Missing <R_ext/sggc-app.h>

[radfordneal]

Missing

from pqr.

[dcegielka]

diff -urN pqR.orig/src/include/Rinternals.h pqR/src/include/Rinternals.h
--- pqR.orig/src/include/Rinternals.h   2019-02-13 22:17:53.000000000 +0100
+++ pqR/src/include/Rinternals.h        2019-02-13 22:18:57.000000000 +0100
@@ -81,8 +81,9 @@

 #ifndef NEED_SGGC_FUNCTIONS
 #define SGGC_NO_FUNCTIONS
-#endif
+#else
 #include <R_ext/sggc-app.h>
+#endif


 #define ConstExtern extern    /* Used for variables defined in const-objs.c */

[dcegielka]

...it need a correct designation where SGGC is used:

x86_64-apple-darwin18-gcc-8.2.0 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include    -fPIC  -march=haswell -pipe -s -O3 -march=native -mtune=native -ffp-contract=off -fno-stack-protector -DNDEBUG  -c add_class.c -o add_class.o
In file included from add_class.c:2:
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:197:9: error: unknown type name 'sggc_cptr_t'
 typedef sggc_cptr_t SEXP32;
         ^~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h: In function 'LOGICAL':
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:502:26: error: 'SGGC_DATA_ALIGNMENT' undeclared (first use in this function); did you mean 'DATAPTR_WITH_ALIGNMENT'?
             (DATAPTR(x), SGGC_DATA_ALIGNMENT, SGGC_DATA_ALIGNMENT_OFFSET)
                          ^~~~~~~~~~~~~~~~~~~
(...)

[radfordneal]

Could you tell me some details of what you're doing? I gather that this is a problem that arose when you tried to install the "xts" package. Is that right? What version of pqR were you using? The most recent stable one, pqR-2019-01-25? You seem to be on a mac, but which version of macOS are you running? Are you trying to use clang or a gcc installed from homebrew (or somewhere else?)? Are you just running bin/R from the build directory, or did you try to install pqR as the system default R, and after that use it to install xts?

I've tried pqR-2019-01-25 on an El Capitan system, using gcc-8 from homebrew, running in the build directory (not installing on the system), and had no problem installing "xts". So it's not a general pqR problem...

[dcegielka]

1. version: pqR version 2.15.1 (2019-01-25)
2. Mojave MacOS
3. gcc-8.2 from MacPorts.
4. R CMD INSTALL xts

xts uses Rinternals.h

https://github.com/joshuaulrich/xts/blob/master/src/add_class.c#L24
https://github.com/joshuaulrich/xts/blob/master/src/any.c#L24

If the header R_ext/sggc-app.h is not available, we simply have an error. I noticed that CGGC is used to compress pointers (in pqR only).

[dcegielka]

Here you have old xts version 0.6-8:

https://github.com/joshuaulrich/xts/tree/8f75b75dbea55ad7ddc1c99056b947f41a55f53a

https://github.com/joshuaulrich/xts/blob/8f75b75dbea55ad7ddc1c99056b947f41a55f53a/src/add_class.c#L24

I'm pretty sure you'll get a error even for this old version: R_ext/sggc-app.h header is not available in /Library/Frameworks/R.framework/Resources/include/R_ext/.

[radfordneal]

From the references to /Library/Frameworks/R, I assume you must have done a "make install" to install pqR as the "system" R, and are then running it as that. Have you tried instead just running bin/R in the build directory? And just running it interactively and then typing install.packages("xts")? I'm not clear on where you've gotten the xts package from. In pqR, install.packages will get it from the pqR repository. That's what works for me.

My best guess at the moment is that the problem relates to setup for paths to find include files when pqR is installed as the system R, but I won't have time to check that out until later tonight.

[dcegielka]

Yes, install.packages("xts") works from pqR build dir, but it fails from system pqR (after make install).

> install.packages("xts")
also installing the dependency ‘zoo’

trying URL 'ftp://price.utstat.utoronto.ca/src/contrib/zoo_1.7-10.tar.gz'
ftp data connection made, file length 813020 bytes
opened URL
==================================================
downloaded 793 Kb

trying URL 'ftp://price.utstat.utoronto.ca/src/contrib/xts_0.9-4.tar.gz'
ftp data connection made, file length 459849 bytes
opened URL
==================================================
downloaded 449 Kb

* installing *source* package ‘zoo’ ...
** package ‘zoo’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin18-gcc-8.2.0 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -march=haswell -pipe -s -O3 -march=native -mtune=native -ffp-contract=off -fno-stack-protector -DNDEBUG  -c coredata.c -o coredata.o
In file included from coredata.c:24:
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:85:10: fatal error: R_ext/sggc-app.h: No such file or directory
 #include <R_ext/sggc-app.h>
          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [coredata.o] Error 1
ERROR: compilation failed for package ‘zoo’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zoo’
ERROR: dependency ‘zoo’ is not available for package ‘xts’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/xts’

[dcegielka]

@radfordneal

My best guess at the moment is that the problem relates to setup for paths to find include files when pqR is installed as the system R

sggc headers are not installed, so CFLAGS+=-Ipath will not help here.:

# system pqR: /Library/Frameworks/R.framework/Versions/2.15
# find /Library/Frameworks/R.framework/ -name sggc-app.h

# and in build dir:
# find . -name sggc-app.h
./pqR/src/extra/sggc/test-sggc4/sggc-app.h
./pqR/src/extra/sggc/test-sggc3/sggc-app.h
./pqR/src/extra/sggc/interp/sggc-app.h
./pqR/src/extra/sggc/test-sggc2/sggc-app.h
./pqR/src/extra/sggc/test-sggc5/sggc-app.h
./pqR/src/extra/sggc/test-sggc7/sggc-app.h
./pqR/src/extra/sggc/test-sggc6/sggc-app.h
./pqR/src/extra/sggc/test-sggc1/sggc-app.h
./pqR/src/extra/sggc/sggc-app.h
./build/include/R_ext/sggc-app.h
./build/src/include/R_ext/sggc-app.h

[radfordneal]

Yes, the sggc and sbset header files are not in the R_ext subdirectory for the installed version. As you may guess, I usually run pqR from the build directory, since I'm often running various different versions of both pqR and R Core implementations, and switching around is more convenient that way.

I'll need to fix "make install" to copy these files correctly to the install directory. In the meantime, it seems that the following workaround is sufficient: After doing "sudo make install", change to the include/R_ext subdirectory of the build directory, and issue the command

sudo cp sbset*.h sggc*.h /Library/Frameworks/R.framework/Headers/R_ext

After doing this, install.packages("xts") works for me. This is on a Mojave system.

Thanks for reporting this problem. Please let me know if the workaround doesn't fix it for you.

[dcegielka]

Of course, copying headers solves the problem.
btw. I'm surprised how little memory pqR consumes.
Thx

[radfordneal]

This is now fixed in a new release, pqR-2019-02-19.