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use of undeclared identifier 'timespec_get' in termux R-4.1.2 #161

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leechaowen opened this issue Dec 13, 2021 · 0 comments
Open

use of undeclared identifier 'timespec_get' in termux R-4.1.2 #161

leechaowen opened this issue Dec 13, 2021 · 0 comments

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@leechaowen
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I fail to install later in termux . i took one night to view the exists issues relate the topic timespec, the way is write something in this file Makevars in the path ~/.R

i had tried one by one , not success. Could you hlep me and give some suggestions? Thanks.

termux version:0.117
android version :11
R version: R version 4.1.2 (2021-11-01) Platform: aarch64-unknown-linux-gnu (64-bit)
g++ version : clang version 13.0.0

> install.packages("later")
trying URL 'https://mirrors.ustc.edu.cn/CRAN/src/contrib/later_1.3.0.tar.gz'
Content type 'application/octet-stream' length 63785 bytes (62 KB)
==================================================
downloaded 62 KB

* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag not needed.
** libs
g++ -std=gnu++11 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c callback_registry.cpp -o callback_registry.o
In file included from callback_registry.cpp:6:
In file included from ./callback_registry.h:10:
./threadutils.h:129:9: error: use of undeclared identifier 'timespec_get'; did you mean 'timespec'?
    if (timespec_get(&ts, TIME_UTC) != TIME_UTC) {
        ^
/data/data/com.termux/files/usr/include/semaphore.h:37:8: note: 'timespec' declared here
struct timespec;
       ^
1 error generated.
make: *** [/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/etc/Makeconf:175: callback_registry.o] Error 1
ERROR: compilation failed for package ‘later’
* removing ‘/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/library/later’

The downloaded source packages are in
        ‘/data/data/com.termux/files/usr/tmp/RtmpZ2DGtQ/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("later") :
  installation of package ‘later’ had non-zero exit status
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-unknown-linux-gnu (64-bit)

Matrix products: default
BLAS:   /data/data/com.termux/files/usr/local/R-4.1.2/lib/R/lib/libRblas.so
LAPACK: /data/data/com.termux/files/usr/local/R-4.1.2/lib/R/lib/libRlapack.so

locale:
[1] C.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
>

g++ version

~ $ g++ --version
clang version 13.0.0
Target: aarch64-unknown-linux-android24
Thread model: posix
InstalledDir: /data/data/com.termux/files/usr/bin
~ $

termux-info


~ $ termux-info
Application version:
0.117
Packages CPU architecture:
aarch64
Subscribed repositories:
# sources.list
deb https://mirrors.tuna.tsinghua.edu.cn/termux/apt/termux-main stable main
# game-repo (sources.list.d/game.list)
deb https://mirrors.tuna.tsinghua.edu.cn/termux/apt/termux-games games stable
# science-repo (sources.list.d/science.list)
deb https://mirrors.tuna.tsinghua.edu.cn/termux/apt/termux-science science stable
# sources.list.d/pointless.list
deb https://its-pointless.github.io/files/21 termux extras
Updatable packages:
All packages up to date
Android version:
11
Kernel build information:
Linux localhost 4.19.113-perf-g41a3186f100e #1 SMP PREEMPT Wed Oct 27 23:23:53 CST 2021 aarch64 Android
Device manufacturer:
Xiaomi
Device model:
M2012K11AC
~ $

the default Makeconf settings:


.../R/etc $ pwd
/data/data/com.termux/files/usr/local/R-4.1.2/lib/R/etc
.../R/etc $ cat Makeconf
# etc/Makeconf.  Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure  '--enable-R-shlib' '--prefix=/data/data/com.termux/files/usr/local/R-4.1.2' '--with-x=no'

## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk

AR = ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY = -fvisibility=hidden
CC = gcc
CFLAGS = -g -O2 $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = g++ -std=gnu++14
CXXFLAGS = -g -O2 $(LTO)
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11FLAGS = -g -O2 $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = g++
CXX14FLAGS = -g -O2 $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = g++
CXX17FLAGS = -g -O2 $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX20 = g++
CXX20FLAGS = -g -O2 $(LTO)
CXX20PICFLAGS = -fpic
CXX20STD = -std=gnu++20
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
## should be used by packges for dylibs, but at the time of writing was not
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F_VISIBILITY = -fvisibility=hidden
## FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran
FCFLAGS = -g -O2 $(LTO_FC)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -g -O2 $(LTO_FC)
FLIBS =  -lgfortran -lm -ldl
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /data/data/com.termux/files/usr/opt/openjdk/bin/jar
JAVA = /data/data/com.termux/files/usr/opt/openjdk/bin/java
JAVAC = /data/data/com.termux/files/usr/opt/openjdk/bin/javac
JAVAH =
## JAVA_HOME might be used in the next three.
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /data/data/com.termux/files/usr/opt/openjdk
JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/server
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
LDFLAGS = -L/usr/local/lib
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR
LIBS = -L/data/data/com.termux/files/usr/lib -lpcre2-8 -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
## set for --enable-lto, --enable-lto=check
LTO =
LTO_FC =
LTO_LD =
## set for --enable-lto=R, used in INSTALL
LTO_OPT =
LTO_FC_OPT =
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
NM = /data/data/com.termux/files/usr/bin/nm -B
OBJC = gcc
OBJCFLAGS = -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = ranlib
SAFE_FFLAGS = -g -O2
SED = /data/data/com.termux/files/usr/bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared# $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD)
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared# $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD)
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared# $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD)
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared# $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD)
SHLIB_CXX20LD = $(CXX20) $(CXX20STD)
SHLIB_CXX20LDFLAGS = -shared# $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD)
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared# $(FCFLAGS) $(FPICFLAGS)
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
## used for add-on packages linked by C
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
## used for standard packages
SHLIB_LDFLAGS_R = -shared# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
SHLIB_LIBADD =
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS = -fopenmp
STRIP_STATIC_LIB = strip --strip-debug
STRIP_SHARED_LIB = strip --strip-unneeded
TCLTK_CPPFLAGS =
TCLTK_LIBS =
YACC = bison -y

## for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(R_HOME)/lib$(R_ARCH)/libR.a" -Wl,--no-whole-archive $(BLAS_LIBS) $(FLIBS)  $(LIBINTL) -lreadline  $(LIBS)

## These are recorded as macros for legacy use in packages
## set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS =
##  was formerly set on HP-UX
R_XTRA_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEBUG
## currently unset
R_XTRA_CXXFLAGS =
## used for gfortran in R > 3.6.0
R_XTRA_FFLAGS = -fno-optimize-sibling-calls

## SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
## SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS =  $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_CXXFLAGS =  $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = -fno-optimize-sibling-calls $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS)
ALL_FCFLAGS = -fno-optimize-sibling-calls $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)

.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o

.c.o:
        $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
        @echo "making $@ from $<"
        @$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
        $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
        $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
        @echo "making $@ from $<"
        @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
        @echo "making $@ from $<"
        @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
        $(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
        @echo "making $@ from $<"
        @$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@
.mm.o:
        $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
        $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
        $(FC) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
        $(FC) $(ALL_FCFLAGS) -c  $< -o $@
.f90.o:
        $(FC) $(ALL_FCFLAGS) -c  $< -o $@
.../R/etc $
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