Re: [sage-release] Re: Sage 8.7.beta6 released
On Thu, Mar 7, 2019 at 5:50 PM kcrisman wrote: > > upgrading from some early 8.6 beta, I get something weird with file > permissions on gap. Everything seems to go well, but: > > > > pkg/laguna-3.9.0 -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg > > pkg/polenta-1.3.8 -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg > > pkg/polycyclic-2.14 -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg > > pkg/resclasses-4.7.1 -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg > > pkg/sophus-1.24 -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg > > pkg/tomlib-1.2.7 -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg > > ../gap -> > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/bin/gap > > > real 2m48.230s > > user 1m30.082s > > sys 0m59.461s > > Copying package files from temporary location > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst to > /Users/.../sage/local > > cp: cannot overwrite directory > /Users/.../sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src > with non-directory > /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src > > cp: /Users/.../sage/local/./share/gap/pkg/ctbllib/tst/docxpl.tst: Permission > denied > > > > Error copying files for gap-4.10.0.p0. > > > > > I have a feeling that there is a typo of some kind in the commit > > > https://github.com/sagemath/sage/commit/ca94bd97d73ee544c273fbb28cb774b3af12ecb6#diff-a9a04fa360dca60daa488241916fdb9c I don't think so but... > though I can't say immediately where, because the full line is > > > non-directory > /Users/karl.crisman/Downloads/sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src > > > and indeed I don't see why there should be a file that has the entire path to > sage/local TWICE; probably should use a temp file if for some reason that was > the desired behavior? I did not do anything unusual in this setup. That's expected. The package build directory is under SAGE_LOCAL ($SAGE_LOCAL/var/tmp/sage/build/gap-4.10.0.p0) but the file's destination path ($SAGE_LOCAL) is appended to this. This is how it's supposed to work (DESTDIR installation). It's probably too late to diagnose now (though it would be good if you could give steps to reproduce). But the question is what type of file was /Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src that it refuses to overwrite because it was supposedly a directory? The GAP package installs a *symlink* at the path $SAGE_LOCAL/share/gap/bin//src When you upgrade GAP, first of all, it should be *uninstalling* the previous gap package, so this link should just be removed. The question is was it a symlink for you in the first place? Or an actual directory? When you run `make clean-gap` does it get removed? I think normally there hasn't been a problem with this, at least not with consistent incremental updates, or else it would show up on the patchbot. In other words, I don't think you'll see this every time your gap package updates. But if you do that would be worth knowing about and investigating. -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAOTD34b1OWiamtEOsntU%2BcYq%3DyL1Qb4TB0q4e1inFmsgOcM2gg%40mail.gmail.com.
Re: [sage-release] Re: Sage 8.7.beta6 released
> That's expected. The package build directory is under SAGE_LOCAL > ($SAGE_LOCAL/var/tmp/sage/build/gap-4.10.0.p0) but the file's > destination path ($SAGE_LOCAL) is appended to this. This is how it's > supposed to work (DESTDIR installation). > > It's probably too late to diagnose now (though it would be good if you > could give steps to reproduce). Yeah, unfortunately my main goal was getting a working Sage install, so the evidence has been eliminated, so to speak. > But the question is what type of file > was > > /Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src > > > > that it refuses to overwrite because it was supposedly a directory? > I can tell you a rough answer to that, after my most recent upgrade the name of the directory seems to have changed slightly though: $ ls -l ~/Downloads/sage/local/share/gap/bin/x86_64-apple-darwin15.6.0-default64-kv3/ total 32 lrwxr-xr-x 1 karl.crisman 78570554 18 Aug 14 14:39 config.h -> ../../gen/config.h lrwxr-xr-x 1 karl.crisman 78570554 9 Aug 14 14:39 gac -> ../../gac lrwxr-xr-x 1 karl.crisman 78570554 9 Aug 14 14:39 gap -> ../../gap lrwxr-xr-x 1 karl.crisman 78570554 9 Aug 14 14:40 src -> ../../src > > The GAP package installs a *symlink* at the path > $SAGE_LOCAL/share/gap/bin//src > > So yes, that is what seems to be happening. > When you upgrade GAP, first of all, it should be *uninstalling* the > previous gap package, so this link should just be removed. The > question is was it a symlink for you in the first place? Apparently. > Or an actual > directory? When you run `make clean-gap` does it get removed? > > Is that something I can do from within Sage? I didn't know that was a make target for us. My assumption is that the symlink was not removed or it wouldn't have complained. -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/02c26f61-e386-4734-b239-79dcae96b476%40googlegroups.com.
Re: [sage-release] Re: Sage 8.7.beta6 released
On Thu, Aug 15, 2019 at 2:22 PM kcrisman wrote: > > >> That's expected. The package build directory is under SAGE_LOCAL >> ($SAGE_LOCAL/var/tmp/sage/build/gap-4.10.0.p0) but the file's >> destination path ($SAGE_LOCAL) is appended to this. This is how it's >> supposed to work (DESTDIR installation). >> >> It's probably too late to diagnose now (though it would be good if you >> could give steps to reproduce). > > > Yeah, unfortunately my main goal was getting a working Sage install, so the > evidence has been eliminated, so to speak. > >> >> But the question is what type of file >> was >> >> /Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src >> >> that it refuses to overwrite because it was supposedly a directory? > > > > I can tell you a rough answer to that, after my most recent upgrade the name > of the directory seems to have changed slightly though: > > $ ls -l > ~/Downloads/sage/local/share/gap/bin/x86_64-apple-darwin15.6.0-default64-kv3/ > > total 32 > > lrwxr-xr-x 1 karl.crisman 78570554 18 Aug 14 14:39 config.h -> > ../../gen/config.h > > lrwxr-xr-x 1 karl.crisman 78570554 9 Aug 14 14:39 gac -> ../../gac > > lrwxr-xr-x 1 karl.crisman 78570554 9 Aug 14 14:39 gap -> ../../gap > > lrwxr-xr-x 1 karl.crisman 78570554 9 Aug 14 14:40 src -> ../../src > > >> >> >> The GAP package installs a *symlink* at the path >> $SAGE_LOCAL/share/gap/bin//src >> > > So yes, that is what seems to be happening. > >> >> When you upgrade GAP, first of all, it should be *uninstalling* the >> previous gap package, so this link should just be removed. The >> question is was it a symlink for you in the first place? > > > Apparently. There was a bug fixed just a few months ago related to this: https://trac.sagemath.org/ticket/27589 Symbolic links were not being removed properly. They should be now, though. It's possible just from an older install something was left behind. Who knows... >> Or an actual >> directory? When you run `make clean-gap` does it get removed? >> > > Is that something I can do from within Sage? I didn't know that was a make > target for us. My assumption is that the symlink was not removed or it > wouldn't have complained. My mistake, that should be `make gap-clean`. But yes, you can do that from the base of SAGE_ROOT. This also happens when you force re-isinstall a package as with `./sage -f gap`. -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAOTD34ZpPi-Avxajhx6F3tS2LXGAQZnDVjhhDE8nnQkxQ5gXbw%40mail.gmail.com.
Re: [sage-release] Re: Sage 8.7.beta6 released
This also happened to me a few weeks ago. The underlying problem seems to be that the uninstall script fails because it tries to call sage-dist-helpers, but cannot find it. This file has recently been moved from src/bin to build/bin, which the uninstall script cannot know about. Once upgraded to Gap 4.10.2.p0, it points to the new location of sage-dist-helpers, so this particular problem should not happen again. This has also been reported on devel [1,2] and might affect more Mac users when upgrading to 8.9. Perhaps a copy of sage-dist-helpers could be added back to src/bin for some deprecation period? [1] https://groups.google.com/forum/#!topic/sage-devel/cdw793St6cE [2] https://groups.google.com/forum/#!topic/sage-devel/h-hXvO2fxgc -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/a4cd4e30-5b2b-4890-a744-9776b2ec2223%40googlegroups.com.
Re: [sage-release] Re: Sage 8.7.beta6 released
Yes, that fits. Now that I know to look, I see buried in my gap install log Uninstalling existing 'gap' Running pre-uninstall script for 'gap' /Users/jpalmier/Desktop/Sage/git/sage/local/var/lib/sage/scripts/gap/spkg-prerm: line 13: /Users/jpalmier/Desktop/Sage/git/sage/src/bin/sage-dist-helpers: No such file or directory Error: failed to source sage-dist-helpers Is /Users/jpalmier/Desktop/Sage/git/sage the correct SAGE_ROOT? Error: The pre-uninstall script for 'gap' failed; the package will not be uninstalled, and some manual intervention may be needed to repair the package's state before uninstallation can proceed. Check further up in this log for more details, or the pre-uninstall script itself at /Users/jpalmier/Desktop/Sage/git/sage/local/var/lib/sage/scripts/gap/spkg-prerm. On Thursday, August 15, 2019 at 10:58:22 AM UTC-7, Markus Wageringel wrote: > > This also happened to me a few weeks ago. The underlying problem seems to > be that the uninstall script fails because it tries to call > sage-dist-helpers, but cannot find it. This file has recently been moved > from src/bin to build/bin, which the uninstall script cannot know about. > Once upgraded to Gap 4.10.2.p0, it points to the new location of > sage-dist-helpers, so this particular problem should not happen again. > > This has also been reported on devel [1,2] and might affect more Mac users > when upgrading to 8.9. Perhaps a copy of sage-dist-helpers could be added > back to src/bin for some deprecation period? > > [1] https://groups.google.com/forum/#!topic/sage-devel/cdw793St6cE > [2] https://groups.google.com/forum/#!topic/sage-devel/h-hXvO2fxgc > > -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/d74a2f9c-c53c-47d9-83f3-045b19353cea%40googlegroups.com.
