Error installing from source in R under Termux

[rrodrigueznt]

Hi! Installation in this environment:

~ $ radian --version
radian version: 0.5.12
r executable: /data/data/com.termux/files/usr/lib/R/bin/R
r version: 4.1.0
python executable: /data/data/com.termux/files/usr/bin/python3
python version: 3.9.7
~ $

Fails with the error:

* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked                                                     ** using staged installation
** libs                                                 
gcc -I"/data/data/com.termux/files/usr/lib/R/include" -DNDEBUG   -I/data/data/com.termux/files/usr/include   -fpic  -g -O2  -c cleancall.c -o cleancall.o               
gcc -I"/data/data/com.termux/files/usr/lib/R/include" -DNDEBUG   -I/data/data/com.termux/files/usr/include   -fpic  -g -O2  -c errors.c -o errors.o                     
gcc -I"/data/data/com.termux/files/usr/lib/R/include" -DNDEBUG   -I/data/data/com.termux/files/usr/include   -fpic  -g -O2  -c init.c -o init.o                         
gcc -I"/data/data/com.termux/files/usr/lib/R/include" -DNDEBUG   -I/data/data/com.termux/files/usr/include   -fpic  -g -O2  -c progress-altrep.c -o progress-altrep.o   
gcc -I"/data/data/com.termux/files/usr/lib/R/include" -DNDEBUG   -I/data/data/com.termux/files/usr/include   -fpic  -g -O2  -c progress.c -o progress.o                 
gcc -I"/data/data/com.termux/files/usr/lib/R/include" -DNDEBUG   -I/data/data/com.termux/files/usr/include   -fpic  -g -O2  -c thread.c -o thread.o                     
thread.c:29:3: warning: implicit declaration of function 'pthread_setcanceltype' is invalid in C99 [-Wimplicit-function-declaration]                                      pthread_setcanceltype(PTHREAD_CANCEL_ASYNCHRONOUS, &old);                                                       ^                                                     
thread.c:29:25: error: use of undeclared identifier 'PTHREAD_CANCEL_ASYNCHRONOUS'                                 pthread_setcanceltype(PTHREAD_CANCEL_ASYNCHRONOUS, &old);                                                                             ^                               
thread.c:80:11: warning: implicit declaration of function 'pthread_cancel' is invalid in C99 [-Wimplicit-function-declaration]                                              
ret = pthread_cancel(tick_thread);                            ^                                             2 warnings and 1 error generated.                       
make: *** 
[/data/data/com.termux/files/usr/lib/R/etc/Makeconf:168: thread.o] Error 1                            
make: *** Waiting for unfinished jobs....               
ERROR: compilation failed for package ‘cli’             
* removing ‘/data/data/com.termux/files/usr/lib/R/library/cli’                                                  
ERROR: dependency ‘cli’ is not available for package ‘pillar’                                                   
* removing ‘/data/data/com.termux/files/usr/lib/R/library/pillar’                                               
ERROR: dependency ‘pillar’ is not available for package ‘tibble’                                                
* removing ‘/data/data/com.termux/files/usr/lib/R/library/tibble’                                                                                                       
The downloaded source packages are in                           ‘/data/data/com.termux/files/usr/tmp/RtmpX0GyDU/downloaded_packages’                                    
Updating HTML index of packages in '.Library'           
Making 'packages.html' ... done                         
Warning messages:                                       
1: In install.packages("tibble") :                        
installation of package ‘cli’ had non-zero exit status
2: In install.packages("tibble") :                        
installation of package ‘pillar’ had non-zero exit status                                                     3: In install.packages("tibble") :                        
installation of package ‘tibble’ had non-zero exit status                                                                                                             r$>

Same error when I use R console.

Please, any clue? Thanks!

[gaborcsardi]

Can you try this? its-pointless/gcc_termux#126 (comment)

[rrodrigueznt]

Thanks. I'm not sure if I'm following the instructions correctly. Here what I have:

~ $ echo $PKG_LIBS
-lbthread
~ $

Same error. Please, any idea? Thanks!

[gaborcsardi]

The same exact error? Did you install libbthread? You need to set PKG_LIBS in the ~/.R/Makevars file.

[rrodrigueznt]

I hope this describe what I'm doing:

~ $ ls ../usr/lib/libb*
../usr/lib/libbfd-2.37.so  ../usr/lib/libblkid.so
../usr/lib/libbfd.a        ../usr/lib/libbthread.so
../usr/lib/libbfd.la       ../usr/lib/libbz2.so
../usr/lib/libbfd.so       ../usr/lib/libbz2.so.1.0
../usr/lib/libblas.so      ../usr/lib/libbz2.so.1.0.8

~ $ head cli/src/thread.c

#include "cli.h"

#ifdef ANDROID
#include <bthread.h>
#endif

#include <pthread.h>
#include <time.h>
#ifndef _WIN32

~ $ cat .R/Makevars
export PKG_LIBS="lbthread"
~ $

I think the error is the same:

thread.c:33:25: error: use of undeclared identifier 'PTHREAD_CANCEL_ASYNCHRONOUS'
  pthread_setcanceltype(PTHREAD_CANCEL_ASYNCHRONOUS, &old);

Only the line changed after editing thread.c.

[gaborcsardi]

This works for me:

#include "cli.h"

#include <pthread.h>
#ifdef __TERMUX__
#include <bthread.h>
#endif

#include <time.h>
#ifndef _WIN32
#include <signal.h>
#endif

and ~/.R/Makevars has to be

PKG_LIBS=-lbthread

[gaborcsardi]

I can update thread.c in cli, but the Makevars is tricker because cli does not currently has a Makevars file, so I would need to generate one from configure.

Btw. set ~/.R/Makevars like this, note the plus sign:

PKG_LIBS+=-lbthread

then it should not break other packages. So if you leave this Makevars file in place then you'll not need anything special for the next version of cli.

[rrodrigueznt]

It is working like a charm! Cli already installed. Other packages on their way! Thanks!

It is still hard to me to understand what I did following your advise. I'll keep reading and, hopefully, when I face a new issue I'll be able to take into account what I learned here!

Allow me to add here a link to a Stack Overflow thread I consider relevant for this issue:

https://stackoverflow.com/questions/43597632/understanding-the-contents-of-the-makevars-file-in-r-macros-variables-r-ma

Cheers!

[gaborcsardi]

Let's keep this open, until I fix thread.c.