Long story short, I'm on Kali rolling 2021.3 and I'm trying to build bison and bison requires m4. I followed this and someone else had the same problem as I am. But while building m4, I'm getting:
freading.c:44:3: error: #error "Please port gnulib freading.c to your platform!"
Here's all my steps with m4 and some truncated output from making m4:
wget ftp://ftp.gnu.org/gnu/m4/m4-1.4.10.tar.gz
Untar and cd in to extracted directory:
./configure --prefix=/opt/m4
make
Then receiving this output(I added the number lines):
68 } | sed '/""/d' > configmake.h-t
69 mv configmake.h-t configmake.h
70 make all-am
71 make[2]: Entering directory '/home/kali/Downloads/m4-1.4.10/lib'
72 gcc -I. -g -O2 -MT freading.o -MD -MP -MF .deps/freading.Tpo -c -o freading.o freading.c
73 freading.c: In function ‘freading’:
74 freading.c:44:3: error: #error "Please port gnulib freading.c to your platform!"
75 44 | #error "Please port gnulib freading.c to your platform!"
76 | ^~~~~
77 make[2]: *** [Makefile:598: freading.o] Error 1
78 make[2]: Leaving directory '/home/kali/Downloads/m4-1.4.10/lib'
79 make[1]: *** [Makefile:451: all] Error 2
80 make[1]: Leaving directory '/home/kali/Downloads/m4-1.4.10/lib'
81 make: *** [Makefile:421: all-recursive] Error 1
Does anyone know how I should handle this kind of error, especially around m4?
Related
I am getting the following error when trying to install the lme4 package in R.
install.packages("lme4")
Installing package into ‘/usr/local/lib/R/4.2/site-library’
(as ‘lib’ is unspecified)
also installing the dependency ‘minqa’
trying URL 'https://cloud.r-project.org/src/contrib/minqa_1.2.4.tar.gz'
Content type 'application/x-gzip' length 53548 bytes (52 KB)
==================================================
downloaded 52 KB
trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-29.tar.gz'
Content type 'application/x-gzip' length 3306026 bytes (3.2 MB)
==================================================
downloaded 3.2 MB
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/local/opt/gcc/bin/gfortran -fno-optimize-sibling-calls -fPIC -g -O2 -c altmov.f -o altmov.o
altmov.f:42:72:
42 | 10 HCOL(K)=ZERO
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
altmov.f:45:72:
45 | DO 20 K=1,NPT
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 20 at (1)
altmov.f:46:72:
46 | 20 HCOL(K)=HCOL(K)+TEMP*ZMAT(K,J)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
altmov.f:53:72:
53 | 30 GLAG(I)=BMAT(KNEW,I)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 30 at (1)
altmov.f:57:72:
57 | 40 TEMP=TEMP+XPT(K,J)*XOPT(J)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)
altmov.f:59:72:
59 | DO 50 I=1,N
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 50 at (1)
altmov.f:60:72:
60 | 50 GLAG(I)=GLAG(I)+TEMP*XPT(K,I)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 50 at (1)
altmov.f:76:72:
76 | 60 DISTSQ=DISTSQ+TEMP*TEMP
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 60 at (1)
altmov.f:172:72:
172 | 90 XNEW(I)=DMAX1(SL(I),DMIN1(SU(I),TEMP))
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 90 at (1)
altmov.f:237:72:
237 | 140 GW=GW+GLAG(I)*W(I)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 140 at (1)
altmov.f:248:72:
248 | 150 TEMP=TEMP+XPT(K,J)*W(J)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 150 at (1)
altmov.f:249:72:
249 | 160 CURV=CURV+HCOL(K)*TEMP*TEMP
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 160 at (1)
altmov.f:255:72:
255 | 170 XALT(I)=DMAX1(SL(I),DMIN1(SU(I),TEMP))
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 170 at (1)
altmov.f:268:72:
268 | 180 W(N+I)=XALT(I)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 180 at (1)
altmov.f:275:72:
275 | 190 XALT(I)=W(N+I)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 190 at (1)
clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'. Try: 'clang (LLVM option parsing) --help'
clang (LLVM option parsing): Did you mean '--x86-slh-loads=false'?
make: *** [altmov.o] Error 1
ERROR: compilation failed for package ‘minqa’
* removing ‘/usr/local/lib/R/4.2/site-library/minqa’
ERROR: dependency ‘minqa’ is not available for package ‘lme4’
* removing ‘/usr/local/lib/R/4.2/site-library/lme4’
The downloaded source packages are in
‘/private/var/folders/02/6dwz1gvd1qz4gml8v_wv6n980000gp/T/RtmpVREiYV/downloaded_packages’
Warning messages:
1: In install.packages("lme4") :
installation of package ‘minqa’ had non-zero exit status
2: In install.packages("lme4") :
installation of package ‘lme4’ had non-zero exit status
I recently upgraded my OS to MacOSX Monterey (12.3.1) in a MacBook 2020 (intel chip).
I have tried reinstalling gcc and gccfortran using brew with no effect.
Can anyone help me with the issue?
Removing xcode command line tools and reinstalling it solved the issue.
$ xcode-select --print-path
/Library/Developer/CommandLineTools
$ sudo rm -r -f /Library/Developer/CommandLineTools
$ xcode-select --install
Im trying to make Github Actions compile my project on windows, but it is failing. When compiling in my machine, it compiles fine. Why does it fail on Github Actions?
I have also tried installing QT using jurplel/install-qt-action#v2.5.3, but I get the same error
The project compiles fine for Mac and Linux
Compile Output:
Info: creating stash file D:\a\dsda-launcher\dsda-launcher\dsda-launcher\build\.qmake.stash
24
C:/ProgramData/Chocolatey/lib/make/tools/install/bin/make.exe -f Makefile.Release
25
make[1]: Entering directory 'D:/a/dsda-launcher/dsda-launcher/dsda-launcher/build'
26
'C:\Qt\5.15.2\mingw81_64\bin\uic.exe' ../mainwindow.ui -o ui_mainwindow.h
27
g++ -c -fno-keep-inline-dllexport -O2 -std=gnu++11 -Wall -Wextra -Wextra -fexceptions -mthreads -DUNICODE -D_UNICODE -DWIN32 -DMINGW_HAS_SECURE_API=1 -DAPP_NAME=dsda-launcher -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CONCURRENT_LIB -DQT_CORE_LIB -DQT_NEEDS_QMAIN -I../../dsda-launcher -I. -IC:/Qt/5.15.2/mingw81_64/include -IC:/Qt/5.15.2/mingw81_64/include/QtWidgets -IC:/Qt/5.15.2/mingw81_64/include/QtGui -IC:/Qt/5.15.2/mingw81_64/include/QtANGLE -IC:/Qt/5.15.2/mingw81_64/include/QtNetwork -IC:/Qt/5.15.2/mingw81_64/include/QtConcurrent -IC:/Qt/5.15.2/mingw81_64/include/QtCore -Irelease -I. -I/include -IC:/Qt/5.15.2/mingw81_64/mkspecs/win32-g++ -o release/main.o ../main.cpp
28
g++ -c -fno-keep-inline-dllexport -O2 -std=gnu++11 -Wall -Wextra -Wextra -fexceptions -mthreads -DUNICODE -D_UNICODE -DWIN32 -DMINGW_HAS_SECURE_API=1 -DAPP_NAME=dsda-launcher -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CONCURRENT_LIB -DQT_CORE_LIB -DQT_NEEDS_QMAIN -I../../dsda-launcher -I. -IC:/Qt/5.15.2/mingw81_64/include -IC:/Qt/5.15.2/mingw81_64/include/QtWidgets -IC:/Qt/5.15.2/mingw81_64/include/QtGui -IC:/Qt/5.15.2/mingw81_64/include/QtANGLE -IC:/Qt/5.15.2/mingw81_64/include/QtNetwork -IC:/Qt/5.15.2/mingw81_64/include/QtConcurrent -IC:/Qt/5.15.2/mingw81_64/include/QtCore -Irelease -I. -I/include -IC:/Qt/5.15.2/mingw81_64/mkspecs/win32-g++ -o release/mainwindow.o ../mainwindow.cpp
29
../mainwindow.cpp: In function 'QString lowerCase(std::__cxx11::string)':
30
../mainwindow.cpp:77:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31
for(int i=0;i<word.length();i++)
32
~^~~~~~~~~~~~~~
33
../mainwindow.cpp: In constructor 'MainWindow::MainWindow(QWidget*)':
34
../mainwindow.cpp:211:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
35
for(int i=0;i<tp.length();i++) // Loop the chars to find the 4 quotes
36
~^~~~~~~~~~~~
37
../mainwindow.cpp:266:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
38
for(int i=0;i<tp.length();i++)
39
~^~~~~~~~~~~~
40
../mainwindow.cpp:308:46: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
41
for(int i=0;i<tp.length();i++)
42
~^~~~~~~~~~~~
43
../mainwindow.cpp: In member function 'void MainWindow::on_LaunchGameButton_clicked(bool, bool)':
44
../mainwindow.cpp:881:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
45
for(int i=0; i<dehFiles.length();i++)
46
~^~~~~~~~~~~~~~~~~~
47
../mainwindow.cpp:893:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
48
for(int i=0; i<files.length();i++)
49
~^~~~~~~~~~~~~~~
50
In file included from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windows.h:65,
51
from ../mainwindow.cpp:1068:
52
C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/excpt.h:14:8: error: expected unqualified-id before string constant
53
extern "C" {
54
^~~
55
In file included from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/minwindef.h:6,
56
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windef.h:8,
57
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windows.h:69,
58
from ../mainwindow.cpp:1068:
59
C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/specstrings.h:18:8: error: expected unqualified-id before string constant
60
extern "C" {
61
^~~
62
In file included from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windef.h:8,
63
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windows.h:69,
64
from ../mainwindow.cpp:1068:
65
C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/minwindef.h:19:8: error: expected unqualified-id before string constant
66
extern "C" {
67
^~~
68
In file included from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/lib/gcc/x86_64-w64-mingw32/8.1.0/include/x86intrin.h:27,
69
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/winnt.h:1554,
70
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/minwindef.h:163,
71
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windef.h:8,
72
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windows.h:69,
73
from ../mainwindow.cpp:1068:
74
C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/lib/gcc/x86_64-w64-mingw32/8.1.0/include/ia32intrin.h:55:25: error: expected '}' before end of line
75
#pragma GCC push_options
76
^
77
../mainwindow.cpp:751:1: note: to match this '{'
78
{
79
^
80
In file included from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/lib/gcc/x86_64-w64-mingw32/8.1.0/include/x86intrin.h:27,
81
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/winnt.h:1554,
82
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/minwindef.h:163,
83
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windef.h:8,
84
from C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/include/windows.h:69,
85
from ../mainwindow.cpp:1068:
86
C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/lib/gcc/x86_64-w64-mingw32/8.1.0/include/ia32intrin.h: At global scope:
87
C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/lib/gcc/x86_64-w64-mingw32/8.1.0/include/ia32intrin.h:55:25: error: expected declaration before end of line
88
#pragma GCC push_options
89
^
90
make[1]: *** [Makefile.Release:725: release/mainwindow.o] Error 1
91
make[1]: Leaving directory 'D:/a/dsda-launcher/dsda-launcher/dsda-launcher/build'
92
make: *** [Makefile:45: release] Error 2
Github Actions code:
steps:
- name: Install qt
run: |
choco install qt5-default
- uses: actions/checkout#v2
- name: build
run: |
C:\Qt\5.15.2\mingw81_64\bin\qmake.exe ..
make.exe
Found the solution. I had to call #include <windows.h> before including any other header. I don't know why, but it works.
https://forum.qt.io/topic/38780/solved-errors-with-windows-h
I also faced an error during Cairo library installation in R. Please, see the messages below.
I get this error:
> install.packages('Cairo')
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 86982 100 86982 0 0 389k 0 --:--:-- --:--:-- --:--:-- 389k
* installing *source* package ‘Cairo’ ...
** package ‘Cairo’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-conda_cos6-linux-gnu-cc
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 x86_64-conda_cos6-linux-gnu-cc accepts -g... yes
checking for x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-conda_cos6-linux-gnu-cc -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/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/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/freetype2 -I/usr/include/libpng12
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=-lfreetype -lz -lpng12 -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 ‘/home/ubuntu/anaconda3/lib/R/library/Cairo’
The downloaded source packages are in
‘/tmp/RtmpAuSLZy/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("Cairo") :
installation of package ‘Cairo’ had non-zero exit status
While session info gives this:
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /home/ubuntu/anaconda3/lib/R/lib/libRblas.so
LAPACK: /home/ubuntu/anaconda3/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RevoUtils_10.0.8
loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3
And capabilities shows I have Cairo available.
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE 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
I believe I read all the corresponding topics and librairo2-dev is already installed:
libcairo2-dev is already the newest version (1.14.6-1).
And, I believe, the .log file:
## --------- ##
## Platform. ##
## --------- ##
hostname = ip-172-31-30-74
uname -m = x86_64
uname -r = 4.4.0-1069-aws
uname -s = Linux
uname -v = #79-Ubuntu SMP Mon Sep 24 15:01:41 UTC 2018
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /home/ubuntu/bin
PATH: /home/ubuntu/.local/bin
PATH: /home/ubuntu/anaconda3/bin
PATH: /home/ubuntu/software/sratoolkit.2.9.0-ubuntu64/bin
PATH: /home/ubuntu/anaconda2/bin
PATH: /home/ubuntu/chenlab_v2/pipeline/bulk_rna_seq/code
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games
PATH: /snap/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2155: checking for gcc
configure:2171: found /home/ubuntu/anaconda3/bin/gcc
configure:2182: result: gcc
configure:2411: checking for C compiler version
configure:2420: gcc --version >&5
gcc (crosstool-NG fa8859cb) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:2431: $? = 0
configure:2420: gcc -v >&5
Reading specs from /home/ubuntu/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/specs
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/home/ubuntu/anaconda3/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/lto-wrapper
Target: x86_64-conda_cos6-linux-gnu
Configured with: /opt/conda/conda-bld/compilers_linux-64_1520532893746/work/.build/src/gcc-7.2.0/configure --build=x86_64-build_pc-linux-gnu --host=x86_64-build_pc-linux-gnu --tar
get=x86_64-conda_cos6-linux-gnu --prefix=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/gcc_built --with-sysroot=/opt/conda/conda-bld/compilers_linux-64_1520532893746/
work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-languages=c,c++,fortran,objc,obj-c++ --with-pkgversion='crosstool-NG fa8859cb' --enable-__cxa_atexit --disable-libmudfl
ap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-libmpx --with-gmp=/opt/conda/conda-bld/compilers_linux-64_152
0532893746/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpfr=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/.build/x86_64-conda_cos6-linux-gnu/buildtools
--with-mpc=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-isl=/opt/conda/conda-bld/compilers_linux-64_152053289374
6/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --enable-lto --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-multilib --
with-local-prefix=/opt/conda/conda-bld/compilers_linux-64_1520532893746/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-long-long --enable-default-pie
Thread model: posix
gcc version 7.2.0 (crosstool-NG fa8859cb)
configure:2431: $? = 0
configure:2420: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2431: $? = 1
configure:2420: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
compilation terminated.
configure:2431: $? = 1
configure:2451: checking whether the C compiler works
configure:2473: gcc -L/home/ubuntu/anaconda3/lib conftest.c >&5
configure:2477: $? = 0
configure:2525: result: yes
configure:2528: checking for C compiler default output file name
configure:2530: result: a.out
configure:2536: checking for suffix of executables
configure:2543: gcc -o conftest -L/home/ubuntu/anaconda3/lib conftest.c >&5
configure:2547: $? = 0
configure:2569: result:
configure:2591: checking whether we are cross compiling
configure:2599: gcc -o conftest -L/home/ubuntu/anaconda3/lib conftest.c >&5
configure:2603: $? = 0
configure:2610: ./conftest
configure:2614: $? = 0
configure:2629: result: no
configure:2634: checking for suffix of object files
configure:2656: gcc -c conftest.c >&5
configure:2660: $? = 0
configure:2681: result: o
configure:2685: checking whether we are using the GNU C compiler
configure:2704: gcc -c conftest.c >&5
configure:2704: $? = 0
configure:2713: result: yes
configure:2722: checking whether gcc accepts -g
configure:2742: gcc -c -g conftest.c >&5
configure:2742: $? = 0
configure:2783: result: yes
configure:2800: checking for gcc option to accept ISO C89
configure:2863: gcc -c -g -O2 conftest.c >&5
configure:2863: $? = 0
configure:2876: result: none needed
configure:2897: checking for gzeof in -lz
configure:2922: gcc -o conftest -g -O2 -L/home/ubuntu/anaconda3/lib conftest.c -lz >&5
/home/ubuntu/anaconda3/lib/libz.so: undefined reference to `memcpy#GLIBC_2.14'
collect2: error: ld returned 1 exit status
configure:2922: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h. */
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char gzeof ();
| int
| main ()
| {
| return gzeof ();
| ;
| return 0;
| }
configure:2931: result: yes
configure:2949: checking how to run the C preprocessor
configure:2980: gcc -E conftest.c
configure:2980: $? = 0
configure:2994: gcc -E conftest.c
conftest.c:10:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:2994: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:3019: result: gcc -E
configure:3039: gcc -E conftest.c
configure:3039: $? = 0
configure:3053: gcc -E conftest.c
conftest.c:10:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:3053: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:3082: checking for grep that handles long lines and -e
configure:3140: result: /bin/grep
configure:3145: checking for egrep
configure:3207: result: /bin/grep -E
configure:3212: checking for ANSI C header files
configure:3232: gcc -c -g -O2 conftest.c >&5
configure:3232: $? = 0
configure:3305: gcc -o conftest -g -O2 -L/home/ubuntu/anaconda3/lib conftest.c -lz >&5
/home/ubuntu/anaconda3/lib/libz.so: undefined reference to `memcpy#GLIBC_2.14'
collect2: error: ld returned 1 exit status
configure:3305: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| /* end confdefs.h. */
| #include <ctype.h>
| #include <stdlib.h>
| #if ((' ' & 0x0FF) == 0x020)
| # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
| # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
| #else
| # define ISLOWER(c) (('a' <= (c) && (c) <= 'i') || ('j' <= (c) && (c) <= 'r') || ('s' <= (c) && (c) <= 'z'))
| # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
| #endif
|
| #define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
| int
| main ()
| {
| int i;
| for (i = 0; i < 256; i++)
| if (XOR (islower (i), ISLOWER (i))
| || toupper (i) != TOUPPER (i))
| return 2;
| return 0;
| }
configure:3316: result: no
configure:3329: checking for sys/types.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for sys/stat.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for stdlib.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for string.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for memory.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for strings.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for inttypes.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for stdint.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3329: checking for unistd.h
configure:3329: gcc -c -g -O2 conftest.c >&5
configure:3329: $? = 0
configure:3329: result: yes
configure:3345: checking size of unsigned long
configure:3350: gcc -o conftest -g -O2 -L/home/ubuntu/anaconda3/lib conftest.c -lz >&5
/home/ubuntu/anaconda3/lib/libz.so: undefined reference to `memcpy#GLIBC_2.14'
collect2: error: ld returned 1 exit status
configure:3350: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_LIBZ 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| static long int longval () { return (long int) (sizeof (unsigned long)); }
| static unsigned long int ulongval () { return (long int) (sizeof (unsigned long)); }
| #include <stdio.h>
| #include <stdlib.h>
| int
| main ()
| {
|
| FILE *f = fopen ("conftest.val", "w");
| if (! f)
| return 1;
| if (((long int) (sizeof (unsigned long))) < 0)
| {
| long int i = longval ();
| if (i != ((long int) (sizeof (unsigned long))))
| return 1;
| fprintf (f, "%ld", i);
| }
| else
| {
| unsigned long int i = ulongval ();
| if (i != ((long int) (sizeof (unsigned long))))
| return 1;
| fprintf (f, "%lu", i);
| }
| /* Do not output a trailing newline, as this causes \r\n confusion
| on some platforms. */
| return ferror (f) || fclose (f) != 0;
|
| ;
| return 0;
| }
configure:3364: result: 0
configure:3527: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by config.status, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on ip-172-31-30-74
config.status:723: creating src/Makevars
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=-L/home/ubuntu/anaconda3/lib
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=no
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_lib_z_gzeof=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_sizeof_unsigned_long=0
## ----------------- ##
## Output variables. ##
## ----------------- ##
CC='gcc'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DHAVE_SYS_TYPES_H=1 -DHAVE
_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=0'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
LDFLAGS='-L/home/ubuntu/anaconda3/lib'
LIBOBJS=''
LIBS='-lz '
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_URL=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
SHELL='/bin/bash'
ac_ct_CC='gcc'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define HAVE_LIBZ 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define SIZEOF_UNSIGNED_LONG 0
configure: exit 0
I would greatly appreciate if someone will be able to help. Thank you in advance.
I am trying to install Rcplex in R on a macbook and I'm following the instruction at this link http://jrzubizarreta.com/INSTALL.
On terminal, in the folder where the unzipped Rcplex directory is, I typed
cd /Library/Frameworks/R.framework/Versions/3.4/Resources/library
R CMD INSTALL --configure-args="PKG_CFLAGS='-m64 -fPIC' PKG_CPPFLAGS=-
I/Applications/CPLEX_Studio_Community129/cplex/include PKG_LIBS='-
l/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic
-m64 -lm -lpthread -framework CoreFoundation -framework IOKit'" Rcplex
as by instructions. However, I get the following error:
configure: error: Could not link CPLEX library using -
L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic
-m64 -lm -lpthread -framework CoreFoundation -framework IOKit
The error persist if I use the sudo option before R CMD INSTALL [...].
The config.log states:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by Rcplex configure 0.3.2, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ ./configure PKG_CFLAGS=-m64 -fPIC PKG_CPPFLAGS=-I/Applications/CPLEX_Studio_Community129/cplex/include PKG_LIBS=-L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
## --------- ##
## Platform. ##
## --------- ##
hostname = Michele.local
uname -m = x86_64
uname -r = 16.7.0
uname -s = Darwin
uname -v = Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
/usr/bin/uname -p = i386
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
hostinfo = Mach kernel version:
Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3
Primary memory available: 16.00 gigabytes
Default processor set: 365 tasks, 1663 threads, 4 processors
Load average: 2.45, Mach factor: 1.68
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /Users/ssandrews/anaconda/bin
PATH: /Library/Frameworks/Python.framework/Versions/2.7/bin
PATH: /Users/ssandrews/anaconda/bin
PATH: /Library/Frameworks/Python.framework/Versions/3.5/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /opt/X11/bin
PATH: /Library/TeX/texbin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1631: checking for gcc
configure:1657: result: clang
configure:1901: checking for C compiler version
configure:1904: clang --version </dev/null >&5
Apple LLVM version 7.0.0 (clang-700.0.72)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
configure:1907: $? = 0
configure:1909: clang -v </dev/null >&5
Apple LLVM version 7.0.0 (clang-700.0.72)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
configure:1912: $? = 0
configure:1914: clang -V </dev/null >&5
clang: error: argument to '-V' is missing (expected 1 value)
clang: error: no input files
configure:1917: $? = 1
configure:1940: checking for C compiler default output file name
configure:1943: clang -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:1946: $? = 0
configure:1992: result: a.out
configure:1997: checking whether the C compiler works
configure:2003: ./a.out
configure:2006: $? = 0
configure:2023: result: yes
configure:2030: checking whether we are cross compiling
configure:2032: result: no
configure:2035: checking for suffix of executables
configure:2037: clang -o conftest -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2040: $? = 0
configure:2065: result:
configure:2071: checking for suffix of object files
configure:2092: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2095: $? = 0
configure:2117: result: o
configure:2121: checking whether we are using the GNU C compiler
configure:2145: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2151: $? = 0
configure:2155: test -z
|| test ! -s conftest.err
configure:2158: $? = 0
configure:2161: test -s conftest.o
configure:2164: $? = 0
configure:2177: result: yes
configure:2183: checking whether clang accepts -g
configure:2204: clang -c -g -I/usr/local/include conftest.c >&5
configure:2210: $? = 0
configure:2214: test -z
|| test ! -s conftest.err
configure:2217: $? = 0
configure:2220: test -s conftest.o
configure:2223: $? = 0
configure:2234: result: yes
configure:2251: checking for clang option to accept ANSI C
configure:2321: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2327: $? = 0
configure:2331: test -z
|| test ! -s conftest.err
configure:2334: $? = 0
configure:2337: test -s conftest.o
configure:2340: $? = 0
configure:2358: result: none needed
configure:2376: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
conftest.c:2:3: error: unknown type name 'choke'
choke me
^
conftest.c:2:11: error: expected ';' after top level declarator
choke me
^
;
2 errors generated.
configure:2382: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
configure:2520: checking how to run the C preprocessor
configure:2638: result: clang -E
configure:2662: clang -E -I/usr/local/include conftest.c
configure:2668: $? = 0
configure:2700: clang -E -I/usr/local/include conftest.c
conftest.c:9:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^
1 error generated.
configure:2706: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "Rcplex"
| #define PACKAGE_TARNAME "rcplex"
| #define PACKAGE_VERSION "0.3.2"
| #define PACKAGE_STRING "Rcplex 0.3.2"
| #define PACKAGE_BUGREPORT ""
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:2756: checking for egrep
configure:2766: result: grep -E
configure:2771: checking for ANSI C header files
configure:2796: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2802: $? = 0
configure:2806: test -z
|| test ! -s conftest.err
configure:2809: $? = 0
configure:2812: test -s conftest.o
configure:2815: $? = 0
configure:2904: clang -o conftest -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit >&5
conftest.c:26:7: warning: implicitly declaring library function 'exit' with type 'void (int) __attribute__((noreturn))'
exit(2);
^
conftest.c:26:7: note: include the header <stdlib.h> or explicitly provide a declaration for 'exit'
1 warning generated.
configure:2907: $? = 0
configure:2909: ./conftest
configure:2912: $? = 0
configure:2927: result: yes
configure:2951: checking for sys/types.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for sys/stat.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for stdlib.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for string.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for memory.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for strings.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for inttypes.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for stdint.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for unistd.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:3019: checking ilcplex/cplex.h usability
configure:3031: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:3037: $? = 0
configure:3041: test -z
|| test ! -s conftest.err
configure:3044: $? = 0
configure:3047: test -s conftest.o
configure:3050: $? = 0
configure:3060: result: yes
configure:3064: checking ilcplex/cplex.h presence
configure:3074: clang -E -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c
configure:3080: $? = 0
configure:3100: result: yes
configure:3135: checking for ilcplex/cplex.h
configure:3142: result: yes
configure:3154: checking for library containing CPXversion
configure:3184: clang -o conftest -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit >&5
Undefined symbols for architecture x86_64:
"_CPXversion", referenced from:
_main in conftest-074e04.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:3190: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "Rcplex"
| #define PACKAGE_TARNAME "rcplex"
| #define PACKAGE_VERSION "0.3.2"
| #define PACKAGE_STRING "Rcplex 0.3.2"
| #define PACKAGE_BUGREPORT ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
|
| /* Override any gcc2 internal prototype to avoid an error. */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
| builtin and then its argument prototype would still apply. */
| char CPXversion ();
| int
| main ()
| {
| CPXversion ();
| ;
| return 0;
| }
configure:3239: clang -o conftest -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c -lcplex -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit >&5
ld: library not found for -lcplex
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:3245: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "Rcplex"
| #define PACKAGE_TARNAME "rcplex"
| #define PACKAGE_VERSION "0.3.2"
| #define PACKAGE_STRING "Rcplex 0.3.2"
| #define PACKAGE_BUGREPORT ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
|
| /* Override any gcc2 internal prototype to avoid an error. */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
| builtin and then its argument prototype would still apply. */
| char CPXversion ();
| int
| main ()
| {
| CPXversion ();
| ;
| return 0;
| }
configure:3273: result: no
configure:3279: error: Could not link CPLEX library using -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=
ac_cv_header_ilcplex_cplex_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_objext=o
ac_cv_prog_CPP='clang -E'
ac_cv_prog_ac_ct_CC=clang
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_egrep='grep -E'
ac_cv_search_CPXversion=no
## ----------------- ##
## Output variables. ##
## ----------------- ##
AWK=''
CC='clang'
CFLAGS='-Wall -g -O2 -m64 -fPIC'
CPLEX_BIN=''
CPP='clang -E'
CPPFLAGS='-I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include'
DEFS=''
ECHO_C='ECHO_N=''
ECHO_T=''
EGREP='grep -E'
EXEEXT=''
LDFLAGS=''
LIBOBJS=''
LIBS='-L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit'
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='Rcplex'
PACKAGE_STRING='Rcplex 0.3.2'
PACKAGE_TARNAME='rcplex'
PACKAGE_VERSION='0.3.2'
PATH_SEPARATOR=':'
PKG_CFLAGS='-m64 -fPIC'
PKG_CPPFLAGS='-I/Applications/CPLEX_Studio_Community129/cplex/include'
PKG_LIBS='-L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit'
SHELL='/bin/sh'
ac_ct_CC='clang'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${prefix}/share'
exec_prefix='NONE'
host_alias=''
includedir='${prefix}/include'
infodir='${prefix}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define HAVE_INTTYPES_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRINGS_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_UNISTD_H 1
#define PACKAGE_BUGREPORT ""
#define PACKAGE_NAME "Rcplex"
#define PACKAGE_STRING "Rcplex 0.3.2"
#define PACKAGE_TARNAME "rcplex"
#define PACKAGE_VERSION "0.3.2"
#define STDC_HEADERS 1
configure: exit 1
The makefile carries the following information:
SYSTEM = x86-64_osx
LIBFORMAT = static_pic
#------------------------------------------------------------
#
# When you adapt this makefile to compile your CPLEX programs
# please copy this makefile and set CPLEXDIR and CONCERTDIR to
# the directories where CPLEX and CONCERT are installed.
#
#------------------------------------------------------------
CPLEXDIR = ../../..
CONCERTDIR = ../../../../concert
# ---------------------------------------------------------------------
# Compiler selection
# ---------------------------------------------------------------------
CCC = clang++ -O0
CC = clang -O0
JAVAC = javac
# ---------------------------------------------------------------------
# Compiler options
# ---------------------------------------------------------------------
CCOPT = -m64 -O -fPIC -fexceptions -DNDEBUG -DIL_STD -stdlib=libc++
COPT = -m64 -fPIC
JOPT = -classpath $(CPLEXDIR)/lib/cplex.jar -O
# ---------------------------------------------------------------------
# Link options and libraries
# ---------------------------------------------------------------------
CPLEXBINDIR = $(CPLEXDIR)/bin/$(BINDIST)
CPLEXJARDIR = $(CPLEXDIR)/lib/cplex.jar
CPLEXLIBDIR = $(CPLEXDIR)/lib/$(SYSTEM)/$(LIBFORMAT)
CONCERTLIBDIR = $(CONCERTDIR)/lib/$(SYSTEM)/$(LIBFORMAT)
# For dynamic linking
CPLEXBINDIR = $(CPLEXDIR)/bin/$(SYSTEM)
CPLEXLIB = cplex$(dynamic:yes=1290)
run = $(dynamic:yes=DYLD_LIBRARY_PATH=$(CPLEXBINDIR))
CCLNDIRS = -L$(CPLEXLIBDIR) -L$(CONCERTLIBDIR) $(dynamic:yes=-L$(CPLEXBINDIR))
CLNDIRS = -L$(CPLEXLIBDIR) $(dynamic:yes=-L$(CPLEXBINDIR))
CCLNFLAGS = -lconcert -lilocplex -l$(CPLEXLIB) -m64 -lm -lpthread -framework CoreFoundation -framework IOKit -stdlib=libc++
CLNFLAGS = -l$(CPLEXLIB) -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
JAVA = java -d64 -Djava.library.path=$(CPLEXDIR)/bin/x86-64_osx -classpath $(CPLEXJARDIR):
all:
make all_c
make all_cpp
make all_java
execute: all
make execute_c
make execute_cpp
make execute_java
CONCERTINCDIR = $(CONCERTDIR)/include
CPLEXINCDIR = $(CPLEXDIR)/include
EXDIR = $(CPLEXDIR)/examples
EXINC = $(EXDIR)/include
EXDATA = $(EXDIR)/data
EXSRCC = $(EXDIR)/src/c
EXSRCCX = $(EXDIR)/src/c_x
EXSRCCPP = $(EXDIR)/src/cpp
EXSRCJAVA = $(EXDIR)/src/java
CFLAGS = $(COPT) -I$(CPLEXINCDIR)
CCFLAGS = $(CCOPT) -I$(CPLEXINCDIR) -I$(CONCERTINCDIR)
JCFLAGS = $(JOPT)
Any idea on how to fix this issue? Thank you
It says
error: unable to open output file '/Volumes/Andrews/R working
Could it be that the blank in the file/folder name causes trouble? Try to install into a path that does not have blanks in its name. And make sure that path exists and you have write permissions for it.
Update after question was updated with new error message: Now the error is this:
error: Could not link CPLEX library using -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
This is the wrong path. The CPLEX libraries are not in examples/x86-64_osx/static_pic but are either in bin/x86-64_osx (dynamic library) or in lib/x86-64_osx/static_pic (static library). I don't know which of the two libraries is required, so just put both pathes into the configuration arguments (including the absolute path to your installation, of course). I am not sure whether you also have to put -lcplex or -lcplex129 (depending on whether the static or the dynamic library is required). So if you get the same error without putting these arguments, then try with them.
I hope someone can help me with this...
This is my first encounter with yosys. For the start, I'm trying to run the very same demo as Clifford explained in his presentation. I downloaded the demo at the following location: https://github.com/cliffordwolf/yosys/tree/master/manual/PRESENTATION_Intro
yosys run beaks at the ABC pass with following message:
12. Executing ABC pass (technology mapping using ABC).
12.1. Extracting gate netlist of module `\counter' to `<abc-temp-dir>/input.blif'..
Extracted 6 gates and 12 wires to a netlist network with 4 inputs and 2 outputs.
12.1.1. Executing ABC.
Running ABC command: <yosys-exe-dir>/yosys-abc -s -f <abc-temp-dir>/abc.script 2>&1
ABC: ABC command line: "source <abc-temp-dir>/abc.script".
ABC:
ABC: + read_blif <abc-temp-dir>/input.blif
ABC: + read_lib -w /home/boris/Documents/Self Learning/yosys_synthesys/mycells.lib
ABC: usage: read_lib [-SG float] [-M num] [-dnvwh] <file>
ABC: reads Liberty library from file
ABC: -S float : the slew parameter used to generate the library [default = 0.00]
ABC: -G float : the gain parameter used to generate the library [default = 0.00]
ABC: -M num : skip gate classes whose size is less than this [default = 0]
ABC: -d : toggle dumping the parsed library into file "*_temp.lib" [default = no]
ABC: -n : toggle replacing gate/pin names by short strings [default = no]
ABC: -v : toggle writing verbose information [default = yes]
ABC: -v : toggle writing information about skipped gates [default = yes]
ABC: -h : prints the command summary
ABC: <file> : the name of a file to read
ABC: ** cmd error: aborting 'source <abc-temp-dir>/abc.script'
ERROR: Can't open ABC output file `/tmp/yosys-abc-KDGya6/output.blif'.
[boris#E7440 yosys_synthesys]$
I have had a look at the file location mentioned in the error statement above, there is no output.blif in there:
[boris#E7440 yosys_synthesys]$ ll /tmp/yosys-abc-KDGya6/
total 12K
-rw-rw-r--. 1 boris boris 542 Jul 5 11:21 abc.script
-rw-rw-r--. 1 boris boris 526 Jul 5 11:21 input.blif
-rw-rw-r--. 1 boris boris 852 Jul 5 11:21 stdcells.genlib
[boris#E7440 yosys_synthesys]$
Buy the way, here is some system/tools info that might be relevant for debugging:
Linux E7440.DELL 4.4.13-200.fc22.x86_64 #1 SMP Wed Jun 8 15:59:40 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Yosys 0.6+141 (git sha1 080f95f, gcc 5.3.1 -fPIC -Os)
UC Berkeley, ABC 1.01 (compiled Mar 8 2015 01:00:49)
The issue has been resolved...
Solution =
Changed rundir from:
/home/boris/Documents/Self Learning/yosys_synthesys/mycells.lib
to:
/home/boris/Documents/SelfLearning/yosys_synthesys/mycells.lib
Lesson learned =
ABC tool does not accept space characters in the path/file name.