Error while compiling Exim (directadmin custombuild) - unix

I'm currently running DirectAdmin on my Debian 6.0.9 and got a message that Exim needed to be updated. So i did my regular commands:
./build update
./build versions
./build update_versions
But, whenever I run these commands, i get the following error:
In file included from tls.c:121:
tlscert-openssl.c: In function ‘asn1_time_copy’:
tlscert-openssl.c:114: warning: passing argument 2 of ‘ASN1_TIME_print’ discards qualifiers from pointer target type
/usr/include/openssl/asn1.h:1006: note: expected ‘struct ASN1_TIME *’ but argument is of type ‘const struct ASN1_TIME *’
gcc tod.c
gcc transport.c
gcc tree.c
gcc verify.c
gcc lookups/lf_quote.c
gcc lookups/lf_check_file.c
gcc lookups/lf_sqlperform.c
gcc local_scan.c
cc perl.c
gcc malware.c
gcc mime.c
gcc regex.c
gcc spam.c
gcc spool_mbox.c
gcc demime.c
gcc bmi_spam.c
gcc spf.c
gcc srs.c
gcc dcc.c
gcc dmarc.c
gcc dane.c
gcc version.c
gcc -o exim
/usr/bin/ld: cannot find -lgdbm
collect2: ld returned 1 exit status
make[1]: *** [exim] Error 1
make[1]: Leaving directory `/usr/local/directadmin/custombuild/exim-4.85/build-Linux-x86_64'
make: *** [all] Error 2
*** The make has failed, would you like to try to make again? (y,n): n
Google doesn't really help and I'm running out of ideas.

Credits go to tripleee
The server was missing libgdbm-dev. So after
sudo apt-get install libgdbm-dev
It was working fine.

Related

R package 'RcppArmadillo' error during installation

I'm trying to install RcppArmadillo in my R environment.
I have created a Docker container starting from a Ubuntu:20.04 image and installing miniconda to manage the environment and install R.
When I install RcppArmadillo I have this error:
checking whether the C++ compiler works... no
configure: error: in `/tmp/Rtmp1znFrE/R.INSTALL3901267e6e22/RcppArmadillo':
configure: error: C++ compiler cannot create executables
I have checked the config.log file to search the error, and I found this:
gcc version 9.4.0 (conda-forge 9.4.0-15)
configure:1931: $? = 0
configure:1920: aarch64-conda-linux-gnu-c++ -std=gnu++14 -V >&5
aarch64-conda-linux-gnu-c++: error: unrecognized command line option '-V'
aarch64-conda-linux-gnu-c++: fatal error: no input files
compilation terminated.
configure:1931: $? = 1
configure:1920: aarch64-conda-linux-gnu-c++ -std=gnu++14 -qversion >&5
aarch64-conda-linux-gnu-c++: error: unrecognized command line option '-qversion'; did you mean '--version'?
aarch64-conda-linux-gnu-c++: fatal error: no input files
compilation terminated.
configure:1931: $? = 1
configure:1951: checking whether the C++ compiler works
configure:1973: aarch64-conda-linux-gnu-c++ -std=gnu++14 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /root/miniconda3/include -fdebug-prefix-map=/drone/src/build_artifacts/r-base-split_1630154255557/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/root/miniconda3=/usr/local/src/conda-prefix conftest.cpp >&5
/root/miniconda3/bin/../lib/gcc/aarch64-conda-linux-gnu/9.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /root/miniconda3/bin/../lib/gcc/aarch64-conda-linux-gnu/9.4.0/libstdc++.so: undefined reference to `__cxa_thread_atexit_impl#GLIBC_2.18'
collect2: error: ld returned 1 exit status
I don't understand if it's a problem of GCC (I have tried to uninstall and install again through apt-get but nothing changed), but seems really strange to me.
If I echo $PATH I get as result /root/miniconda3/bin:/usr/bin:/bin, but If I find / -name gcc I get:
/root/miniconda3/lib/R/library/BH/include/boost/mpl/aux_/preprocessed/gcc
/root/miniconda3/lib/gcc
/root/miniconda3/libexec/gcc
/root/miniconda3/libexec/gcc/aarch64-conda-linux-gnu/9.4.0/gcc
/root/miniconda3/share/licenses/gcc
/root/miniconda3/pkgs/gcc_impl_linux-aarch64-9.4.0-h603953f_15/libexec/gcc
/root/miniconda3/pkgs/gcc_impl_linux-aarch64-9.4.0-h603953f_15/libexec/gcc/aarch64-conda-linux-gnu/9.4.0/gcc
/root/miniconda3/pkgs/gcc_impl_linux-aarch64-9.4.0-h603953f_15/share/licenses/gcc
/root/miniconda3/pkgs/gcc_impl_linux-aarch64-9.4.0-h603953f_15/lib/gcc
/root/miniconda3/pkgs/libgcc-devel_linux-aarch64-9.4.0-h85f5abf_15/lib/gcc
/root/miniconda3/pkgs/libstdcxx-devel_linux-aarch64-9.4.0-h85f5abf_15/lib/gcc
/root/miniconda3/pkgs/gfortran_impl_linux-aarch64-9.4.0-h54cdb55_15/libexec/gcc
/root/miniconda3/pkgs/gfortran_impl_linux-aarch64-9.4.0-h54cdb55_15/lib/gcc
/root/miniconda3/pkgs/gxx_impl_linux-aarch64-9.4.0-h603953f_15/libexec/gcc
/usr/share/gcc
/usr/share/doc/gcc
/usr/share/doc/gcc-9-base/gcc
/usr/lib/gcc
/usr/bin/gcc
so maybe there are some mistakes in all these GCC instances.
Thanks for your help

Error in R CMD SHLIB compiling Fortran code

I'm trying to compile a Fortran subroutine in the remote machine, when I run:
R CMD SHLIB -fPIC vintp2p_afterburner_wind.f
I get the following error:
gcc -shared -L/sw/installed/R/3.6.2-fosscuda-2019b/lib64/R/lib -L/sw/installed/pocl/1.4-GCC-8.3.0/lib64 -L/sw/installed/ImageMagick/7.0.9-5-GCCcore-8.3.0/lib -L/sw/installed/GSL/2.6-GCC-8.3.0/lib -L/sw/installed/UDUNITS/2.2.26-GCCcore-8.3.0/lib -L/sw/installed/HDF5/1.10.5-gompic-2019b/lib -L/sw/installed/ICU/64.2-GCCcore-8.3.0/lib -L/sw/installed/libsndfile/1.0.28-GCCcore-8.3.0/lib -L/sw/installed/FFTW/3.3.8-gompic-2019b/lib -L/sw/installed/NLopt/2.6.1-GCCcore-8.3.0/lib64 -L/sw/installed/GMP/6.1.2-GCCcore-8.3.0/lib -L/sw/installed/libxml2/2.9.9-GCCcore-8.3.0/lib -L/sw/installed/cURL/7.66.0-GCCcore-8.3.0/lib -L/sw/installed/Tk/8.6.9-GCCcore-8.3.0/lib -L/sw/installed/Java/11.0.2/lib -L/sw/installed/LibTIFF/4.0.10-GCCcore-8.3.0/lib -L/sw/installed/libjpeg-turbo/2.0.3-GCCcore-8.3.0/lib64 -L/sw/installed/libpng/1.6.37-GCCcore-8.3.0/lib -L/sw/installed/PCRE/8.43-GCCcore-8.3.0/lib -L/sw/installed/SQLite/3.29.0-GCCcore-8.3.0/lib -L/sw/installed/zlib/1.2.11-GCCcore-8.3.0/lib -L/sw/installed/XZ/5.2.4-GCCcore-8.3.0/lib -L/sw/installed/bzip2/1.0.8-GCCcore-8.3.0/lib -L/sw/installed/ncurses/6.1-GCCcore-8.3.0/lib -L/sw/installed/libreadline/8.0-GCCcore-8.3.0/lib -L/sw/installed/cairo/1.16.0-GCCcore-8.3.0/lib -L/sw/installed/libGLU/9.0.1-GCCcore-8.3.0/lib -L/sw/installed/Mesa/19.1.7-GCCcore-8.3.0/lib -L/sw/installed/X11/20190717-GCCcore-8.3.0/lib -L/sw/installed/ScaLAPACK/2.0.2-gompic-2019b/lib -L/sw/installed/OpenBLAS/0.3.7-GCC-8.3.0/lib -L/sw/installed/GCCcore/8.3.0/lib64 -L/sw/installed/GCCcore/8.3.0/lib -L/sw/installed/CUDA/10.1.243/lib64 -o vintp2p_afterburner_wind.so vintp2p_afterburner_wind.o -fPIC -lgfortran -L/sw/installed/R/3.6.2-fosscuda-2019b/lib64/R/lib -lR
/sw/installed/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: vintp2p_afterburner_wind.o: requires dynamic R_X86_64_PC32 reloc against 'log' which may overflow at runtime; recompile with -fPIC
collect2: error: ld returned 1 exit status
make: *** [vintp2p_afterburner_wind.so] Error 1
The subroutine has a log() function. I'm totally new to this error and I don't know where to start with!
Maybe someone will find it useful: compiling is done by :
gfortran -fPIC -shared -ffree-form vintp2p_afterburner_wind.f -o vintp2p_afterburner_wind.so

Torch '!./install.sh' returns error in Colab when installing Torch

I followed http://torch.ch/docs/getting-started.html#_ to install Torch.
I always get the following error when running
!./install.sh
in google colab
error:
...
-- Installing: /root/torch/install/include/luaT.h
-- Installing: /root/torch/install/share/cmake/torch/luaTConfig.cmake
Updating manifest for /root/torch/install/lib/luarocks/rocks
torch scm-1 is now built and installed in /root/torch/install/ (license: BSD)
Updating manifest for /root/torch/install/lib/luarocks/rocks
dok scm-1 is now built and installed in /root/torch/install/ (license: BSD)
gcc -O2 -fPIC -I/root/torch/install/include -c utils.c -o utils.o
gcc -shared -o treplutils.so -L/root/torch/install/lib utils.o
gcc -O2 -fPIC -I/root/torch/install/include -c readline.c -o readline.o
readline.c:8:10: fatal error: readline/readline.h: No such file or directory
#include <readline/readline.h>
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Error: Build error: Failed compiling object readline.o
.
Please I need help fixing this error.
Probably you need something like
!apt-get install libreadline-dev
before attempting to run the install.sh script.

Install RODBC Mac OS Sierra 10.12.3

Fresh install at 10.12.1 with upgrades to 10.12.3.
I did the brew install unixodbc.
I then tried R CMD INSTALL RODBC_1.3-14.tar.gz
with error:
checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
checking whether the C compiler works... no
configure: error: in `/private/var/folders/7f/3n9kqyy13glcwlrx7h8cb5dc0000gn/T/RtmpYQnA2y/R.INSTALL354a771740af/RODBC':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘RODBC’
I then unpacked RODBC and tried to ./configure and got the following error message in the log:
configure:2690: /usr/local/opt/llvm/bin/clang -fopenmp -v >&5
clang version 3.9.1 (tags/RELEASE_391/final)
Target: x86_64-apple-darwin16.4.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
configure:2701: $? = 0
configure:2690: /usr/local/opt/llvm/bin/clang -fopenmp -V >&5
clang: error: argument to '-V' is missing (expected 1 value)
clang: error: no input files
configure:2701: $? = 1
configure:2690: /usr/local/opt/llvm/bin/clang -fopenmp -qversion >&5
clang: error: unknown argument: '-qversion'
clang: error: no input files
configure:2701: $? = 1
configure:2721: checking whether the C compiler works
configure:2743: /usr/local/opt/llvm/bin/clang -fopenmp -Wall -mtune=core2 -g -O2 -I/usr/local/opt/llvm/include -I. conftest.c >&5
ld: library not found for -lomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:2747: $? = 1
configure:2785: result: no
I had the same issue For me, the problem was that the R installer was relying on the clang compiler that shipped with OS X (Sierra, 10.12.4), which does not support openmp.
I also couldn't get any of the usual means for specifying a different compiler to configure to work (such as examples here) because, as it turns out, RODBC's configure script is hard-coded to use the compilers and lib/include paths specified by your R installation, which are described here.
I was able to resolve the problem by editing ~/.R/Makevars to point to a version of gcc I installed via macports (sudo port install gcc6), as such:
CC=/opt/local/bin/gcc-mp-6 -fopenmp
CXX=/opt/local/bin/g++-mp-6
LDFLAGS=-L/opt/local/lib -L/usr/local/opt/llvm/lib
CPPFLAGS=-I/opt/local/include -I/usr/local/opt/llvm/include
Then the normal installation process (R CMD INSTALL ./RODBC_1.3-15.tar.gz) worked as expected.

Unable to compile thrift-0.9.0 on Centos6.4

I have followed all the instructions mentioned in the Apache thrift wiki. I downloaded the thrift source code, then installed the dependencies
sudo yum install automake libtool flex bison pkgconfig gcc-c++ boost-devel libevent-devel zlib-devel python-devel ruby-devel
Then ran
./configure
(didn't run bootstrap.sh because there is no bootstrap.sh in the thrift-0.9.0 codebase). Finally, I get this error. Any idea why this is happening?
libtool: link: ( cd ".libs" && rm -f "libthriftz.la" && ln -s "../libthriftz.la" "libthriftz.la" )
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I./src -I./src/thrift -DQT_SHARED -I/usr/include/QtCore -I/usr/include/QtNetwork -Wall -g -O2 -MT libthriftqt_la-moc_TQTcpServer.lo -MD -MP -MF .deps/libthriftqt_la-moc_TQTcpServer.Tpo -c -o libthriftqt_la-moc_TQTcpServer.lo `test -f 'src/thrift/qt/moc_TQTcpServer.cpp' || echo './'`src/thrift/qt/moc_TQTcpServer.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I./src -I./src/thrift -DQT_SHARED -I/usr/include/QtCore -I/usr/include/QtNetwork -Wall -g -O2 -MT libthriftqt_la-moc_TQTcpServer.lo -MD -MP -MF .deps/libthriftqt_la-moc_TQTcpServer.Tpo -c src/thrift/qt/moc_TQTcpServer.cpp -fPIC -DPIC -o .libs/libthriftqt_la-moc_TQTcpServer.o
src/thrift/qt/moc_TQTcpServer.cpp:14:2: error: #error "This file was generated using the moc from 4.8.1. It"
src/thrift/qt/moc_TQTcpServer.cpp:15:2: error: #error "cannot be used with the include files from this version of Qt."
src/thrift/qt/moc_TQTcpServer.cpp:16:2: error: #error "(The moc has changed too much.)"
src/thrift/qt/moc_TQTcpServer.cpp:47: error: no 'void apache::thrift::async::TQTcpServer::qt_static_metacall(QObject*, QMetaObject::Call, int, void**)' member function declared in class 'apache::thrift::async::TQTcpServer'
src/thrift/qt/moc_TQTcpServer.cpp:62: error: 'const QMetaObjectExtraData apache::thrift::async::TQTcpServer::staticMetaObjectExtraData' is not a static member of 'class apache::thrift::async::TQTcpServer'
src/thrift/qt/moc_TQTcpServer.cpp:63: error: 'qt_static_metacall' was not declared in this scope
src/thrift/qt/moc_TQTcpServer.cpp:64: error: too many initializers for 'const QMetaObjectExtraData'
src/thrift/qt/moc_TQTcpServer.cpp:68: error: 'staticMetaObjectExtraData' was not declared in this scope
src/thrift/qt/moc_TQTcpServer.cpp:69: error: too many initializers for 'QMetaObject::<anonymous struct>'
src/thrift/qt/moc_TQTcpServer.cpp: In member function 'virtual int apache::thrift::async::TQTcpServer::qt_metacall(QMetaObject::Call, int, void**)':
src/thrift/qt/moc_TQTcpServer.cpp:95: error: 'qt_static_metacall' was not declared in this scope
make[4]: *** [libthriftqt_la-moc_TQTcpServer.lo] Error 1
make[4]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0/lib/cpp'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0/lib/cpp'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0/lib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0'
make: *** [all] Error 2
I download the source from: http://www.apache.org/dyn/closer.cgi?path=/thrift/0.9.0/thrift-0.9.0.tar.gz
Your qt-devel is out of date for thrift. Just remove the qt-devel rpm and rerun the configure script which will skip this part. It works for me.
First of all, check your qt related rpms by executing the following command
rpm -qa | grep qt-devel
If you find qt-devel is installed version below 4.6, please remove this package by executing command
rpm -qa | grep qt-devel | xargs rpm -e
If this is done, the qt part of thrift will be skipped.
It looks like the version of Qt that is on your system is older than what this program expects. Can you try updating Qt to a later version?
sudo yum install qt4-devel

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