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R has no graphics abilities on Debian buster #27163

Closed 7822f248-ba56-45f1-ab3d-4de7482bdf9f closed 5 years ago

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago

Seen in 8.7.beta1, but probably from 8.6 (i. e. the switch to using th library):

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

Similarly, one can't install the R package "Cairo". This entails the loss of creating graphics files from R, which is exceedingly annoying...

One of the strengths of R being its graphical abilities, losing them is, IMNSHO, a critical problem.

CC: @timokau @dimpase @embray @slel

Component: packages: standard

Reviewer: Emmanuel Charpentier

Issue created by migration from https://trac.sagemath.org/ticket/27163

dimpase commented 5 years ago
comment:1

What exactly is meant by can't install the R package "Cairo"?

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:2

Look for yourself :

charpent@p-202-021:~$ sage -R

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"

[ Snip... ]

[Sauvegarde de la session précédente restaurée]

> install.packages("Cairo")
--- SVP sélectionner un miroir CRAN pour cette session ---

[ re-Snip... ]

Selection: 32
essai de l'URL 'https://cran.univ-paris1.fr/src/contrib/Cairo_1.5-9.tar.gz'
Content type 'application/x-gzip' length 86982 bytes (84 KB)
==================================================
downloaded 84 KB

* installing *source* package ‘Cairo’ ...
** package ‘Cairo’ correctement décompressé et sommes MD5 vérifiées
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/local/sage-8/local/bin/pkg-config
checking whether pkg-config knows about cairo... yes
checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender
configure: CAIRO_CFLAGS=-I/usr/local/sage-8/local/include -I/usr/local/sage-8/local/include/freetype2 -I/usr/local/sage-8/local/include -I/usr/local/sage-8/local/include/libpng16 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid
checking if R was compiled with the RConn patch... no
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=-L/usr/local/sage-8/local/lib -lfreetype -lz -lpng16 -lz -lcairo -lXext -lXrender -lX11
checking for library containing deflate... no
checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’
* removing ‘/usr/local/sage-8/local/lib/R/library/Cairo’

Les packages source téléchargés sont dans
    ‘/tmp/RtmphJPGGK/downloaded_packages’
Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  impossible de charger l'objet partagé '/usr/local/sage-8/local/lib/R//modules//R_X11.so':
  /usr/lib/x86_64-linux-gnu/libcairo.so.2: undefined symbol: FT_Done_MM_Var
2: In install.packages("Cairo") :
  l'installation du package ‘Cairo’ a eu un statut de sortie non nul
>

Note that R tries to use the system's cairo libraries...

dimpase commented 5 years ago
comment:3

It all works for me on a Debian stretch system after apt install libcairo-dev. (without it, Sage's R cannot even find cairo.h header).

dimpase commented 5 years ago
comment:4

There is of course no telling in general whether your cairo installation is compatible with Sage's R, I guess this problem was always there, it's just that you finally hit this incompatibility.

dimpase commented 5 years ago
comment:5

I am inclined to close this as worksforme. I think the best way to proceed is to add capability to use system R installation, via adding appropriate spkg-configure.m4 to build/pkgs/r.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:6

Replying to @dimpase:

I am inclined to close this as worksforme. I think the best way to proceed is to add capability to use system R installation, via adding appropriate spkg-configure.m4 to build/pkgs/r.

I disagree :

charpent@p-202-021:~$ apt-get install -s libcairo-dev
NOTE: Ceci n'est qu'une simulation !
      apt-get a besoin des privilèges du superutilisateur
      pour pouvoir vraiment fonctionner.
      Veuillez aussi noter que le verrouillage est désactivé,
      et la situation n'est donc pas forcément représentative
      de la réalité !
Lecture des listes de paquets... Fait
Construction de l'arbre des dépendances       
Lecture des informations d'état... Fait
Note : sélection de « libcairo2-dev » au lieu de « libcairo-dev »
libcairo2-dev est déjà la version la plus récente (1.16.0-2).
0 mis à jour, 0 nouvellement installés, 0 à enlever et 0 non mis à jour.

Something else has changed... Maybe because I'm running buster (i. e. testing) rather than stretch (i. e. stable) ?

ISTR that Erik Madison Bray once had a proposal to use system's R as the Sage R interpreter. I'd be interested in knowing more...

dimpase commented 5 years ago
comment:7

zhe ne kompran pa your error messages :-)

Naturally all bets are off for a testing distro. You might try installing system's R ans check whether you get Cairo there.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:8

Replying to @dimpase:

zhe ne kompran pa your error messages :-)

My systems has fr_FR.UTF8 locale...

Naturally all bets are off for a testing distro.

I am aware of very few people running stable on a desktop. testing is usually the right compromise.

(Of course, on a server, stable is probably de rigueur ;-).

And since testing is the next stable (trnsition underway), I don't think that detecting a problem on it is irrelevant to Sage...

You might try installing system's R

Done since about 21 years (R is my professional bread and butter, replacing SAS), and religiously maintained (following Debian's packaging).

ans check whether you get Cairo there.

I do :

charpent@p-202-021:~$ R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.

R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.

Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.

[Sauvegarde de la session précédente restaurée]

> "Cairo" %in% row.names(installed.packages())
[1] TRUE
>

I'm maintaining Sage's R installation because :

BTW : the "Cairo" issue blocks a couple of R packages that depend on it. And the lack of any graphical ability is much more preoccupying...

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:9

I stand by my statement that this needs fixing.

dimpase commented 5 years ago
comment:10

So a quick solution would be to upgrade Sage's R to 3.5.2 and pray that such an upgrade won't break things on, say, debian stable (which I am running in a container on a ChromeOS laptop, not on a server :-))

timokau commented 5 years ago
comment:11

I'm pretty sure this has nothing to do with my recent change in the R interface. sage -R doesn't actually have much (if anything) to do with sage. It just starts the version of R that sage uses. That wasn't touched by my changes.

If you're sure the issue is new and was introduced by some sage update, maybe try git-bisect.

dimpase commented 5 years ago
comment:12

25674 will fix it - this is libraries incompatibility, nothing to do with rpy2.

dimpase commented 5 years ago
comment:13

Please review #25674 - I checked that installing Cairo still works on Debian stretch, please check whether this fixes graphics problems on Debian buster.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:14

Replying to @dimpase:

Please review #25674 - I checked that installing Cairo still works on Debian stretch,

Did you chheck that you had graphics capabilities() ?

please check whether this fixes graphics problems on Debian buster.

Underway...

dimpase commented 5 years ago
comment:15

I get, after installing Cairo,

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

It looks good enough to me.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:16

Replying to @dimpase:

I get, after installing Cairo,

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

It looks good enough to me.

png() is essential and here, ditto for cairo() ; tiff() is sometimes necessary to fulfill (exceedingly) retro desiderata of some medical journals' instructions to authors, and jpeg() is handy for some HTML tools who dislike png() for some unreasonable reason.

So, yes, that's good enough, if I can get that under buster.

Build still underway on another buster machine (merging develop and #25674).

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:17

Replying to @dimpase:

I get, after installing Cairo,

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

It looks good enough to me.

No such luck on buster. After getting #25674 and merging develop, I get :

charpent@zen-book-flip:/usr/local/sage-8$ sage -R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.

R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.

Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
      FALSE       FALSE       FALSE        TRUE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE       FALSE       FALSE        TRUE        TRUE        TRUE 
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  impossible de charger l'objet partagé '/usr/local/sage-8/local/lib/R//modules//R_X11.so':
  /usr/lib/x86_64-linux-gnu/libcairo.so.2: undefined symbol: FT_Done_MM_Var
>

For comparison, on the same machine, nut using system's R:

charpent@zen-book-flip:/usr/local/sage-8$ R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.

R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.

Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE        TRUE       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 
>

Therefore, I think that this is a distinct issue.

dimpase commented 5 years ago
comment:18

Have you tried reinstalling Cairo into Sage's R?

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:19

Replying to @dimpase:

Have you tried reinstalling Cairo into Sage's R?

No such bloody luck:

> install.packages("Cairo")
--- SVP sélectionner un miroir CRAN pour cette session ---
Secure CRAN mirrors 

 1: 0-Cloud [https]                   2: Algeria [https]                
 3: Australia (Canberra) [https]      4: Australia (Melbourne 1) [https]
 5: Australia (Melbourne 2) [https]   6: Australia (Perth) [https]      
 7: Austria [https]                   8: Belgium (Ghent) [https]        
 9: Brazil (PR) [https]              10: Brazil (RJ) [https]            
11: Brazil (SP 1) [https]            12: Brazil (SP 2) [https]          
13: Bulgaria [https]                 14: Chile 1 [https]                
15: Chile 2 [https]                  16: China (Hong Kong) [https]      
17: China (Guangzhou) [https]        18: China (Lanzhou) [https]        
19: China (Shanghai 1) [https]       20: China (Shanghai 2) [https]     
21: Colombia (Cali) [https]          22: Czech Republic [https]         
23: Denmark [https]                  24: East Asia [https]              
25: Ecuador (Cuenca) [https]         26: Ecuador (Quito) [https]        
27: Estonia [https]                  28: France (Lyon 1) [https]        
29: France (Lyon 2) [https]          30: France (Marseille) [https]     
31: France (Montpellier) [https]     32: France (Paris 2) [https]       
33: Germany (Erlangen) [https]       34: Germany (Göttingen) [https]    
35: Germany (Münster) [https]        36: Greece [https]                 
37: Iceland [https]                  38: India [https]                  
39: Indonesia (Jakarta) [https]      40: Ireland [https]                
41: Italy (Padua) [https]            42: Japan (Tokyo) [https]          
43: Japan (Yonezawa) [https]         44: Korea (Busan) [https]          
45: Korea (Gyeongsan-si) [https]     46: Korea (Seoul 1) [https]        
47: Korea (Ulsan) [https]            48: Malaysia [https]               
49: Mexico (Mexico City) [https]     50: Norway [https]                 
51: Philippines [https]              52: Serbia [https]                 
53: Spain (A Coruña) [https]         54: Spain (Madrid) [https]         
55: Sweden [https]                   56: Switzerland [https]            
57: Turkey (Denizli) [https]         58: Turkey (Mersin) [https]        
59: UK (Bristol) [https]             60: UK (London 1) [https]          
61: USA (CA 1) [https]               62: USA (IA) [https]               
63: USA (KS) [https]                 64: USA (MI 1) [https]             
65: USA (OR) [https]                 66: USA (TN) [https]               
67: USA (TX 1) [https]               68: Uruguay [https]                
69: (other mirrors)                  

Selection: 32
essai de l'URL 'https://cran.univ-paris1.fr/src/contrib/Cairo_1.5-9.tar.gz'
Content type 'application/x-gzip' length 86982 bytes (84 KB)
==================================================
downloaded 84 KB

* installing *source* package ‘Cairo’ ...
** package ‘Cairo’ correctement décompressé et sommes MD5 vérifiées
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/local/sage-8/local/bin/pkg-config
checking whether pkg-config knows about cairo... yes
checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender
configure: CAIRO_CFLAGS=-I/usr/local/sage-8/local/include -I/usr/local/sage-8/local/include/freetype2 -I/usr/local/sage-8/local/include -I/usr/local/sage-8/local/include/libpng16 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid
checking if R was compiled with the RConn patch... no
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=-L/usr/local/sage-8/local/lib -lfreetype -lz -lpng16 -lz -lcairo -lXext -lXrender -lX11
checking for library containing deflate... no
checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’
* removing ‘/usr/local/sage-8/local/lib/R/library/Cairo’

Les packages source téléchargés sont dans
    ‘/tmp/Rtmp5RTdn4/downloaded_packages’
Warning message:
In install.packages("Cairo") :
  l'installation du package ‘Cairo’ a eu un statut de sortie non nul
>

Same as before...

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-Seen in 8.7.beta1, but probably from 8.6 (i. e. the switch to using th library):
+On a Debian `buster` machine, seen in 8.7.beta1, but probably from 8.6 (i. e. the switch to using th library):

capabilities() @@ -12,4 +12,6 @@

Similarly, one can't install the R package "Cairo". This entails the loss of creating graphics files from R, which is exceedingly annoying...

+It should be noted that the problem cannot be reproduced on a Debian stretch machine. + One of the strengths of R being its graphical abilities, losing them is, IMNSHO, a critical problem.

dimpase commented 5 years ago
comment:21
checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’

and what's in this config.log?

dimpase commented 5 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-On a Debian `buster` machine, seen in 8.7.beta1, but probably from 8.6 (i. e. the switch to using th library):
+Seen in 8.7.beta1, but probably from 8.6 (i. e. the switch to using th library):

capabilities() @@ -12,6 +12,4 @@

Similarly, one can't install the R package "Cairo". This entails the loss of creating graphics files from R, which is exceedingly annoying...

-It should be noted that the problem cannot be reproduced on a Debian stretch machine.

One of the strengths of R being its graphical abilities, losing them is, IMNSHO, a critical problem.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:22

Replying to @dimpase:

checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’

and what's in this config.log?

This is deleted by R's mechanism :-(. I do not know how to keep the intermediate files).

But I think that the problem exists before Cairo attempts : I should get png(), tiff() and jpeg() at the very minimum...

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:23

Replying to @EmmanuelCharpentier:

Replying to @dimpase:

checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’

and what's in this config.log?

This is deleted by R's mechanism :-(. I do not know how to keep the intermediate files).

But I think that the problem exists before Cairo attempts : I should get png(), tiff() and jpeg() at the very minimum... without cairo !

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago

Configuration log of an attempt to manually install Cairo

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:24

Attachment: config.log

Replying to @dimpase:

checking whether Cairo programs can be compiled... configure: error: Cannot compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’

and what's in this config.log?

Found how to do that : you have to manually download the tarball, untar it and R CMD INSTAZLL Cairo.

See attachment (pretty uninformative...).

embray commented 5 years ago
comment:25

I'm not exactly sure what you expect here.

As with Python, what capabilities get build when you configure and build R is going to depend heavily on what system packages you have installed (and most likely their -devel counterparts), and whether or not the versions of those packages are supported for building whatever feature you care about. I don't think Sage includes SPKGs for all the potential dependencies for something like R (e.g. Cairo).

I don't think this has anything to do either way with the use of rpy2 to access the R interpreter.

embray commented 5 years ago
comment:26

Replying to @dimpase:

I am inclined to close this as worksforme. I think the best way to proceed is to add capability to use system R installation, via adding appropriate spkg-configure.m4 to build/pkgs/r.

+1

One thing this will probably have to do (which I don't think any of our other spkg-configure.m4 files do yet, though it's certainly a possibility I've considered) is output a file containing the results of its findings; for example, the path to the system R. This would need to be output to a file that can be read by the Sage sources, or possibly even just a variable added to the existing src/bin/sage-env-config.in.

(Though I also think, in the spirit of #27040, there should be some kind of src/sage/env_config.py.in which results in a src/sage/env_config.py which is imported by sage.env to add additional package data that can be used by sagelib without first having to source some environment variables.)

dimpase commented 5 years ago
comment:27

Somewhere around line 350 of the log you will a compiler/linker call, and the code it is called on. And the error libcairo.so.2: undefined symbol: FT_Done_MM_Var - same as in the comment 2 above.

The reason is that libfreetype shipped with Sage is older (2.8) than the one on your system (2.9), and it does not even have FT_Done_MM_Var, whereas cairo expects it to be available. So the wrong library is pulled in, resulting in this error. For instance, upgrading freetype to version 2.9.1 should fix this, at least on buster. Whether such an upgrade will break cairo on older systems, is a question I don't know the answer to.

It could also be an R or Cairo bug, I don't know.

For sure this has absolutely nothing to do with rpy2.

embray commented 5 years ago
comment:28

libfreetype is another one that should be high priority to get an spkg-configure.m4. This is not the first time I've encountered an incompatibility with it over that exact same symbol, though I forget the rest of the context.

dimpase commented 5 years ago
comment:29

I'd also say the freetype upgrade should include spkg-configure.m4 to pull in the system library if one is available - this would preclude this sort of mess we see here, that comes from duplicate libs being pulled from different places...

See #27168 for a followup.

dimpase commented 5 years ago
comment:30

Replying to @embray:

libfreetype is another one that should be high priority to get an spkg-configure.m4. This is not the first time I've encountered an incompatibility with it over that exact same symbol, though I forget the rest of the context.

I've beaten you to opening #27168 :-)

slel commented 5 years ago
comment:31

Meanwhile I opened #27169 to upgrade to freetype 2.9.1. Will post a branch soon.

slel commented 5 years ago
comment:32

Note that #27040 was initially opened as "R 3.4.2 has no graphics capabilities" and its summary was later changed to "Upgrade freetype to 2.8.1".

slel commented 5 years ago
comment:33

Please check if upgrading to freetype 2.9.1 (#27169) fixes the problem described here.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago
comment:34

27169 fixes this with either R 3.4.4 (current now) or R 3.5.2 (as prepared in #25674). This can be considered as a duplicate of #27169.

==>positive_review with a invalid/duplicate/wontfix milestone.

7822f248-ba56-45f1-ab3d-4de7482bdf9f commented 5 years ago

Reviewer: Emmanuel Charpentier

embray commented 5 years ago
comment:36

Presuming these are all correctly reviewed as either duplicate, invalid, or wontfix.