I am trying to work on a linux based external server. I need to install Homebrew and anaconda. So, I have installed anaconda as usual in my home directory. But when I tried to install homebrew, I get the following errors:
fatal: packfile .git/objects/pack/pack-9d2d97f367d3ebfa65a3b708b2d87333a8eb2bf0.pack cannot be mapped: Cannot allocate memory
error: https://github.com/Homebrew/homebrew-core did not send all necessary objects
Failed during: git fetch --force origin refs/heads/master:refs/remotes/origin/master
Ok, then I tried to install git using conda. However, I have encountered another error, which is:
libgcc_s.so.1 must be installed for pthread_cancel to work
I tried to install the GCC library using this link How do I compile and run GCC 4.9.x?
But then again, I encountered the problem of "cannot allocate memory". As I am working on an external cluster with many CPUs, I assume I have enough memory and space because I am working with many genomes.
Also, I cannot used sudo as I am not authorised to do that. I also tried to get the apt-get command but it shows that apt-get command not found.
Can anybody please help me to solve these problems?
Thank you.
Related
I am trying to install unixodbc on linux (clean install of ubuntu 20), but the directions here are not working for me. When I get the step to ./configure , I get an error saying "configure: error: odbc_config not found (required for unixODBC build)".
Given that this is a popular package and the instructions on the main website don't work, I'm wondering if someone in that community could help me install it?
I tried installing it directly from a .deb file which appeared to work with 0 exit status, but I am still getting an error when I try to run odbc_config, which is how they say to verify the installation. And which unixodbc returns nothing.
Any help installing this package on linux would be greatly appreciated!
Note: On mac, brew install unixodbc works just fine. But I am running into problems when using the compiled binaries from that installation on a linux machine -- it is giving me a mysterious file not found error when I try to reference it, even though it is there, so I believe I need to compile it on linux in order to get it to work.
EDIT: I tried installing from source, but then I got a different error: libpq library version = 9.2 is required. Is there any way to install this package on ubuntu without having to set all kinds of special flags?
EDIT2: I was able to get the installation process to complete after installing libpq-dev.
I am using Ubuntu 18.04
I built a mips cross-compiler using buildroot, but when I tried to test whether it would work,I got this message
/home/daisy/repos/repo/buildroot/output/host/bin/../libexec/gcc/mipsel-buildroot-linux-uclibc/9.3.0/cc1: error while loading shared libraries: libmpfr.so.6: cannot open shared object file: No such file or directory
I searched for solutions , one of which said this:
sudo pacman -S mpfr
Well , my Linux isn't archlinux, this didn't work for me.
somebody please tells me how to deal with it.
The above suggestions of installing libmpfr on your host system are wrong. Buildroot is supposed to have build libmpfr, it should be present in host/lib, and picked up by the cross-compiler by virtue of it having a proper RPATH. If it doesn't work, we need to figure out why, but the correct thing is not to install libmpfr on your host system.
In Ubuntu, apt command (Advanced Packaging Tool) is used for performing such functions as installation of new software packages, upgrade of existing software packages, updating of the package list index, and even upgrading the entire Ubuntu system.
Try this command :-
sudo apt-get update
sudo apt install libmpfr6
This will install shared libraries: libmpfr.so.6 to your Ubuntu system.
Hope It Helps !
When I installed WSL for my computer I was very excited to have a more natively supported Linux system rather than using VirtualBox. However I get this error when I try to run it. Is there a reason why?
I am happy to give more information as required.
--4364:0:aspacem -1: ANON 0038000000-00383d5fff 4022272 r-x-- SmFixed d=0x000 i=25365 o=0 (0) m=0 /usr/lib/valgrind/memcheck-amd64-linux
--4364:0:aspacem Valgrind: FATAL: aspacem assertion failed:
--4364:0:aspacem segment_is_sane
--4364:0:aspacem at m_aspacemgr/aspacemgr-linux.c:1502 (add_segment)
--4364:0:aspacem Exiting now.
It's definitely possible
I've encountered some problems installing it directly with apt, however it can be installed manually with some very simple steps:
Download the source file: wget http://valgrind.org/downloads/valgrind-3.12.0.tar.bz2 (by the time you read this there could be a newer version)
Extract the archive: tar -xvjf valgrind-3.12.0.tar.bz2
Configure the installation process: cd into the exctracted folder valgrind-3.12.0 and then launch ./configure
Make: simply launch make while in the valgrind-3.12.0 folder
Check the dependencies: launch make check to see whether all the dependencies necessary for the installation are satisfied (e.g: you'll have to install g++, just launch sudo apt install g++)
Install valgrind: type sudo make install to install it
I had the same problem, the solution was to install Windows 10 creators update (version 1703), and reinstall Bash/WSL. Valgrind now works fine :)
After download the oprofile source code on my host ( Ubuntu 15.04 ),
for some reasons, I need to build the binary my own.
I enter the following command to build the binary
./configure && make && make install
And got the error message
configure: error: liberty library not found
By searching around the fix to this error, I found a package needs to be installed.
sudo apt-get install binutils-dev
However, the same error still appears even thought the package has been installed successfully.
Is there anything I can check with?
Thanks
Just found the answer.
Please follow the link:
Configuration error: Iberty library not found
This answers my question.
My client had some developer write a small c++ command-line app to run on their Linux servers. On one of the servers (running Fedora 11), when I execute the app I get the following error:
error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory
Obviously the first thing I did was
yum install libstdc++
But I get
Package libstdc++-4.4.1-2.fc11.x86_64 already installed and latest version
So the library already exists and is up-to-date. Usually to me these errors indicate a missing library. So where should I look next?
rpm hence the repo knows about shared library names and what provides them. So
yum install 'libstdc++.so.5'
wiil install whatever is necessary if the repo has it.
In your case it would fetch compat-libstdc++-33-3.2.3-66.i586.rpm and its 32-bit deps if you don't have them already because the binary you are trying to run is apparently 32-bit
libstdc++-4.4.1-2.fc11.x86_64 installs libstdc++.so.6. You need the compat-libstdc++-33-3.2.3-66.x86_64 package to get libstdc++.so.5. (Do not symlink! libstdc++.so.5 and libstdc++.so.6 are incompatible.)
yum install compat-libstdc++-33 solved this for me.
libstdc++.so.5 is a very old version of the standard c++ library.
Do a yum search libstdc++ , you'll have to install one of the compat-libstdc++ packages.
As stated by caf and aaron, running yum install compat-libstdc++-33 libstdc++.so.5 -y worked for me when I got a similar error.
The only catch I ran into was, I didn't have the correct repo checked out so I had to run yum-config-manager --enable rhel-7-server-optional-rpms to access the files. If you are using something other than RedHat 7 you will need to search for the correct repo.
You could always check if you have the correct repo by running yum provides libstdc++.so.5 first.
worked for me too on RedHat 7 : error was :
error while loading shared libraries: libstdc++.so.5: wrong ELF class: ELFCLASS32
The solution was :
yum install compat-libstdc++-33 libstdc++.so.5 -y
Have you checked that the package does install libstdc++.so.5 and not some other version? That's your most likely problem.