu/store/f8fdzi1hp7b3ln2zz6z87p3cj3gf0ac5-guix-translated-texinfo.drv' failed due to signal 11 (Segmentation fault) --8<---cut here---end--->8--- So the comment is still valid, I'm afraid :-/. Thanks, Maxim
bug#48903: guix substitute: error: TLS error in procedure 'read_from_session_record_port': Error decoding the received TLS packet.
Hi! Ludovic Courtès writes: > Maxim Cournoyer skribis: > >> Ludovic Courtès writes: >> >>> Hi, >>> >>> Maxim Cournoyer skribis: >>> I've tried with the following modified version which runs multiple threads in parallel (to mimic --max-jobs=4 on the daemon), and I've yet to trigger it, although the hard drive is grinding heavily: >>> >>> Note that ‘--max-jobs=4’ leads guix-daemon to spawn 4 ‘guix substitute’ >>> processes, which is not what the script is doing here. >> >> Oh! I had overlooked that. What the modified version did is create >> threads rather than processes, right? > > Yes. > > So I’m not sure how to better test this. Perhaps you could try > introducing random delays in the loop (which could cause connections to > go stale), using different substitute URLs, things like that. I've tried some to reproduce the issue with the modified scripts below, but in vain. I'm not sure if my delay is inserted at the right place. I also suspect that my attempt to shuffle the substitute-urls is not really useful, as that's probably what would have happened anyway (although I haven't followed in the code deeply enough to confirm). substitute-stress-launcher.sh Description: Bourne shell script substitute-stress.scm Description: Binary data Thanks, Maxim
bug#48335: Emacs is broken
Hello Xinglu, Xinglu Chen writes: > On Fri, May 21 2021, Maxim Cournoyer wrote: > >> Hi, >> >> Xinglu Chen writes: >> >>> ~/src/guix $ guix environment --ad-hoc emacs -- emacs --version >>> The following derivation will be built: >>>/gnu/store/js53a7lydr66bk3wpwkaj1j8j43mirrm-profile.drv >>> >>> building CA certificate bundle... >>> listing Emacs sub-directories... >>> building fonts directory... >>> generating GLib schema cache... >>> creating GTK+ icon theme cache... >>> building cache files for GTK+ input methods... >>> building directory of Info manuals... >>> building database for manual pages... >>> building XDG desktop file cache... >>> building XDG MIME database... >>> building profile with 1 package... >>> /gnu/store/gbzd8hc6360vaxmk2xh5bzkx7dkkwl8q-profile/bin/emacs: >>> error while loading shared libraries: libm17n-core.so.0: cannot >>> open shared object file: No such file or directory [...] Using the same commit you were using last, 652a03888e1609bd1a687326760436867fe2abb7, I can obtain the same Emacs (same store hash): $ guix time-machine --commit=652a03888e1609bd1a687326760436867fe2abb7 -- environment --ad-hoc emacs [env]$ which emacs /gnu/store/gbzd8hc6360vaxmk2xh5bzkx7dkkwl8q-profile/bin/emacs Have you tried it in a container, like so: $ guix time-machine --commit=652a03888e1609bd1a687326760436867fe2abb7 \ -- environment -C --ad-hoc emacs -- emacs --version to ensure there are no contaminants from your host. Perhaps NixOS, being similar to Guix, is somehow interfering? Maxim
bug#49467: python-scanpy 1.7.2 tests failing with SIGILL
On an x86_64 machine, I’ve seen this: --8<---cut here---start->8--- $ guix build python-scanpy --no-grafts --check […] starting phase `check' = test session starts == platform linux -- Python 3.8.2, pytest-5.3.5, py-1.8.1, pluggy-0.13.1 rootdir: /tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2 plugins: hypothesis-5.4.1, cov-2.8.1, black-0.3.8 Fatal Python error: Illegal instruction Current thread 0x7785c300 (most recent call first): File "", line 219 in _call_with_frames_removed File "", line 1109 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "", line 219 in _call_with_frames_removed File "", line 1042 in _handle_fromlist File "/gnu/store/368d0i579ga5sbc3mms4bg7bd4lzj6km-python-numcodecs-0.6.4/lib/python3.8/site-packages/numcodecs/__init __.py", line 45 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/python3.8/site-packages/zarr/codecs.py", line 3 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/python3.8/site-packages/zarr/__init__.py", li ne 3 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "", line 219 in _call_with_frames_removed File "", line 961 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/compat/__i nit__.py", line 19 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/views.py", line 13 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/aligned_mapping.py", line 13 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/raw.py", line 11 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/anndata.py", line 26 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/__init__.py", line 7 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/_utils.py", line 18 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/__init__.py", line 5 in File "", line 219 in _call_with_frames_removed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/tests/conftest.py", line 11 in File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/assertion/rewrite.py", line 143 in exec_module File "", line 671 in _load_unlocked
bug#49477: [core-updates] python-pyyaml fails on sanity-check
Perhaps due to recent addition/changes for python sanity-check? Here is the relevant portion of the log from running ./pre-inst-env guix build python-pyyaml on core-updates: warning: build_py: byte-compiling is disabled, skipping. running build_ext building 'yaml._yaml' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/yaml gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -I/gnu/store/4nrih35yjsz2kwhr4pwxnkdzjmkgxxfq-python-3.9.5/include/python3.9 -c yaml/_yaml.c -o build/temp.linux-x86_64-3.9/yaml/_yaml.o gcc: error: yaml/_yaml.c: No such file or directory gcc: fatal error: no input files compilation terminated. Error compiling module, falling back to pure Python phase `build' succeeded after 0.3 seconds starting phase `install' running "python setup.py" with command "install" and parameters ("--prefix=/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1" "--no-compile" "--single-version-externally-managed" "--root=/") running install running build running build_py warning: build_py: byte-compiling is disabled, skipping. running build_ext building 'yaml._yaml' extension gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -I/gnu/store/4nrih35yjsz2kwhr4pwxnkdzjmkgxxfq-python-3.9.5/include/python3.9 -c yaml/_yaml.c -o build/temp.linux-x86_64-3.9/yaml/_yaml.o gcc: error: yaml/_yaml.c: No such file or directory gcc: fatal error: no input files compilation terminated. Error compiling module, falling back to pure Python running install_lib creating /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1 creating /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib creating /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9 creating /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages creating /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml copying build/lib.linux-x86_64-3.9/_yaml/__init__.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml creating /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/__init__.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/composer.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/constructor.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/cyaml.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/dumper.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/emitter.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/error.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/events.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/loader.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/nodes.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/parser.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/reader.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/representer.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/resolver.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/scanner.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/serializer.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml copying build/lib.linux-x86_64-3.9/yaml/tokens.py -> /gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml warning: install_lib: byte-compiling is disabled, skipping. runni