Unfortunately, the new version fails its test suite AGAIN when the recommended
packages are not build. Makes one wonder whether maybe we should offer the R
developers CI builds that check this. I've reported the issue upstream, let's
see what happens.
The `geogebra` package is subject to break as upstream removes versioned
packages from their download server when five new releases are comming.
This is why I had to fix almost monthly the package by bumping the
version (these can be found by running `git log --online | grep
geogebra:`). As the package didn't cause any issues for several months
now I guess that using `archive.org` seems to be a suitable solution for
now.
/cc @sternenseemann @matthewbauer
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:
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- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 4.3.0 with grep in /nix/store/aw897502z5bcn6dw6rp7jca90flfrjab-JAGS-4.3.0
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:
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- ran `/nix/store/phmgqwmf0fa3q2d62zq220zpgi64hssj-gp2c-0.0.10pl1/bin/gp2c -h` got 0 exit code
- ran `/nix/store/phmgqwmf0fa3q2d62zq220zpgi64hssj-gp2c-0.0.10pl1/bin/gp2c -v` and found version 0.0.10pl1
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- ran `/nix/store/phmgqwmf0fa3q2d62zq220zpgi64hssj-gp2c-0.0.10pl1/bin/gp2c-run -h` got 0 exit code
- ran `/nix/store/phmgqwmf0fa3q2d62zq220zpgi64hssj-gp2c-0.0.10pl1/bin/gp2c-run --help` got 0 exit code
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- ran `/nix/store/phmgqwmf0fa3q2d62zq220zpgi64hssj-gp2c-0.0.10pl1/bin/gp2c-run --help` and found version 0.0.10pl1
- found 0.0.10pl1 with grep in /nix/store/phmgqwmf0fa3q2d62zq220zpgi64hssj-gp2c-0.0.10pl1
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Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:
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- ran `/nix/store/gbxxlzids227g9xaiqyqp2hp8ccmkfvq-fricas-1.3.3/bin/fricas -h` got 0 exit code
- ran `/nix/store/gbxxlzids227g9xaiqyqp2hp8ccmkfvq-fricas-1.3.3/bin/fricas -h` and found version 1.3.3
- ran `/nix/store/gbxxlzids227g9xaiqyqp2hp8ccmkfvq-fricas-1.3.3/bin/efricas --help` got 0 exit code
- found 1.3.3 with grep in /nix/store/gbxxlzids227g9xaiqyqp2hp8ccmkfvq-fricas-1.3.3
The tests failed for a good reason on Darwin and should not have been
disabled. The issue has been resolved upstream with version 1.8 which
now also supports AArch64.
Semi-automatic update. These checks were done:
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Semi-automatic update. These checks were done:
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Semi-automatic update. These checks were done:
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- found 0.6.2 with grep in /nix/store/gdzrfmvi5x26is0hbv0yyg5s61cxm7dy-gfan-0.6.2
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Semi-automatic update. These checks were done:
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- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere -V` and found version 2.12.6.6
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- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere --version` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere version` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere -h` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere --help` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/4dsphere help` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/fproduct -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/fproduct --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/fproduct help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/mersenne -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/mersenne --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/mersenne help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/piforever -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/piforever -v` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus -v` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus --version` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus version` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus --help` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/plus help` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/powerterm -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/powerterm --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/powerterm help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/simple -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/simple --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/simple help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/simple -v` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/square -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/square --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/square help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/cscript/square -v` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/calc -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/calc --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/calc help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/calc -v` and found version 2.12.6.6
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/.calc-wrapped -h` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/.calc-wrapped --help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/.calc-wrapped help` got 0 exit code
- ran `/nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6/bin/.calc-wrapped -v` and found version 2.12.6.6
- found 2.12.6.6 with grep in /nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6
- found 2.12.6.6 in filename of file in /nix/store/mdjaq6pgxp9qrfg9s7iaavj2rsvjqh9q-calc-2.12.6.6
Semi-automatic update. These checks were performed:
- built on NixOS
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/tex2mail help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gphelp --help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gphelp help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -h` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 --help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -V` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -v` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 --version` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -h` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 --help` and found version 2.9.4
- found 2.9.4 with grep in /nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4
- found 2.9.4 in filename of file in /nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4
cc "@ertes @raskin @AndersonTorres"
Semi-automatic update. These checks were performed:
- built on NixOS
- found 18.02.0 with grep in /nix/store/q3pav5f98v0imlk0bsr295k8xf2w8njr-wxmaxima-18.02.0
- found 18.02.0 in filename of file in /nix/store/q3pav5f98v0imlk0bsr295k8xf2w8njr-wxmaxima-18.02.0
cc "@peti"
Semi-automatic update. These checks were performed:
- built on NixOS
- ran `/nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5/bin/lp_solve -h` got 0 exit code
- ran `/nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5/bin/lp_solve -h` and found version 5.5.2.5
- found 5.5.2.5 with grep in /nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5
- found 5.5.2.5 in filename of file in /nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5
cc "@smironov"
Semi-automatic update. These checks were performed:
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- ran `/nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2/bin/fricas -h` got 0 exit code
- ran `/nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2/bin/fricas -h` and found version 1.3.2
- ran `/nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2/bin/efricas --help` got 0 exit code
- found 1.3.2 with grep in /nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2
cc "@sprock"
Semi-automatic update. These checks were performed:
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- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/clp help` got 0 exit code
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/clp version` and found version 2.9.9
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/clp help` and found version 2.9.9
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/cbc help` got 0 exit code
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/cbc version` and found version 2.9.9
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/cbc help` and found version 2.9.9
- found 2.9.9 with grep in /nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9
- found 2.9.9 in filename of file in /nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9
openblas is used since it's propagated from OpenCV and ATLAS compiled without
architecture-specific optimizations is generally slower than OpenBLAS as I
heard.
This makes the HTML-docs an default-off option. Inline documentation
(`matrix-plot??`) is still available and HTML docs are available online.
Motivation: Get below the Hydra output size limit.
The build was failing on some machines because of a `find` command that
touched files in different orders on different machines.
That confused `make`s timestamp mechanism.
The sandboxed build was failing, because it relied heavily on
/usr/bin/env. This is fixed with a lot of shebang patching (both
to system packages and to sage-internal packages).
For now English (default) and Japanese editions only.
Fill out information in `l10ns.nix` to add the other localized editions.
Example usage: `mathematica.override { lang = "ja"; }` derives Japanese edition.
This "un-breaks" sage while also updating it to 8.0.
It compiles sage with its dependencies as one big pile, which is not
the best approach but definately better than nothing for now.
To be able to shrink the huge output pile a little, it also splits
docs from the rest of the output.
* pkgs: refactor needless quoting of homepage meta attribute
A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.
* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit
* Fixed some instances
The new version needs TZ configured to a value other than "UTC" for the test
suite to succeed. Otherwise, an assumption in "reg-tests-1d.R" won't hold that
expects
d <- as.POSIXlt("2016-12-06"); d$zone <- 1; format(d)
to throw an error about an invalid time zone.
Darwin build fails from conflicts in libSystem:
In file included from altdom.c:1:
In file included from /private/var/folders/7t/4vz31njj37b8y_bg6z3t7tk00000gn/T/nix-build-LiE-2.2.2.drv-0/LiE/lie.h:34:
In file included from /nix/store/9ll4m9yx854hr64fn1w9ra3qimm3pzdk-Libsystem-osx-10.9.5/include/string.h:176:
/nix/store/9ll4m9yx854hr64fn1w9ra3qimm3pzdk-Libsystem-osx-10.9.5/include/strings.h:73:7: error: redefinition of 'index' as different kind of symbol
char *index(const char *, int) __POSIX_C_DEPRECATED(200112L);
^
/private/var/folders/7t/4vz31njj37b8y_bg6z3t7tk00000gn/T/nix-build-LiE-2.2.2.drv-0/LiE/lie.h:6:14: note: previous definition is here
typedef long index;
^
1 error generated.
The Sage derivation had texLive, the old TeX Live packaging which
is now marked as broken, as a build input. This replaces it by the
current TeX Live packaging.
However, the build remains broken. One of the problems can be
solved by patching the hashbangs at the beginning of build scripts,
but the build still gets stuck while building ncurses.
A built-from-source Scilab 5 package looks to be a lot more work, and some
dependencies are missing from Nixpkgs, but the binary version with bundled
dependencies works.
In line with the Nixpkgs manual.
A mechanical change, done with this command:
find pkgs -name "*.nix" | \
while read f; do \
sed -e 's/description\s*=\s*"\([a-z]\)/description = "\u\1/' -i "$f"; \
done
I manually skipped some:
* Descriptions starting with an abbreviation, a user name or package name
* Frequently generated expressions (haskell-packages.nix)
The following parameters are now available:
* hardeningDisable
To disable specific hardening flags
* hardeningEnable
To enable specific hardening flags
Only the cc-wrapper supports this right now, but these may be reused by
other wrappers, builders or setup hooks.
cc-wrapper supports the following flags:
* fortify
* stackprotector
* pie (disabled by default)
* pic
* strictoverflow
* format
* relro
* bindnow
This option compiles R with --enable-strict-barrier. Doing so is
enables extra memory diagnostics in R that very useful for debugging
memory leak or memory protections issues in extensions to R written in
C, or for any apps embedding R (e.g. Haskell aps embedding R via
HaskellR).
This seems to have been confusing people, using both xlibs and xorg, etc.
- Avoided renaming local (and different) xlibs binding in gcc*.
- Fixed cases where both xorg and xlibs were used.
Hopefully everything still works as before.
Fixes#9044, close#9667. Thanks to @taku0 for suggesting this solution.
Now we have no modes starting with `/` or `+`.
Rewrite the `-perm` parameters of find:
- completely safe: rewrite `/0100` and `+100` to `-0100`,
- slightly semantics-changing: rewrite `+111` to `-0100`.
I cross-verified the `find` manual pages for Linux, Darwin, FreeBSD.
Many (less easily automatically converted) old-style strings
remain.
Where there was any possible ambiguity about the exact version or
variant intended, nothing was changed. IANAL, nor a search robot.
Use `with stdenv.lib` wherever it makes sense.
(My OCD kicked in today...)
Remove repeated package names, capitalize first word, remove trailing
periods and move overlong descriptions to longDescription.
I also simplified some descriptions as well, when they were particularly
long or technical, often based on Arch Linux' package descriptions.
I've tried to stay away from generated expressions (and I think I
succeeded).
Some specifics worth mentioning:
* cron, has "Vixie Cron" in its description. The "Vixie" part is not
mentioned anywhere else. I kept it in a parenthesis at the end of the
description.
* ctags description started with "Exuberant Ctags ...", and the
"exuberant" part is not mentioned elsewhere. Kept it in a parenthesis
at the end of description.
* nix has the description "The Nix Deployment System". Since that
doesn't really say much what it is/does (especially after removing
the package name!), I changed that to "Powerful package manager that
makes package management reliable and reproducible" (borrowed from
nixos.org).
* Tons of "GNU Foo, Foo is a [the important bits]" descriptions
is changed to just [the important bits]. If the package name doesn't
contain GNU I don't think it's needed to say it in the description
either.
