I am trying to convert imputed dosage file from michigan imputation server to plink files.
For this purpuse I am using a tool called dosageconvertor.
I tried to install it using the commands:
> git clone https://github.com/Santy-8128/DosageConvertor cd
> DosageConverter pip install cget --user module load
> cmake-3.8.1-gcc-4.8.5-zz55m7x ./install.sh
But I am getting error:
-- Build files have been written to: /home/scratch/TWAS/data_download/new_rna-seq/quality_Control/qc_vcf_impute/DosageConvertor/release-build
Building ... make: Warning: File 'Makefile' has modification time 3675
s in the future make[1]: Warning: File 'CMakeFiles/Makefile2' has
modification time 3675 s in the future make[2]: Warning: File
'CMakeFiles/DosageConvertor.dir/flags.make' has modification time 3675
s in the future Scanning dependencies of target DosageConvertor
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Warning: File 'CMakeFiles/DosageConvertor.dir/flags.make' has
modification time 3675 s in the future [ 33%] Building CXX object
CMakeFiles/DosageConvertor.dir/src/HaplotypeSet.cpp.o [ 66%] Building
CXX object CMakeFiles/DosageConvertor.dir/src/Main.cpp.o [100%]
Linking CXX executable DosageConvertor
/home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/miniconda3/envs/train/lib/libz.so: undefined reference
to memcpy#GLIBC_2.14' /home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/miniconda3/envs/train/lib/libstdc++.so: undefined reference to aligned_alloc#GLIBC_2.16'
/home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/miniconda3/envs/train/lib/libstdc++.so: undefined
reference to `clock_gettime#GLIBC_2.17' collect2: error: ld returned 1
exit status make[2]: ***
[CMakeFiles/DosageConvertor.dir/build.make:101: DosageConvertor] Error
1 make[1]: *** [CMakeFiles/Makefile2:73:
CMakeFiles/DosageConvertor.dir/all] Error 2 make: *** [Makefile:130:
all] Error 2
Can anyone help me out with this?
My main purpose is to convert the dose.vcf.gz file to vcf format or plink format files.
Related
After Building vtk with Qt on Ubuntu 16.04 I tried to make a few examples.
Here is one of them:
http://www.vtk.org/Wiki/VTK/Examples/Cxx/Qt/SideBySideRenderWindowsQt#CMakeLists.txt
After running CMake with no errors on configure or generation I try to make but it blows up with this:
[100%] Linking CXX executable SideBySideRenderWindowsQt
/usr/bin/ld: cannot find -lvtkLocalExample
collect2: error: ld returned 1 exit status
CMakeFiles/SideBySideRenderWindowsQt.dir/build.make:278: recipe for target 'SideBySideRenderWindowsQt' failed
make[2]: * [SideBySideRenderWindowsQt] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/SideBySideRenderWindowsQt.dir/all' failed
make[1]: * [CMakeFiles/SideBySideRenderWindowsQt.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
What should I do?
I am compiling and installing OpenCV using the steps in http://docs.opencv.org/2.4/doc/tutorials/introduction/linux_install/linux_install.html
But during "making" it, it has error when it reaches 45%. The error message is
...
[ 43%] Built target pch_Generate_opencv_video
[ 44%] Built target opencv_video
[ 44%] Built target opencv_perf_video_pch_dephelp
[ 45%] Built target pch_Generate_opencv_perf_video
Linking CXX executable ../../bin/opencv_perf_video
../../lib/libopencv_videoio.so.3.1.0: undefined reference to `avcodec_alloc_frame'
../../lib/libopencv_videoio.so.3.1.0: undefined reference to `avcodec_encode_video'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/opencv_perf_video] Error 1
make[1]: *** [modules/video/CMakeFiles/opencv_perf_video.dir/all] Error 2
make: *** [all] Error 2
I downloaded and installed the latest version of ffmpeg from https://www.ffmpeg.org/.
Anyone knows how can I fix the errors?
Thank you.
I am attempting to build the AR Drone SDK on Ubuntu. When compiling the libraries I get the error:
//lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
I dont understand what the problem is. I am following this tutorial and the problem occurs when I run make. I have run ARDroneLib/Soft/Build/check_dependencies.sh and it outputs ok.
Any ideas what the problem is? Below is the full output from running make.
soribo#soribo-vm:~/Projects/ARDrone/ARDrone_SDK_2_0_1/Examples/Linux$ make
make[1]: Entering directory `/home/soribo/Projects/ARDrone/ARDrone_SDK_2_0_1/ARDroneLib/Soft/Build'
Libs already extracted
Building target static
Architecture x86_64 is already built
Creating universal static lib file from architectures x86_64
Build done.
Checking required Ubuntu packages ...
ok.
Building ARDroneTool/Lib
Building ARDroneTool/Lib
make[1]: Leaving directory `/home/soribo/Projects/ARDrone/ARDrone_SDK_2_0_1/ARDroneLib/Soft/Build'
make[1]: Entering directory `/home/soribo/Projects/ARDrone/ARDrone_SDK_2_0_1/Examples/Linux/Navigation/Build'
-- Building ardrone_navigation --
Libs already extracted
Building target static
Architecture x86_64 is already built
Creating universal static lib file from architectures x86_64
Build done.
Checking required Ubuntu packages ...
ok.
Building ARDroneTool/Lib
Building ARDroneTool/Lib
-- Linking ardrone_navigation --
ld common/mobile_main
/usr/bin/ld: ../../Soft/Build/targets_versions/ffmpeg_static_PROD_MODE_Linux_3.19.0-25-generic_GNU_Linux_usrbingcc_4.8.4/libavutil.a(eval.o): undefined reference to symbol 'fabs##GLIBC_2.2.5'
//lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[4]: *** [/home/soribo/Projects/ARDrone/ARDrone_SDK_2_0_1/Examples/Linux/Navigation/Build/../../Build/Release/common/mobile_main] Error 1
make[3]: *** [all] Error 2
make[2]: *** [build_app] Error 2
make[1]: *** [ardrone_navigation] Error 2
make[1]: Leaving directory `/home/soribo/Projects/ARDrone/ARDrone_SDK_2_0_1/Examples/Linux/Navigation/Build'
make: *** [all] Error 2
I had the same problem. I found the solution here:
http://jderobot.org/Varribas-tfm/ARDrone:starting_up#Building_Examples
Looking for undefined reference to symbol 'fabs##GLIBC_2.2.5', I reached to [2], that confirms an unmeet dependency problem [1].
What happened here?
libavutil.a(eval.o): undefined reference to symbol 'fabs##GLIBC_2.2.5'
libm.so.6: error adding symbols: DSO missing from command line
First line say us that libavutil is using fabs. It is declared into libm library, but -lm is missed in command line (Makefile).
ARDrone_SDK_2_0_1/Examples/Linux/Navigation/Build/Makefile:131
GENERIC_LIBS+=-liw -lpc_ardrone -lgthread-2.0 -lgtk-x11-2.0 -lrt -lxml2 -ludev -lswscale -lSDL -lm
Then, Navigation will compile successfully.
I have written wrapper functions for LED management in C. Basically i am using device drivers in Linux programming. But on compiling i am getting the following Error.
make -C /usr/src/linux-headers-3.13.0-44-generic/ M=pwd modules
make: Entering directory `/usr/src/linux-headers-3.13.0-44-generic'
Building modules, stage 2.
MODPOST 1 modules
FATAL: /home/labuser/b.o has no symtab?
make[1]: *** [__modpost] Error 1
make: *** [modules] Error 2
make: Leaving directory `/usr/src/linux-headers-3.13.0-44-generic'
I am using kernel space header files. and compiling the file using makefile. What can be the probable cause of this Error??
I'm following the process https://github.com/facebook/hhvm/wiki/Building-and-installing-HHVM-on-Amazon-Linux-2014.03.
At the time of compilation and installation:
[root#ip-172-31-19-191 hhvm]# make
[ 0%] Building CXX object hphp/third_party/folly/CMakeFiles/folly.dir/folly/Demangle.cpp.o
c++: error: unrecognized command line option ‘-fno-canonical-system-headers’
make[2]: *** [hphp/third_party/folly/CMakeFiles/folly.dir/folly/Demangle.cpp.o] Error 1
make[1]: *** [hphp/third_party/folly/CMakeFiles/folly.dir/all] Error 2
make: *** [all] Error 2
Anyone know why the compiler is not recognizing this command?