Installation fails on Termux #349

rrodrigueznt · 2021-10-03T08:18:42Z

Hi! Installing from source on R 4.1.0 on Termux, I get this error:

id.cc:109:17: error: use of undeclared identifier 'getpwent'; did you mean 'getgrent'?                            passwd* pwd = getpwent();                                             ^~~~~~~~                                                getgrent                                /data/data/com.termux/files/usr/include/grp.h:55:22: note: 'getgrent' declared here                             static struct group* getgrent(void) { return 0; }                            ^                                  id.cc:109:11: error: cannot initialize a variable of type 'passwd *' with an rvalue of type 'struct group *'      passwd* pwd = getpwent();                                       ^     ~~~~~~~~~~                              id.cc:113:11: error: use of undeclared identifier 'getpwent'; did you mean 'getgrent'?                              pwd = getpwent();                                             ^~~~~~~~                                                getgrent                                      /data/data/com.termux/files/usr/include/grp.h:55:22: note: 'getgrent' declared here                             static struct group* getgrent(void) { return 0; }                            ^                                  id.cc:113:11: error: incompatible pointer types assigning to 'passwd *' from 'struct group *'                       pwd = getpwent();                                             ^~~~~~~~~~                                    4 errors generated.                                     make: *** [/data/data/com.termux/files/usr/lib/R/etc/Makeconf:173: id.o] Error 1                                make: *** Waiting for unfinished jobs....               ERROR: compilation failed for package ‘fs’              * removing ‘/data/data/com.termux/files/usr/lib/R/library/fs’

Please, any idea? Thanks!

The text was updated successfully, but these errors were encountered:

jimhester · 2021-10-04T15:27:05Z

It looks like there are a couple of patches at https://github.com/its-pointless/gcc_termux/blob/master/R-patches/rcran-fs-id.cc.patch and https://github.com/its-pointless/gcc_termux/blob/master/R-patches/rcran-fs-Makevars.patch, did you apply those?

rrodrigueznt · 2021-10-05T05:02:24Z

Working on that! Thanks!

rrodrigueznt · 2021-10-06T01:10:41Z

Working on that! Thanks!

I'm failing in my attempts of applying both patches. Here what I get:

~ $ git apply rcran-fs-Makevars.patch --verbose --ignore-whitespace
rcran-fs-Makevars.patch:5: trailing whitespace.
HOST :=
Checking patch fs/src/Makevars...
error: while searching for:
PKG_LIBS += -lkvm
endif
ifeq ($(UNAME), Linux)
OBJECTS +=  bsd/setmode.o bsd/strmode.o bsd/reallocarray.o
endif


error: patch failed: fs/src/Makevars:18
error: fs/src/Makevars: patch does not apply
~ $

~ $ git apply rcran-fs-id.cc.patch --verbose --ignore-whitespace
Checking patch fs/src/id.cc...
error: while searching for:
List users_() {
  std::vector<std::string> names;
  std::vector<int> ids;
#ifndef __WIN32
  passwd* pwd = getpwent();
  while (pwd != NULL) {
    names.push_back(pwd->pw_name);

error: patch failed: fs/src/id.cc:69
error: fs/src/id.cc: patch does not apply
~ $

I guess both patches are outdated and shouldn't work as they are without editing and updating them. Please, am I correct?
I'm new to git. Please, is there anyway of getting updated patches? I'm not sure if my question has any sense. Thanks!

jimhester · 2021-10-06T12:11:01Z

I think you could look at what the patches do and then apply the edits manually to the current sources.

leechaowen · 2021-11-10T09:00:18Z

i have compiled r-base 4.1.2 source code in termux for my phone today. how to fix such issue? Thanks.

> install.packages("fs")
trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/fs_1.5.0.tar.gz'
Content type 'application/octet-stream' length 796244 bytes (777 KB)
==================================================
downloaded 777 KB

* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c dir.cc -o dir.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c error.cc -o error.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c file.cc -o file.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c fs.cc -o fs.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c getmode.cc -o getmode.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c id.cc -o id.o
id.cc:109:17: error: use of undeclared identifier 'getpwent'; did you mean 'getgrent'?
  passwd* pwd = getpwent();
                ^~~~~~~~
                getgrent
/data/data/com.termux/files/usr/include/grp.h:55:22: note: 'getgrent' declared here
static struct group* getgrent(void) { return 0; }
                     ^
id.cc:109:11: error: cannot initialize a variable of type 'passwd *' with an rvalue of type 'struct group *'
  passwd* pwd = getpwent();
          ^     ~~~~~~~~~~
id.cc:113:11: error: use of undeclared identifier 'getpwent'; did you mean 'getgrent'?
    pwd = getpwent();
          ^~~~~~~~
          getgrent
/data/data/com.termux/files/usr/include/grp.h:55:22: note: 'getgrent' declared here
static struct group* getgrent(void) { return 0; }
                     ^
id.cc:113:11: error: incompatible pointer types assigning to 'passwd *' from 'struct group *'
    pwd = getpwent();
          ^~~~~~~~~~
4 errors generated.
make: *** [/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/etc/Makeconf:173: id.o] Error 1
ERROR: compilation failed for package ‘fs’
* removing ‘/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/fs’

The downloaded source packages are in
        ‘/data/data/com.termux/files/usr/tmp/RtmpadY3y2/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("fs") :
  installation of package ‘fs’ had non-zero exit status

leechaowen · 2021-11-15T02:48:18Z

It looks like there are a couple of patches at https://github.com/its-pointless/gcc_termux/blob/master/R-patches/rcran-fs-id.cc.patch and https://github.com/its-pointless/gcc_termux/blob/master/R-patches/rcran-fs-Makevars.patch, did you apply those?

how to use these patches? i have no knowledge about how to run patches. i think it's better update fs for termux. Could you mind take some time update it ? Thanks .

gaborcsardi · 2021-12-08T13:19:42Z

I don't have termux, does libuv compile on termux?

I can consider patches to make fs compile on termux.

leechaowen · 2021-12-09T03:24:33Z

I don't have termux, does libuv compile on termux?

I can consider patches to make fs compile on termux.

Thanks your support. i run pkg install libuv in termux, show below.

~ $ pkg install libuv
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libuv is already the newest version (1.42.0-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
~ $

rrodrigueznt · 2021-12-14T19:49:48Z

Hi! @gaborcsardi, @jimhester, it seems that the change introduced by https://github.com/its-pointless/gcc_termux/blob/master/R-patches/rcran-fs-id.cc.patch is simple and easy to introduce at line 108 of the current version of id.cc in https://github.com/r-lib/fs/blob/main/src/id.cc. I guess I should fork the project, edit the file, and submit changes to the original repository with pull requests. Please, am I right? Thanks!

gaborcsardi · 2021-12-14T20:15:43Z

Yeah, please do that. Thanks!

rrodrigueznt · 2021-12-15T17:39:48Z

Yeah, please do that. Thanks!

Done, I think! The message about getpwent() has gone. And using this Makevars:

https://github.com/rrodrigueznt/fs/blob/8e60e9e84fc244d9060f53b8d15cb4628d5751c3/src/Makevars

Here what I get now:

~ $ R CMD INSTALL fs --preclean
* installing to library ‘/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library’
* installing *source* package ‘fs’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c dir.cc -o dir.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c error.cc -o error.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c file.cc -o file.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c fs.cc -o fs.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c getmode.cc -o getmode.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c id.cc -o id.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c init.cc -o init.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c link.cc -o link.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c path.cc -o path.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c utils.cc -o utils.o
g++ -std=gnu++14 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c unix/getmode.cc -o unix/getmode.o
gcc -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c bsd/setmode.c -o bsd/setmode.o
gcc -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c bsd/strmode.c -o bsd/strmode.o
gcc -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread  -I/usr/local/include   -fpic  -g -O2  -c bsd/reallocarray.c -o bsd/reallocarray.o
g++ -std=gnu++14 -shared -L/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/lib -L/usr/local/lib -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv-1.38.1/.libs/libuv.a -pthread -lbthread -L/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/lib -lR
installing to /data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/00LOCK-fs/00new/fs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘fs’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/00LOCK-fs/00new/fs/libs/fs.so':
  dlopen failed: cannot locate symbol "uv__pthread_sigmask" referenced by "/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/00LOCK-fs/00new/fs/libs/fs.so"...
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/fs’
~ $

I don't find information about uv__pthread_sigmask.

Please, any idea? Thanks!

gaborcsardi · 2021-12-15T18:44:40Z

pthread is lacking on Termux, see here: r-lib/cli#358 (comment) and the comments below.

rrodrigueznt · 2021-12-17T07:21:32Z

Still working hard to understand where I am lost, I founded this pthread-sigmask.patch

rrodrigueznt · 2021-12-18T19:59:07Z

pthread is lacking on Termux, see here: r-lib/cli#358 (comment) and the comments below.

I'm still lost. I'm afraid that I've no skills enough to understand why you are pointing me to my own comments in a different issue, and you say that pthread is lacking on Termux.

In Termux I find:

~ $ ls ../usr/lib/libpthr*                           
../usr/lib/libpthread.so
~ $ ls ../usr/include/pthread*
../usr/include/pthread.h
~ $

Please, does it mean that pthread is available on Termux? Also, here what I get when I try to list the symbols available in libpthread.so:

~ $ nm -gD ../usr/lib/libpthread.so
nm: ../usr/lib/libpthread.so: file format not recognized
~ $

However, I'm able to list them for any other installed library. Please, does it make any sense to you? Any further help will be truly appreciated! Thanks!

gaborcsardi · 2021-12-18T21:05:30Z

Because libpthread is missing some functions on termux, that are provided by libbthread. Maybe this is why uv__pthread_sigmask is missing for you. But it is just a guess, I don't have a termux system, so I can't actually try any of this, sorry.

kurokirasama · 2022-05-28T02:05:16Z

someone has the right patches, the mentioned before do not work for me?

yfyang86 · 2024-03-23T09:22:00Z

compile the libuv-1.44.2 manually should work. Although it is an ugly fix.

download the R package and extract it;
patch whatever the above threads told;
Compile libuv manunally

rm -rf fs/src/libuv-1.44.2`
cd fs/src
wget https://codeload.github.com/libuv/libuv/tar.gz/refs/tags/v1.44.2
tar vxf v1.44.2
cd libuv-1.44.2
mkdir .libs
cd .libs
cmake ..
make
cp -rf libuv* /data/data/com.termux/files/usr/lib

Change srv/Makevars

UNAME := $(shell uname)

LIBUV := libuv-1.44.2

PKG_LIBS = ./$(LIBUV)/.libs/libuv.so -pthread

SOURCES = $(wildcard *.cc unix/*.cc)
OBJECTS = $(SOURCES:.cc=.o)

ifeq ($(UNAME), SunOS)
PKG_LIBS += -lkstat -lsendfile -lsocket -lxnet
OBJECTS +=  bsd/setmode.o bsd/strmode.o bsd/reallocarray.o
endif
ifeq ($(UNAME), FreeBSD)
PKG_LIBS += -lkvm
endif
ifeq ($(UNAME), OpenBSD)
PKG_LIBS += -lkvm
endif
ifneq ($(filter $(UNAME), Linux AIX OS400),)
OBJECTS +=  bsd/setmode.o bsd/strmode.o bsd/reallocarray.o
endif

PKG_CPPFLAGS = -I./$(LIBUV)/include -I. -pthread

all: $(SHLIB)

$(SHLIB): $(LIBUV)/.libs/libuv.so

.PHONY: shlib-clean clean

# shlib-clean: clean

clean:
	$(MAKE) --directory=$(LIBUV) distclean
	rm -f $(OBJECTS)

INSTALL R package

In the folder the fs package locates

R CMD INSTALL fs

rrodrigueznt changed the title ~~Installation fails in Termux~~ Installation fails on Termux Oct 3, 2021

rrodrigueznt mentioned this issue Oct 3, 2021

Error when installing fs on R running on Termux its-pointless/its-pointless.github.io#87

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gaborcsardi added the help wanted ❤️ we'd love your help! label Dec 8, 2021

gaborcsardi mentioned this issue Dec 8, 2021

error: use of undeclared identifier 'getpwent' #351

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Installation fails on Termux #349

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Installation fails on Termux #349

Installation fails on Termux #349

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