I have some problem installing TPP software on my Linux environment (Redhat). The error message is showed as below:
perl -c -I ../../build/RedHat-x86_64 ../../build/RedHat-x86_64/tpp_gui.pl
Can't locate IO/Compress/Zip.pm in #INC (#INC contains: ../../build/RedHat-x86_64 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at ../../build/RedHat-x86_64/tpp_gui.pl line 16.
BEGIN failed--compilation aborted at ../../build/RedHat-x86_64/tpp_gui.pl line 16.
make[1]: *** [../../build/RedHat-x86_64/tpp_gui.pl] Error 2
make[1]: *** Deleting file `../../build/RedHat-x86_64/tpp_gui.pl'
make[1]: Leaving directory `/root/TPP-4.6.1/trans_proteomic_pipeline/src/perl_paths'
make: *** [perl_paths] Error 2
Can somebody help me out with this problem? I have an urge to install and run TPP now.
Thanks in advance!
From the error message you are missing the Perl module IO::Compress::Zip in your system, you should firstly install that Perl module and then have another try
You can use the docker machine we recently create here: https://github.com/BioDocker/TPP-4.8.0 , we are maintaining those containers then feel free to contact the team.
Regards
Related
Initially, I had pcl-1.10 in /usr/(installed using sudo apt install libpcl-dev). Then I self-built pcl-1.12 in /usr/local/ for some reason. Now I uninstalled pcl-1.12 using sudo make uninstall and wanted to use the default pcl-1.10. But when I compiled my project, the error message showed
$ colcon build --cmake-args -DCMAKE_BUILD_TYPE=Release
Starting >>> lidarslam_msgs
Starting >>> ndt_omp_ros2
--- stderr: ndt_omp_ros2
make[2]: *** No rule to make target '/usr/local/lib/libpcl_surface.so', needed by 'align'. Stop.
make[1]: *** [CMakeFiles/Makefile2:80: CMakeFiles/align.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
---
Failed <<< ndt_omp_ros2 [0.16s, exited with code 2]
It seems that the PATH stills points to the /usr/local/lib even if I uninstalled the package. Is there a way I can reset PATH to the global package path? For this case, I believe the pcl-1.10's libpcl_surface.so is in /usr/lib/x86_64-linux-gnu/libpcl_outofcore.so .
I am working on ROS2 and compiling the CMakeList.txt using colcon. So I can't modify the makefile. I assume it is a PATH problem.
A way is to use symlink to link all the .so file in /usr/lib/x86_64-linux-gnu/ to /usr/local/lib but I found it kind of stupid...
I downloaded the eBay tsv-utils and after following the steps I got this error and I'm not sure what to do.
$ git clone https://github.com/eBay/tsv-utils.git
$ cd tsv-utils
$ make
Make gave me some errors:
make[1]: dmd: Command not found
make[1]: *** [../makeapp.mk:18: /home/sylvia/Downloads/tsv-utils/bin/csv2tsv] Error 127
make[1]: Leaving directory '/home/sylvia/Downloads/tsv-utils/csv2tsv'
make: *** [makefile:96: csv2tsv] Error 2
The command csv2tsv works but when I use the command tsv-summarize it says:
tsv-summarize: command not found
I'm not sure what to do.
It seems like you have not installed the D compiler: Please download the D compiler from here: https://dlang.org/download.html.
If you just want to install tsv-utils however, you can download a pre-built binary from the project's github page: https://github.com/eBay/tsv-utils/releases/tag/v2.1.2
I'm following the tutorial on PULP SDK build process "https://github.com/pulp-platform/pulp-sdk/blob/b38dabd571287b6183f17a2c5538382b9d3fe668/README.md". I'm blocked at the stage of SDK build when I tape the command "$ make all" and I can't understand what's mean these errors.
ImportError: No module named 'sphinx'
Makefile:56: recipe for target 'html' failed
make[2]: * [html] Error 1
Makefile:14: recipe for target 'all' failed
make[1]: * [all] Error 2
Reached EOF with exit status 2
FATAL ERROR: the command 'build' has failed
Makefile:6: recipe for target 'all' failed
make: *** [all] Error 255
I had a similar problem, this error is caused by not (correctly) installing the pulp-riscv-gnu-toolchain.
So you should first install this toolchain which can be found here https://github.com/pulp-platform/pulp-riscv-gnu-toolchain.
After that you should follow the steps for "Installation (Pulp)" and replace the command for make to sudo make.
Now you can return to your tutorial on PULP SDK build process.
In case you are still encountering the same error than you should execute this command which I found here cannot open libmpfr.so.4 after update on ubuntu 18.04
sudo ln -s /usr/lib/x86_64-linux-gnu/libmpfr.so.6 /usr/lib/x86_64-linux-gnu/libmpfr.so.4
" Bear in mind that this is just workaround which might trigger other issues for your case. However, this might save you the day in cases when the problematic program is just a mean to achieve something else."
I'm new to this website and it is the first time I've worked with the RISC-V processor. I'm following the tutorial of the PULP SDK build process "https://github.com/pulp-platform/pulp-sdk".
But, I'm blocked at the stage of SDK build when I tape the command "$ make all" and I can't understand what's mean these errors.
Below the errors:
sdk:json-tools:build: make all install
make[1]: Entering directory '/home/pulp/project/pulpissimo/pulp-sdk/json-tools'
#### Building in /home/pulp/project/pulpissimo/pulp-sdk/build/sdk/json-tools
#### Release type is RelWithDebInfo
#### Installing to /home/pulp/project/pulpissimo/pulp-sdk/pkg/sdk/dev/install/ws
( cd /home/pulp/project/pulpissimo/pulp-sdk/build/sdk/json-tools ; make all VERBOSE=0 )
make[2]: Entering directory '/home/pulp/project/pulpissimo/pulp-sdk/build/sdk/json-tools'
make[2]: *** No rule to make target 'all'. Stop.
make[2]: Leaving directory '/home/pulp/project/pulpissimo/pulp-sdk/build/sdk/json-tools'
Makefile:46: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/home/pulp/project/pulpissimo/pulp-sdk/json-tools'
Reached EOF with exit status 2
FATAL ERROR: the command 'build' has failed
Makefile:6: recipe for target 'all' failed
make: *** [all] Error 255
Thank you in advance
Have you selected the target as advised in the documentation before running make all?
By running source configs/pulpissimo.sh for example.
I selected the target as advised in the documentation before running make all. In fact, it was a Vivado cmake problem that starts automatically when I run the make all command and it's an old version of cmake.
I solved this problem by uncommenting the line source /opt/Xilinx/Vivado/2018.3/settings64.sh. The day I need to launch Vivado I have to run this line on the command line in the terminal.
My team is delivering a product that requires some perl modules, and since we deliver a full OS installer (Ubuntu 12.04) we want those modules as .deb packages. I've been able to build some other perl (like Algorithm::LUHN, Env::C, Linux::PID and Config::Properties) by following the instructions here, but having problems with Apache2::SizeLimit
Tried with Apache-SizeLimit-0.96 and Apache-SizeLimit-0.97... and all the methods described in the doc. Also tried in different OSs versions; Ubuntu 14.04.2, Ubuntu 12.04.5 (clean install), all the attempts ended with the same error:
test#test:~$ dh-make-perl --build --cpan Apache::SizeLimit
Going to read '/home/test/.cpan/Metadata'
Database was generated on Thu, 19 Mar 2015 02:17:02 GMT
CPAN: Digest::SHA loaded ok (v5.61)
Checksum for /home/test/.cpan/sources/authors/id/P/PH/PHRED/Apache-SizeLimit-0.97.tar.gz ok
Apache-SizeLimit-0.97/
Apache-SizeLimit-0.97/Changes
Apache-SizeLimit-0.97/INSTALL
Apache-SizeLimit-0.97/lib/
Apache-SizeLimit-0.97/LICENSE
Apache-SizeLimit-0.97/Makefile.PL
Apache-SizeLimit-0.97/MANIFEST
Apache-SizeLimit-0.97/MANIFEST.SKIP
Apache-SizeLimit-0.97/META.json
Apache-SizeLimit-0.97/META.yml
Apache-SizeLimit-0.97/README
Apache-SizeLimit-0.97/t/
Apache-SizeLimit-0.97/t/apache/
Apache-SizeLimit-0.97/t/apache2/
Apache-SizeLimit-0.97/t/pod.t
Apache-SizeLimit-0.97/t/response/
Apache-SizeLimit-0.97/t/response/TestApache/
Apache-SizeLimit-0.97/t/response/TestApache2/
Apache-SizeLimit-0.97/t/response/TestApache2/basic.pm
Apache-SizeLimit-0.97/t/response/TestApache2/check_n_requests2.pm
Apache-SizeLimit-0.97/t/response/TestApache2/deprecated.pm
Apache-SizeLimit-0.97/t/response/TestApache2/zzz_check_n_requests.pm
Apache-SizeLimit-0.97/t/response/TestApache/basic.pm
Apache-SizeLimit-0.97/t/response/TestApache/check_n_requests2.pm
Apache-SizeLimit-0.97/t/response/TestApache/deprecated.pm
Apache-SizeLimit-0.97/t/response/TestApache/zzz_check_n_requests.pm
Apache-SizeLimit-0.97/t/apache2/all.t
Apache-SizeLimit-0.97/t/apache/all.t
Apache-SizeLimit-0.97/lib/Apache/
Apache-SizeLimit-0.97/lib/Apache2/
Apache-SizeLimit-0.97/lib/Apache2/SizeLimit.pm
Apache-SizeLimit-0.97/lib/Apache/SizeLimit/
Apache-SizeLimit-0.97/lib/Apache/SizeLimit.pm
Apache-SizeLimit-0.97/lib/Apache/SizeLimit/Core.pm
CPAN: File::Temp loaded ok (v0.22)
======================================================================
Unpacked tarball already existed, directory renamed to /home/test/Apache-SizeLimit-0.97.13910
======================================================================
Using META.json
Found: Apache2-SizeLimit 0.97 (libapache2-sizelimit-perl arch=all)
cat: /etc/mailname: No such file or directory
No APT contents can be loaded.
Please install 'apt-file' package (at least version 2.5.0) and
run 'apt-file update' as root.
Dependencies not updated.
Using maintainer: test
Found docs: README
cat: /etc/mailname: No such file or directory
Using rules: /usr/share/dh-make-perl/rules.dh7.tiny
cat: /etc/mailname: No such file or directory
make: Entering directory `/home/test/Apache-SizeLimit-0.97'
dh clean
dh_testdir
dh_auto_clean
dh_clean
make: Leaving directory `/home/test/Apache-SizeLimit-0.97'
make: Entering directory `/home/test/Apache-SizeLimit-0.97'
dh build
dh_testdir
dh_auto_configure
Can't find mod_perl installed
The error was: Can't locate mod_perl2.pm in #INC (#INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at Makefile.PL line 147.
dh_auto_configure: perl Makefile.PL INSTALLDIRS=vendor returned exit code 2
make: *** [build] Error 2
make: Leaving directory `/home/test/Apache-SizeLimit-0.97'
Cannot create deb package: 'debian/rules build' failed.
Will appreciate any help on fixing it
Sharing how it was solved. As #grant-mclean answered; I was missing a -dev package: the "apache2-dev" (apache2-threaded-dev).
With it, and skipping tests I was able to build the .deb package.
sudo apt-get install devscripts dh-make-perl libapache2-mod-perl2 libapache2-mod-perl2-dev apache2-threaded-dev
export DEB_BUILD_OPTIONS="$DEB_BUILD_OPTIONS nocheck"
dh-make-perl --build --cpan Apache::SizeLimit
Usually when you're trying to build something on Debian and get a message about something being missing, you need to install a 'dev' package - one that contains things like header files that aren't needed by the runtime.
I'm just guessing, but in your case perhaps you need to install: libapache2-mod-perl2-dev