New core plan for R #571

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therealpadams commented May 24, 2017

Signed-off-by: Paul Adams paul@baggerspion.net

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thesentinels May 24, 2017

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Thanks for the pull request! Here is what will happen next:

  1. Your PR will be reviewed by the maintainers
  2. If everything looks good, one of them will approve it, and your PR will be merged.

Thank you for contributing!

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thesentinels commented May 24, 2017

Thanks for the pull request! Here is what will happen next:

  1. Your PR will be reviewed by the maintainers
  2. If everything looks good, one of them will approve it, and your PR will be merged.

Thank you for contributing!

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stevendanna May 24, 2017

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👍 This looks like a good start to me. It would be nice if we could get some of the graphical output devices enabled:

  Interfaces supported:
  External libraries:        readline, curl
  Additional capabilities:   NLS
  Options enabled:           shared BLAS, R profiling

  Capabilities skipped:      PNG, JPEG, TIFF, cairo, ICU
  Options not enabled:       memory profiling

  Recommended packages:      yes

Because of dependency shenanigans I've had trouble getting some of those enabled without at least getting some parts of xorg packaged, which is started over in the xorg org.

I don't think we need those immediately, just wanted to mention it as I'm happy to help get those enabled over time.

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stevendanna commented May 24, 2017

👍 This looks like a good start to me. It would be nice if we could get some of the graphical output devices enabled:

  Interfaces supported:
  External libraries:        readline, curl
  Additional capabilities:   NLS
  Options enabled:           shared BLAS, R profiling

  Capabilities skipped:      PNG, JPEG, TIFF, cairo, ICU
  Options not enabled:       memory profiling

  Recommended packages:      yes

Because of dependency shenanigans I've had trouble getting some of those enabled without at least getting some parts of xorg packaged, which is started over in the xorg org.

I don't think we need those immediately, just wanted to mention it as I'm happy to help get those enabled over time.

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therealpadams May 24, 2017

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Thanks for the heads-up!

I can enable PNG, JPEG, TIFF and ICU with no problem. Will need to work with others to get core/cairo shipped.

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therealpadams commented May 24, 2017

Thanks for the heads-up!

I can enable PNG, JPEG, TIFF and ICU with no problem. Will need to work with others to get core/cairo shipped.

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therealpadams May 25, 2017

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I'm going to leave this PR open to keep conversation going (other people are interested in this core/R). But if we want image export, I, at least, additionally need to work on:

  • core/cairo
  • core/Xlibs

This is currently a do-not-merge PR.

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therealpadams commented May 25, 2017

I'm going to leave this PR open to keep conversation going (other people are interested in this core/R). But if we want image export, I, at least, additionally need to work on:

  • core/cairo
  • core/Xlibs

This is currently a do-not-merge PR.

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robbkidd commented May 25, 2017

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Status update:
When compiling R, during the .configure step, pkg-config cannot find cairo (despite being correctly present in PKG_PATH). There is some anecdotal evidence that this happens when pango is not present.

So now I am working on:

  • core/cairo
  • core/pango
  • core/harfbuzz
  • core/R

Thanks to @eeyun and @stevendanna for their help in the hack day yesterday. This PR is staying open for further comment.

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therealpadams commented May 26, 2017

Status update:
When compiling R, during the .configure step, pkg-config cannot find cairo (despite being correctly present in PKG_PATH). There is some anecdotal evidence that this happens when pango is not present.

So now I am working on:

  • core/cairo
  • core/pango
  • core/harfbuzz
  • core/R

Thanks to @eeyun and @stevendanna for their help in the hack day yesterday. This PR is staying open for further comment.

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stevendanna May 26, 2017

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I was able to get cairo recognized with a small fix to pixman (in another PR) and by explicitly adding some transitive dependencies to the R pkg_deps array.

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stevendanna commented May 26, 2017

I was able to get cairo recognized with a small fix to pixman (in another PR) and by explicitly adding some transitive dependencies to the R pkg_deps array.

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stevendanna May 26, 2017

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PR for pixman: #577

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stevendanna commented May 26, 2017

PR for pixman: #577

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therealpadams May 28, 2017

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@stevendanna That's great news. Do you have a branch somewhere that I can merge into this PR so I can grab your R plan.sh?

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therealpadams commented May 28, 2017

@stevendanna That's great news. Do you have a branch somewhere that I can merge into this PR so I can grab your R plan.sh?

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** Status update **
Builds:

  • core/pango
  • core/harfbuzz
  • core/cairo

WIP:

  • core/R

In terms of builds, I'm pretty close to wrapping this up now. Once everything is building nicely, there will need to be some work to cleanup the plans. Note: this PR assumes that #577 is merged.

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therealpadams commented May 28, 2017

** Status update **
Builds:

  • core/pango
  • core/harfbuzz
  • core/cairo

WIP:

  • core/R

In terms of builds, I'm pretty close to wrapping this up now. Once everything is building nicely, there will need to be some work to cleanup the plans. Note: this PR assumes that #577 is merged.

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@stevendanna when you have a moment, I'd hugely appreciate a review of this PR. I cannot work out why I am not getting R to build with all the graphical device support. I assume that once cairo works, jpeg, png etc will all enable, too.
Cannot work out why cairo is not being enabled, though.

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therealpadams commented May 29, 2017

@stevendanna when you have a moment, I'd hugely appreciate a review of this PR. I cannot work out why I am not getting R to build with all the graphical device support. I assume that once cairo works, jpeg, png etc will all enable, too.
Cannot work out why cairo is not being enabled, though.

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@therealpadams Thanks for pushing this forward. I'll pull down your recent changes and see what I can find.

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stevendanna commented May 29, 2017

@therealpadams Thanks for pushing this forward. I'll pull down your recent changes and see what I can find.

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OK. I've made some progress, but don't get too excited, lots of caveats below:

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua
       TRUE        TRUE        TRUE       FALSE       FALSE       FALSE
   http/ftp     sockets      libxml        fifo      cledit       iconv
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
        NLS     profmem       cairo         ICU long.double     libcurl
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
> png("foo.png", type="cairo")
> plot(c(1,2,3,4,5))
> dev.off()
null device
          1
>
Save workspace image? [y/n/c]: n
[157][default:/src:0]# file foo.png
foo.png: PNG image data, 480 x 480, 8-bit colormap, non-interlaced

This is available on my branch which I forked off of yours: therealpadams/core-plans@core/R...stevendanna:core/R-ssd

Here is a brief summary of where I've gotten:

  1. A lot of things were in pkg_build_deps that needed to be in pkg_deps. I've sorted most of them out, but we'll want to do another pass once everything is working.

  2. I've added some "transitive" deps directly to pkg_deps so that they are correctly added to PKG_CONFIG_PATH. This is how I got the configure script recognizing pango and cairo. A good trick for figuring out why pkg-config isn't finding something is to have it tell you by exporting the same PKG_CONFIG_PATH that the build is using and then running pkg-config directly with the --print-errors flag:

    [52][default:/src:0]# /hab/pkgs/core/pkg-config/0.29/20170513212944/bin/pkg-config cairo --print-errors
    Package fontconfig was not found in the pkg-config search path.
    Perhaps you should add the directory containing `fontconfig.pc'
    to the PKG_CONFIG_PATH environment variable
    Package 'fontconfig', required by 'cairo', not found
    
  3. The configure script that R ships, expect that cairo-xlib is there no matter how cairo has been compiled. Here are the two tests programs it might execute:

    Pango and Cairo:

    #include <pango/pango.h>
    #include <pango/pangocairo.h>
    #include <cairo-xlib.h>
    #if CAIRO_VERSION  < 10200
    #error cairo version >= 1.2 required
    #endif
    int main(void) {
        cairo_t  *CC = NULL; // silence picky compilers
        cairo_arc(CC, 0.0, 0.0, 1.0, 0.0, 6.28);
        pango_cairo_create_layout(CC);
        pango_font_description_new();
        return 0;
     }
    

    Cairo-only:

    #include <cairo.h>
    #include <cairo-xlib.h>
    #if CAIRO_VERSION  < 10200
    #error cairo version >= 1.2 required
    #endif
    int main(void) {
        cairo_t  *CC;
        cairo_arc(CC, 0.0, 0.0, 1.0, 0.0, 6.28);
        cairo_select_font_face (CC, "Helvetica", CAIRO_FONT_SLANT_NORMAL,
                                 CAIRO_FONT_WEIGHT_BOLD);
        return 0;
     }
    

    To get around this I removed pango so I just had to deal with one of the tests and then ran sed on the configure script to remove the include <cairo-xlib.h>. The test still passes without this include. My guess is the same is true for the pango+cairo test, the cairo-only test just seemed like the place to start.

    To be honest, this makes me a bit nervous since I don't know much about cairo and whether not having cairo-xlib will be a problem down the road. I might be "OK" with it for now until we can get xlib in core.

  4. Even after all that, lots of code won't work "out-of-the-box" since the default "type" parameter for devices like png still seems to be "xlib" even though we compiled it completely without xlib. It would be nice if we could figure out how to make the default "cairo".

  5. Editing the configuration file also led to some failures during building some package that requires java config. I haven't dug into it at all yet. It might have to do with the timestamp on the configure script or it could have been environmental.

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stevendanna commented May 30, 2017

OK. I've made some progress, but don't get too excited, lots of caveats below:

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua
       TRUE        TRUE        TRUE       FALSE       FALSE       FALSE
   http/ftp     sockets      libxml        fifo      cledit       iconv
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
        NLS     profmem       cairo         ICU long.double     libcurl
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
> png("foo.png", type="cairo")
> plot(c(1,2,3,4,5))
> dev.off()
null device
          1
>
Save workspace image? [y/n/c]: n
[157][default:/src:0]# file foo.png
foo.png: PNG image data, 480 x 480, 8-bit colormap, non-interlaced

This is available on my branch which I forked off of yours: therealpadams/core-plans@core/R...stevendanna:core/R-ssd

Here is a brief summary of where I've gotten:

  1. A lot of things were in pkg_build_deps that needed to be in pkg_deps. I've sorted most of them out, but we'll want to do another pass once everything is working.

  2. I've added some "transitive" deps directly to pkg_deps so that they are correctly added to PKG_CONFIG_PATH. This is how I got the configure script recognizing pango and cairo. A good trick for figuring out why pkg-config isn't finding something is to have it tell you by exporting the same PKG_CONFIG_PATH that the build is using and then running pkg-config directly with the --print-errors flag:

    [52][default:/src:0]# /hab/pkgs/core/pkg-config/0.29/20170513212944/bin/pkg-config cairo --print-errors
    Package fontconfig was not found in the pkg-config search path.
    Perhaps you should add the directory containing `fontconfig.pc'
    to the PKG_CONFIG_PATH environment variable
    Package 'fontconfig', required by 'cairo', not found
    
  3. The configure script that R ships, expect that cairo-xlib is there no matter how cairo has been compiled. Here are the two tests programs it might execute:

    Pango and Cairo:

    #include <pango/pango.h>
    #include <pango/pangocairo.h>
    #include <cairo-xlib.h>
    #if CAIRO_VERSION  < 10200
    #error cairo version >= 1.2 required
    #endif
    int main(void) {
        cairo_t  *CC = NULL; // silence picky compilers
        cairo_arc(CC, 0.0, 0.0, 1.0, 0.0, 6.28);
        pango_cairo_create_layout(CC);
        pango_font_description_new();
        return 0;
     }
    

    Cairo-only:

    #include <cairo.h>
    #include <cairo-xlib.h>
    #if CAIRO_VERSION  < 10200
    #error cairo version >= 1.2 required
    #endif
    int main(void) {
        cairo_t  *CC;
        cairo_arc(CC, 0.0, 0.0, 1.0, 0.0, 6.28);
        cairo_select_font_face (CC, "Helvetica", CAIRO_FONT_SLANT_NORMAL,
                                 CAIRO_FONT_WEIGHT_BOLD);
        return 0;
     }
    

    To get around this I removed pango so I just had to deal with one of the tests and then ran sed on the configure script to remove the include <cairo-xlib.h>. The test still passes without this include. My guess is the same is true for the pango+cairo test, the cairo-only test just seemed like the place to start.

    To be honest, this makes me a bit nervous since I don't know much about cairo and whether not having cairo-xlib will be a problem down the road. I might be "OK" with it for now until we can get xlib in core.

  4. Even after all that, lots of code won't work "out-of-the-box" since the default "type" parameter for devices like png still seems to be "xlib" even though we compiled it completely without xlib. It would be nice if we could figure out how to make the default "cairo".

  5. Editing the configuration file also led to some failures during building some package that requires java config. I haven't dug into it at all yet. It might have to do with the timestamp on the configure script or it could have been environmental.

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We now successfully have all graphics drivers enabled and cairo enabled as the default bitmap type:

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE       FALSE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
> options("bitmapType")
$bitmapType
[1] "cairo"
Contributor

therealpadams commented May 30, 2017

We now successfully have all graphics drivers enabled and cairo enabled as the default bitmap type:

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE       FALSE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
> options("bitmapType")
$bitmapType
[1] "cairo"

therealpadams and others added some commits May 24, 2017

New core plan for R
Signed-off-by: Paul Adams <paul@baggerspion.net>
Paul Adams
Fix: R plan cleaning
Signed-off-by: Paul Adams <paul.adams@endocode.com>
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These plans now have all their pkg_build_deps and pkg_deps corrected and the EXPORTS removed. I reckon these are now OK to merge.

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therealpadams commented May 31, 2017

These plans now have all their pkg_build_deps and pkg_deps corrected and the EXPORTS removed. I reckon these are now OK to merge.

therealpadams added some commits May 31, 2017

Fixed dependencies in order to remove the ugly EXPORTS that were all …
…over these plans.

Signed-off-by: Paul Adams <paul@baggerspion.net>
Added missing upstream URLS and descriptions
Signed-off-by: Paul Adams <paul@baggerspion.net>
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So here's a problem:
It's one thing to have FontConfig installed. It's totally another to have fonts installed...
rplot_360

I was able to show that the output is correct, by installing some fonts manually into my studio:
rplot_360-1

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therealpadams commented Jun 1, 2017

So here's a problem:
It's one thing to have FontConfig installed. It's totally another to have fonts installed...
rplot_360

I was able to show that the output is correct, by installing some fonts manually into my studio:
rplot_360-1

Add core/liberation-fonts-ttf pkg and update harfbuzz and R to use it
Signed-off-by: Paul Adams <paul@baggerspion.net>
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This PR is getting a little crazy :) It now contains:
core/cairo
core/harfbuzz
core/pango
core/R
core/liberation-fonts-ttf

The Liberation Fonts pkg simply downloads and untars the Liberations Fonts for use by, for example, R. Problem, we need to run fc-cache $(pkg_path_for core/liberation-fonts-ttf) at some point before the fonts can actually be used. Not entirely sure when.

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therealpadams commented Jun 3, 2017

This PR is getting a little crazy :) It now contains:
core/cairo
core/harfbuzz
core/pango
core/R
core/liberation-fonts-ttf

The Liberation Fonts pkg simply downloads and untars the Liberations Fonts for use by, for example, R. Problem, we need to run fc-cache $(pkg_path_for core/liberation-fonts-ttf) at some point before the fonts can actually be used. Not entirely sure when.

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bdangit Jun 3, 2017

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While we could do this in init but I suspect this is more of a cli command than a service that is to be managed underneath Hab sup.

Alternatively, you could always make a "R" wrapper where it will execute the command you need as well setup any other additional exports/variables/etc.

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bdangit commented Jun 3, 2017

While we could do this in init but I suspect this is more of a cli command than a service that is to be managed underneath Hab sup.

Alternatively, you could always make a "R" wrapper where it will execute the command you need as well setup any other additional exports/variables/etc.

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Looking good!

R/plan.sh
+ core/diffutils
+ core/file
+ core/gcc
+ core/icu

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No need to call this out here if it's defined in pkg_deps

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No need to call this out here if it's defined in pkg_deps

R/plan.sh
+ core/file
+ core/gcc
+ core/icu
+ core/liberation-fonts-ttf

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If you need this during runtime, you'll want to make sure this is placed in pkg_deps

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If you need this during runtime, you'll want to make sure this is placed in pkg_deps

R/plan.sh
+ core/icu
+ core/liberation-fonts-ttf
+ core/libjpeg-turbo
+ core/libpng

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Remove here if called out in pkg_deps

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Remove here if called out in pkg_deps

R/plan.sh
+ core/gcc
+ core/icu
+ core/liberation-fonts-ttf
+ core/libjpeg-turbo

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Remove this if defined in pkg_deps

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Remove this if defined in pkg_deps

R/plan.sh
+do_build() {
+ sed -i '/#include.*<cairo-xlib.h>/d' ./configure
+ ./configure --prefix="${pkg_prefix}" \
+ --with-x=no \

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Alignment seems off by one space

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Alignment seems off by one space

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These alignment errors are super weird... don't see them in VIM. Will guess my way around them :)

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These alignment errors are super weird... don't see them in VIM. Will guess my way around them :)

R/plan.sh
+ sed -i '/#include.*<cairo-xlib.h>/d' ./configure
+ ./configure --prefix="${pkg_prefix}" \
+ --with-x=no \
+ --disable-java \

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Alignment

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Alignment

harfbuzz/plan.sh
+pkg_origin=core
+pkg_version=1.3.1
+pkg_maintainer="The Habitat Maintainers <humans@habitat.sh>"
+pkg_license=('mit')

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Minor nit but would Uppercase to MIT

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Minor nit but would Uppercase to MIT

harfbuzz/plan.sh
+
+do_build() {
+ ./configure --prefix="$pkg_prefix" \
+ --with-gobject=yes

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Alignment off by one space

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Alignment off by one space

pango/plan.sh
+ core/patch
+ core/perl
+ core/pkg-config
+ core/util-linux

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Alignment by one space

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Alignment by one space

Fixes from @bdangit's comments
Signed-off-by: Paul Adams <paul@baggerspion.net>
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Thanks for the review, @bdangit. Alignment issues all fixed and I've sorted out pkg_deps vs pkg_build_deps (thought I'd already done that).

I think this is mergeable now. The issue with updating the font-cache is something that can be fixed with documentation.

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therealpadams commented Jun 4, 2017

Thanks for the review, @bdangit. Alignment issues all fixed and I've sorted out pkg_deps vs pkg_build_deps (thought I'd already done that).

I think this is mergeable now. The issue with updating the font-cache is something that can be fixed with documentation.

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👍

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bdangit commented Jun 4, 2017

👍

@eeyun eeyun added S-DO-NOT-MERGE and removed DO NOT MERGE labels Jun 6, 2017

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@eeyun Wondering if we can remove the DO-NOT-MERGE label? This looks good to me. While there is the fc-cache issue, I think it is best to "document and iterate" on that issue.

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stevendanna commented Jun 7, 2017

@eeyun Wondering if we can remove the DO-NOT-MERGE label? This looks good to me. While there is the fc-cache issue, I think it is best to "document and iterate" on that issue.

@eeyun eeyun removed the S-DO-NOT-MERGE label Jun 7, 2017

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LGTM!

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eeyun commented Jun 7, 2017

LGTM!

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core/pixman/0.34.0/20170623171747 has been built and uploaded to the depot. 💖
core/cairo/1.14.8/20170623172008 has been built and uploaded to the depot. 💖
core/liberation-fonts-ttf/2.00.1/20170623172912 has been built and uploaded to the depot. 💖
core/harfbuzz/1.3.1/20170623172916 has been built and uploaded to the depot. 💖
core/pango/1.40.6/20170623172955 has been built and uploaded to the depot. 💖
core/R/3.4.0/20170623173042 has been built and uploaded to the depot. 💖

The following reverse dependencies in the chain have also been rebuilt:
core/qemu/2.7.0/20170623173821 has been built and uploaded to the depot. 💖
core/grub/2.02/20170623174156 has been built and uploaded to the depot. 💖

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eeyun commented Jun 23, 2017


core/pixman/0.34.0/20170623171747 has been built and uploaded to the depot. 💖
core/cairo/1.14.8/20170623172008 has been built and uploaded to the depot. 💖
core/liberation-fonts-ttf/2.00.1/20170623172912 has been built and uploaded to the depot. 💖
core/harfbuzz/1.3.1/20170623172916 has been built and uploaded to the depot. 💖
core/pango/1.40.6/20170623172955 has been built and uploaded to the depot. 💖
core/R/3.4.0/20170623173042 has been built and uploaded to the depot. 💖

The following reverse dependencies in the chain have also been rebuilt:
core/qemu/2.7.0/20170623173821 has been built and uploaded to the depot. 💖
core/grub/2.02/20170623174156 has been built and uploaded to the depot. 💖

@eeyun eeyun merged commit 8585f28 into habitat-sh:master Jun 23, 2017

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