I'm super new to coding in general so apologies for any lack of clarity or conciseness. I'm attempting to make a build for Kallisto to use in RNA sequence alignment and I'm getting stuck at the "make" stage. The cmake was successful after a little fiddling and downloading a CXX compiler, but the make keep exiting with an error status:
[ 27%] Built target htslib
[ 93%] Built target kallisto_core
[ 96%] Linking CXX executable kallisto
/home/wahanson/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
make[2]: *** [src/CMakeFiles/kallisto.dir/build.make:88: src/kallisto] Error 1
make[1]: *** [CMakeFiles/Makefile2:130: src/CMakeFiles/kallisto.dir/all] Error 2
the main error appears to be "cannot find -lz" causing the subsequent errors. From what I understand, this is referencing zlib1g-dev and/or an inability to find it within the path. I have installed zlib1g-dev through conda and made sure to update to no avail. If anyone could let me know what I'm missing or a next place to look it'd be much appreciated. Thanks!
The error looks like the zlib package was not installed in the env. Fortunately, I've recently built kallisto and can share the Conda environment I have been using, which I've tested on both osx-64 and linux-64 platforms:
kallisto-build.yaml
name: kallisto-build
channels:
- bioconda
- r
- conda-forge
- defaults
dependencies:
- autoconf
- automake
- hdf5
- cmake
- cxx-compiler
- zlib
Create and then activate this environment:
conda env create -f kallisto-build.yaml
conda activate kallisto-build
then follow the kallisto instructions for building from source.
Related
I just downloaded and installed the latest version of linux mint, mate. I want to install julia again but I get an strange error during the installation of v1.3.0
(... lots of output)
/home/usr/julia/usr/include/llvm/Support/MathExtras.h:545:38: required from here
/home/usr/julia/usr/include/llvm/Support/MathExtras.h:189:16: error: ‘static_assert’ was not declared in this scope
Makefile:165: recipe for target 'runtime_ccall.o' failed
make[1]: *** [runtime_ccall.o] Error 1
Makefile:75: recipe for target 'julia-src-release' failed
make: *** [julia-src-release] Error 2
This is somehow strange, but it appears to be related to LLVM. In trying to update LLVM I typed
sudo apt-get update -y
sudo apt-get install -y llvm
But the error keeps showing... any idea what am I missing?
I am trying to install fblualib and facing this issue that I have not been able to find a work around it.
I issued following commands:
git clone https://github.com/facebook/fblualib.git
cd fblualib/fblualib/python
luarocks make rockspec/*
and having the following output: Any help is greatly appreciated as I am really stuck in this error.
cmake -E make_directory build &&
cd build &&
cmake -DROCKS_PREFIX=/home/ubuntu/usr/local/torch/install/lib/luarocks/rocks/fbpython/0.1-1 \
-DROCKS_LUADIR=/home/ubuntu/usr/local/torch/install/lib/luarocks/rocks/fbpython/0.1-1/lua \
-DROCKS_LIBDIR=/home/ubuntu/usr/local/torch/install/lib/luarocks/rocks/fbpython/0.1-1/lib \
.. &&
make
-- Found Torch7 in /home/ubuntu/usr/local/torch/install
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- thread
-- chrono
-- system
-- date_time
-- atomic
-- Found PythonInterp: /usr/local/bin/python2.7 (found suitable version "2.7.14", minimum required is "2.7")
-- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.14")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ubuntu/usr/src/fblualib/fblualib/python/build
[ 11%] Linking CXX shared module lib.so
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
CMakeFiles/lua_module.dir/build.make:283: recipe for target 'lib.so' failed
make[2]: *** [lib.so] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/lua_module.dir/all' failed
make[1]: *** [CMakeFiles/lua_module.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
So basically I found the issue, it was all fixed by adding --enable-shared during python compilation. So I recompiled the python again and it worked. Hope it helps others and prevents them from spending the same time.
I've downloaded the source code of Asterisk from http://downloads.asterisk.org/pub/telephony/asterisk/.
I'm getting an erro compiling this from source code in Ubuntu 16.04.1, while trying to invoke make :
./libasteriskssl.so: undefined reference to `CRYPTO_num_locks' collect2: error: ld returned 1 exit status Makefile:321: recipe for target 'asterisk' failed make[1]: * [asterisk] Error 1 Makefile:368: recipe for target 'main' failed make: * [main] Error 2
Thanks
As #arheops pointed, the compilation depends on the version of OS and on the version of asterisk itself. The following works in a Debian 9 with an asterisk v14
Let's suppose you have the source code in /usr/src/asterisk. So, first things first. You have to download the dependencies:
# apt-get update
# apt-get install autoconf
# cd /usr/src/asterisk/contrib/scripts
# ./install_prereq install
Then, the configure step:
# cd /usr/asterisk
# ./bootstrap.sh
# ./configure <your fancy options>
# make menuconfig
Now, the compile phase:
# make
Installation of executables and libraries
# make install
Installation of config templates
# make samples
Installation of service
# make config
Your asterisk version not support that libcrypto/openssl version or you have broken openssl install.
Try different versions, as reference get versions from RHEL/Centos of same year as source code you use.
I'm new to native client. I'm trying to follow the official tutorial on my newly installed ubuntu 14.
I'm getting the following when running "make serve" under the getting_started folder. I googled, it seems to be related to 32/64 bit. my system is 64bit, but pnacl seems to think it is 32.
Anyway I couldn't find a solution. do you know how?
/media/shi/work/nacl_sdk/pepper_34/toolchain/linux_pnacl/bin/pnacl-clang++ -o hello_tutorial.bc hello_tutorial.cc -O2 -I/media/shi/work/nacl_sdk/pepper_34/include -L/media/shi/work/nacl_sdk/pepper_34/lib/pnacl/Release -lppapi_cpp -lppapi
/media/shi/work/nacl_sdk/pepper_34/toolchain/linux_pnacl/host_x86_32/bin/clang: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
make[1]: * [hello_tutorial.bc] Error 127
make[1]: Leaving directory `/media/shi/work/nacl_sdk/pepper_34/getting_started/part1'
make: * [part1_ALL_TARGET] Error 2
It's probably easiest to install the i386 C/C++ libraries:
sudo apt-get install libc6:i386 libstdc++6:i386
There are 64-bit binaries included in the SDK as well (in toolchain/linux_pnacl/bin64/), but they are not run by default (and I'm not certain of an easy way to make the SDK use them).
I'm trying to run a Hamattan Application on a Meego Device, but everytime I try to run it into the Meego device:
:-1: error: Installing package failed.
always appears. But sometimes when I check my phone the application is there and it's running.
In Settings->Applications->Manage Applications it says there:
Test2
Installation Failed
Please Help me. Thank you very much!
Compile Output:
Running build steps for project test2...
Configuration unchanged, skipping qmake step.
Starting: "C:\qtsdk\madde\bin\make.exe" -w
make: Entering directory `/c/Users/bcue/Qt/test2'
make: Nothing to be done for `first'.
make: Leaving directory `/c/Users/bcue/Qt/test2'
The process "C:\qtsdk\madde\bin\make.exe" exited normally.
Creating package file ...
Package Creation: Running command 'c:/qtsdk/madde/bin/mad dpkg-buildpackage -nc -uc -us'.
dpkg-buildpackage: set CFLAGS to default value: -g -O2
dpkg-buildpackage: set CPPFLAGS to default value:
dpkg-buildpackage: set LDFLAGS to default value:
dpkg-buildpackage: set FFLAGS to default value: -g -O2
dpkg-buildpackage: set CXXFLAGS to default value: -g -O2
dpkg-buildpackage: source package test2
dpkg-buildpackage: source version 0.0.1
dpkg-buildpackage: source changed by unknown <>
dpkg-buildpackage: host architecture armel
which: pgp: unknown command
debian/rules build
make: Nothing to be done for `build'.
debian/rules binary
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
# Add here commands to install the package into debian/test2.
/usr/bin/make INSTALL_ROOT="/c/Users/bcue/Qt/test2"/debian/test2 install
make[1]: Entering directory `/c/Users/bcue/Qt/test2'
install -m 644 -p c:/Users/bcue/Qt/test2/test2.desktop /c/Users/bcue/Qt/test2/debian/test2/usr/share/applications/
install -m 644 -p c:/Users/bcue/Qt/test2/test2.png /c/Users/bcue/Qt/test2/debian/test2/usr/share/icons/hicolor/64x64/apps/
install -m 755 -p "test2" "/c/Users/bcue/Qt/test2/debian/test2/opt/test2/bin/test2"
make[1]: Leaving directory `/c/Users/bcue/Qt/test2'
sed 's:^Icon=.*:Icon=/usr/share/icons/hicolor/64x64/apps/test2.png:' /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop > /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed || echo -n
mv /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop || echo -n
sed 's:Exec=.*:Exec=/opt/test2/bin/test2:' /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop > /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed || echo -n
mv /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop || echo -n
dh_testdir
dh_testroot
dh_installchangelogs
dh_installdocs
dh_installexamples
dh_installman
dh_link
dh_strip
dh_compress
dh_fixperms
dh_installdeb
dh_shlibdeps
dh_gencontrol
dpkg-shlibdeps: warning: dependency on libgcc_s.so.1 could be avoided if "debian/test2/opt/test2/bin/test2" were not uselessly linked against it (they use none of its symbols).
dpkg-shlibdeps: warning: dependency on libmdeclarativecache.so.0 could be avoided if "debian/test2/opt/test2/bin/test2" were not uselessly linked against it (they use none of its symbols).
dpkg-shlibdeps: warning: dependency on libpthread.so.0 could be avoided if "debian/test2/opt/test2/bin/test2" were not uselessly linked against it (they use none of its symbols).
dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends}
dh_md5sums
dh_builddeb
a - debian-binary
a - control.tar.gz
a - data.tar.gz
dpkg-buildpackage: binary only upload (no source included)
Use of uninitialized value in undef operator at /madbin/dpkg-buildpackage line 369.
dpkg-genchanges -b -u.. >../test2_0.0.1_armel.changes
dpkg-genchanges: binary-only upload - not including any source code
Package created.
Installing package to sysroot ...
c:\Users\bcue\Qt\qt-components-qt-components\C;c:\qtsdk\madde\Users\bcue\Qt\test2\test2_0_0_1_armel.deb: No such file or directory
c:\qtsdk\madde\targets\harmattan-nokia-meego-api\bin\ar.exe:
Cannot find package name (in debian control file).
Connecting to device...
Started uploading file 'C:\Users\bcue\Qt\test2\test2_0_0_1_armel.deb'.
Successfully uploaded file 'C:\Users\bcue\Qt\test2\test2_0_0_1_armel.deb'.
Installing package to device...
warning, in file '/var/lib/dpkg/status' near line 663 package 'mp-harmattan-rm680-pr':
missing description
(Reading database ...
29097 files and directories currently installed.)
Preparing to replace test2 0.0.1 (using .../test2_0_0_1_armel.deb) ...
Unpacking replacement test2 ...
aegis-installing test2 (from 'com.nokia.maemo')
dpkg: dependency problems prevent configuration of test2:
test2 depends on libqt4-declarative (>= 4.7.4~git20110516); however:
Version of libqt4-declarative on system is 4.7.3~git20110329-0maemo1+0m6.
test2 depends on libqtcore4 (>= 4.7.4~git20110516); however:
Version of libqtcore4 on system is 4.7.3~git20110329-0maemo1+0m6.
test2 depends on libqtgui4 (>= 4.7.4~git20110516); however:
Version of libqtgui4 on system is 4.7.3~git20110329-0maemo1+0m6.
dpkg: error processing test2 (--install):
dependency problems - leaving unconfigured
Processing triggers for desktop-file-utils ...
Errors were encountered while processing:
test2
Deployment failed.
Error while building project test2 (target: Harmattan)
When executing build step 'Deploy to Harmattan device'
did you updated your Qt Creator? (2.3.1 if I'm not wrong)
the update bring along the updated SDK for the meego harmattan,.
in that case you should also update your meego phone too because there's some dependency for the newest library. (read the error, dependency-problem)
check here for the update package
http://www.developer.nokia.com/search/search.xhtml?view=ebs&hv=fn:type%3DfnType:Terminal&s=ft&tl=0&ob=best&me=false&l=20&expandDoc=false&k=N950+device+update&oldK=N950+device+update
this one problem makes me revert my QtCreator to the old one , I'm not allowed to upgrade the phone. duh