Closed boyoungzheng closed 4 years ago
Hello,
This formula is broken because of some issue in the tcl/tk needed by xcrysden, which is an outdated version. I’ll try to fix the x11 issue but that’s not the main problem…
Regards, Agilio
On 19 Jul 2018, at 21:16, boyoungzheng notifications@github.com wrote:
Homebrew does not have formula "x11". By the way, I have Xquatz installed. Are there any options to use "my" available xquartz? Thank you.
==> Installing xcrysden from agiliopadua/extras Error: No available formula with the name "x11" (dependency of agiliopadua/extras/xcrysden) ==> Searching for a previously deleted formula (in the last month)... Error: No previously deleted formula found. ==> Searching for similarly named formulae... This similarly named formula was found: x11vnc To install it, run: brew install x11vnc ==> Searching taps... ==> Searching taps on GitHub... Error: No formulae found in taps.
Homebrew 1.7.0 Homebrew/homebrew-core (git revision b47f6e; last commit 2018-07-19) MacOS 10.13.5 XQuartz 2.7.11 (xorg-server 1.18.4)
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@boyoungzheng, I agree with @agiliopadua x11 is not the main problem, I have tried tcl/tk 8.5, 8.6, 8.7 and mac os default, none of them works. you can view all my attempts at https://gist.github.com/specter119/4f630e538d39edcf67ec742f78c23aab .
The Macport can successfully build Xcrysden. I have absolutely no idea how it works. Maybe you code genius can look into it and do the same trick in homebrew? I prefer installing through homebrew :-)
@boyoungzheng I know MacPort and Fink can build it. But their codes haven't change for quite a long time.
Thanks to @agiliopadua, I believe that he has made all the most necessary modifications (you can compare the modification in MacPort and Fink I provide). Also his codes could also help you build xcrysden in the near past.
But the New issue is:
5156 Segmentation fault: 11 ${XCRYSDEN_XCRYS_DIR}/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH "$@" > /dev/null
when xcrysden launches (you can successfully build xcrysden with tcl/tk 8.5/8.6/8.7/system with the code in my gist).
This issue is more related to homebrew tcl/tk or even MacOS itself I guess, and few useful message in xcrysden mail list mentioned this.
I also eager to use xcrysden on Mac natively, but I finally turn to linux instead. I think you should consider MacPort, Fink, Linux or even WSL on windows as an alternative way.
I know nothing about tcl/tk, so that I'm not able to fix this at all. If you find any one can fix this, I am happy to merge it to brewsci/homebrew-science.
Thanks to @agiliopadua patch. I can successfully build XCrysden from source package. Although there is the error( http://www.democritos.it/pipermail/xcrysden/2015-October/001750.html ), we can solve its error( http://www.democritos.it/pipermail/xcrysden/2015-October/001754.html) from xcrysden_root/F/gengeom.f.
Before compiling, I performed export PATH="/usr/local/bin:$PATH"
,brew install tcl-tk --with-threads --with-x11
and brew link tcl-tk --overwrite --force
.
I hope to become clue of problem solving.
@Tomoki9684 tcl-tk
no longer have --with-threads
and --with-x11
options
@specter119 I'm sorry that I forget to tell about changing the formula. we can download this address (https://www.dropbox.com/s/tq2dsvtclsmt0ec/tcl-tk.rb?dl=0) with --with-threads
and --with-x11
options. Please, overwrite homebrew/core formula. However, I cannot open the bxsf format (ex. Fermi Surface) because of Segmentation fault: 11
.
Dear all, according to @Tomoki9684's opinion, I have add --with-x11
to tcl-tk
, and add xcrysden
to brewsci/homebrew-science. you can see:
add with-x11 option for tcl-tk add xcrysden
you can wait for the 2 prs merging, or build them by modify your local homebrew.
update:
because homebrew-science has been archive and is not maintained.
you can install xcrysden by my fork of homebrew-science
by the way, bxsf related functions work well.
Homebrew does not have formula "x11". By the way, I have Xquatz installed. Are there any options to use "my" available xquartz? Thank you.
==> Installing xcrysden from agiliopadua/extras Error: No available formula with the name "x11" (dependency of agiliopadua/extras/xcrysden) ==> Searching for a previously deleted formula (in the last month)... Error: No previously deleted formula found. ==> Searching for similarly named formulae... This similarly named formula was found: x11vnc To install it, run: brew install x11vnc ==> Searching taps... ==> Searching taps on GitHub... Error: No formulae found in taps.
Homebrew 1.7.0 Homebrew/homebrew-core (git revision b47f6e; last commit 2018-07-19) MacOS 10.13.5 XQuartz 2.7.11 (xorg-server 1.18.4)