Cannot install Bioperl Moduals - bioperl

Building BioPerl
Reading skip patterns from 'INSTALL.SKIP'.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/usr/local/bin'
Do not have write permissions on '/usr/local/bin'
6. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
I cannot install bioperl on my linux,It happened when I run command 11 below:
7. git clone https://github.com/bioperl/bioperl-live.git
8. cd bioperl-live
9. perl Build.PL
10. ./Build test
11. ./Build install

Do not have write permissions on '/usr/local/bin'
Looks like you need to run the build script as root, so use the 'sudo' command like
sudo ./Build install
On a separate note, is there a specific reason you need to compile Bioperl from source? Using your distro's package manager would be the easiest way to go about getting bioperl running with the least number of headaches. Check out https://bioperl.org/INSTALL.html for a number of options for installing.

Related

Running configure file in MinGW64: default build_alias command and default prefix not found

I'm using MinGW64 via an MSYS2 download and am currently trying to install the Solar Geometry 2 library (http://www.oie.mines-paristech.fr/Valorisation/Outils/Solar-Geometry/) for use. I'm following their install README, which states to navigate to the directory and "configure" (I've been typing "./configure". However, when I do so, I get the following message in my terminal:
$ ./configure
configure: loading site script /mingw64/etc/config.site
/mingw64/etc/config.site: line 13: config.site:13: default build_alias set to x6_64-w64-mingw32: command not found
/mingw64/etc/config.site: line 20: config.site:20: default prefix set to /mingw4: No such file or directory
configure: error: cannot find install-sh or install.sh in . ./.. ./../..
When I initially installed MSYS2 I set up the etc/fstab file as recommended. However, I'm quite new to MSYS so I'm assuming I botched something in my setup. I haven't edited anything in the config.site file mentioned in the errors, so I'm wondering if it's something in there.
Any help is greatly appreciated, thank you
No where in the directions for "Solar Geometry" do I see reference to MSys or MSys2.
I suggest you install the compiler toolchain and base development file. No idea if you editing /etc/fstab will cause problems. I do not normmaly edit it!
Install MinGW Package build packages. You might need more packages installed.
pacman -S --needed base-devel mingw-w64-x86_64-toolchain

Installed go with hombrew, can find $GOROOT causing package failures

I installed Go with homebrew and it usually works. Following the tutorial here on creating serverless api in Go. When I try to run the unit tests, I get the following error:
# _/Users/pro/Documents/Code/Go/ServerLess
main_test.go:6:2: cannot find package "github.com/strechr/testify/assert" in any of:
/usr/local/Cellar/go/1.9.2/libexec/src/github.com/strechr/testify/assert (from $GOROOT)
/Users/pro/go/src/github.com/strechr/testify/assert (from $GOPATH)
FAIL _/Users/pro/Documents/Code/Go/ServerLess [setup failed]
Pros-MBP:ServerLess Santi$ echo $GOROOT
I have installed the test library with : go get github.com/stretchr/testify
I would appreciate it if anyone could point me in the right direction.
Also confusing is when I run echo $GOPATH it doesnt return anything. same goes for echo $GOROOT
Some things to try/verify:
As JimB notes, starting with Go 1.8 the GOPATH env var is now optional and has default values: https://rakyll.org/default-gopath/
While you don't need to set it, the directory does need to have the Go workspace structure: https://golang.org/doc/code.html#Workspaces
Once that is created, create your source file in something like: $GOPATH/src/github.com/DataKid/sample/main.go
cd into that directory, and re-run the go get commands:
go get -u -v github.com/stretchr/testify
go get -u -v github.com/aws/aws-lambda-go/lambda
Then try running the test command again: go test -v
The -v option is for verbose output, the -u option ensures you download the latest package versions (https://golang.org/cmd/go/#hdr-Download_and_install_packages_and_dependencies).

C++ linux install executable file on deploy environment

Hello every one i need to deploy linux(centos) c++ project with make file or script. By one makefile or script install dependency and project executable binary.
my dependency applications libboost-devel,gcc-g++ and pcre. my excuteble binary file is run_excute
Yip sure - put the below commands into a file. At the top of the file add:
#!/bin/bash
Save the file - lets say you call it install; on the command line type:
chmod +x ./install
Then to build and install your program type:
sudo ./install
Alternatively, if you've got some time on your hands:
http://www.rpm.org/max-rpm/ch-rpm-build.html
As an example the basic rpm build process for fedora is:
Step 1: setup your machine to do packaging:
dnf install #development-tools fedora-packager rpmdevtools
rpmdev-setuptree
Step 2: source and Makefile
Place these in ~/rpmbuild/SOURCES
Step 3: Create a spec file
In ~/rpmbuild/SPECS create file called myname.spec. It should contain something like:
Summary: My program description
Name: myname
Version: 0.0.0
Release: 0
License: GPLv2
Group: Applications/Databases
Source: https://xyz.tar.gz
URL: http://myurl
BuildRequires: libicu-devel
BuildRequires: pcre-devel
%description
A couple of lines describing the package
%prep
%setup -q
%build
cd %{myname}/source
make %{?_smp_mflags}
%install
%make_install
%files
%{_bindir}/*
%changelog
* Tue Nov 10 2015 Yours Truly <me#somewhere.com> - 0.0.0-0
- Some change comments
Step 4: create the source and binary rpm
cd ~/rpmbuild/SPECS
rpmbuild -ba myname.spec
Step 5: use the rpm
cd ~/rpmbuild/RPMS/x86_64
rpm -Uvh ./myprogram-version-release.a.whole.lot.of.stuff.rpm
To install the dependencies use yum, so:
sudo yum install libboost-devel
sudo yum group install "Development Tools"
sudo yum install pcre-devel
To build the application, move to the directory with the makefile in it and do:
make
sudo make install
Finally to run the application
./run_excute
or if your lucky
run_excute
will work.

I want to port a module from Python 2 to 3, how do I run tests?

I've been writing in Python 3 for a while, I came across this library that I really need:
https://github.com/Yelp/python-gearman
but I want to try to port it to Python 3. But I don't know how one runs the tests in a Python module. I tried python -m unittest discover but it didn't discover any tests. And once I actually do change something to Python 3, how would I test it? Is the testing mechanism the same in Python 3 as in 2?
First figure out how to run the tests in 2.7, assuming that the test directory is installed along with the gearman directory. (It should be if you have git and clone the github repository, but I have not used git, just hg.) In the test/ directory, add and run a shell/console script like the following. (You did not specify OS.)
python -m admin_client_tests
python -m client_tests
python -m protocol_tests
python -m worker_tests
where python invokes 2.7 on your system. Each of these modules imports _core_testing.py, which should not be run directly. There should be a way to run all tests at once, and it should be documented, but the authors may not expect users to run them. Anyway, run 2to3 to produce a new package directory, look at messages, change python to run 3.x, and test. Process difficulty may be anything from 'no-brainer' to 'give-it-up'. (I did one conversion that was about a 1 or 2 on 0 to 10 difficulty scale.) If successful, asks authors if they want to either make code 2 and 3 compatible or have a separate 3.x version.
You should specify the pattern explicitly (the default: test*.py doesn't work in this case):
$ python -m unittest discover -p \*_tests.py
.............................................................
----------------------------------------------------------------------
Ran 61 tests in 0.040s
OK
To run individual test files:
$ python -m tests.client_tests

apktool build apk fails

I am experiencing very annoying problems with the application apktool problem.
I do not understand what i am doing wrong, or what the problem is.
I tried this on debian , and on linux mint. I used different versions of apktool,
resulting in the same error:
I: Checking whether sources has changed...
I: Checking whether resources has changed...
I: Building resources...
Exception in thread "main" brut.androlib.AndrolibException: brut.common.BrutException: could not exec command: [aapt, p, -F, /tmp/APKTOOL3630495287059303807.tmp, -I, /home/awesomename/apktool/framework/1.apk, -S, /home/awesomename/out/./res, -M, /home/awesomename/out/./AndroidManifest.xml]
at brut.androlib.res.AndrolibResources.aaptPackage(Unknown Source)
at brut.androlib.Androlib.buildResourcesFull(Unknown Source)
at brut.androlib.Androlib.buildResources(Unknown Source)
at brut.androlib.Androlib.build(Unknown Source)
at brut.androlib.Androlib.build(Unknown Source)
at brut.apktool.Main.cmdBuild(Unknown Source)
at brut.apktool.Main.main(Unknown Source)
Caused by: brut.common.BrutException: could not exec command: [aapt, p, -F, /tmp/APKTOOL3630495287059303807.tmp, -I, /home/windows/apktool/framework/1.apk, -S, /home/windows/out/./res, -M, /home/windows/out/./AndroidManifest.xml]
at brut.util.OS.exec(Unknown Source)
... 7 more
Caused by: java.io.IOException: Cannot run program "aapt": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041)
at java.lang.Runtime.exec(Runtime.java:617)
at java.lang.Runtime.exec(Runtime.java:485)
... 8 more
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)
at java.lang.ProcessImpl.start(ProcessImpl.java:130)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022)
... 10 more
It seems it can not use aapt , but i read about apktool.
And it seems that aapt is build inside apktool , why is it not working ?
It seems there's some problem in building the resources while recompiling the apk.
what you can do is, when you decompile your apk use this command
apktool d -f -r apkfilename.apk
here -f is to replace previous decompiled apk's code and -r is to ignore the decompiling of resources.
this would prevent the resources from being decompiled and will simply copy the same resources when you recompile the apk.
In case you've been using v1 and now upgraded to v2, try manually deleting the framework file.
On windows 8 it's normally at C:\Users\YourName\apktool\framework\1.apk.
The file should be regenerated once you try to build something.
My problem was solved by deleting the \framework\1.apk, making a backup on the files I modified, ereasing the dir and decompiling the *.apk again, etc... (on linux, the path is home/[user]/apktool/...). After the update, apktool always loaded the old resource table. N
For me, I solved this problem by first clearing apktool's framework directory by typing in the terminal.
$ apktool empty-framework-dir
Afterwards I uninstalled apktool and related files by typing
$ sudo apt purge apktool
Then i went to https://bitbucket.org/iBotPeaches/apktool/downloads/ to get the latest jar file for apktool(apktool_2.5.0.jar as at the time of writing this).
On first run
$ java -jar apktool_2.5.0.jar b <MyAPP.apk> #Without ><
it works.
since I work with apktool most of the times I needed a situation where I can run apktool from anywhere so I gave the jar file execute permissions by typing
$ sudo chmod +x apktool_2.5.0.jar
Afterwards I moved it /usr/bin/ by typing
$ sudo apktool_2.5.0.jar /usr/bin/
Definitely seems like the aapt PATH problem I had awhile back. Have you added aapt to PATH? If you still have problems, I have made a good apk kit in bash to avoid all these dependency problems. It supports apktool, signapk, zipalign,adb, fastboot, and heimdall. Check it out. All you need is a current java install.
http://forum.xda-developers.com/android/development/toolkit-apk-munky-rench-t3026757/post58747626#post58747626
There isn’t really enough information to give you a definite answer.
How ever you mentioned using different versions but the aapt issue was solved in version 2.4. Dependencies have been reduced to java version 1.8 or greater and the framework.
I use Debian and have the following:
Apktool 2.4
java version 11
Android framework
That’s all it took to get rid of the aapt path error.
The last error I came across was unrelated to aapt but was on the framework so I ran this command
apktool empty-framework-dir
And it solved it.
try to put the dir which include aapt file to your PATH. for example, export PATH=$PATH:./ ./apktool b
try to install ia32-libs and update latest version of apktool. (if possible restart)
apktool requires "ia32-libs" which is not available after Ubuntu 12.04. install ia32-libs
sudo apt-get install lib32z1 lib32ncurses5 lib32bz2-1.0 lib32stdc++6
Download latest version of apktools.jar - https://bitbucket.org/iBotPeaches/apktool/downloads
apktool complete installation guide - http://ibotpeaches.github.io/Apktool/install/
I just encounter same problem when run apktool d foo.apk(decompiled success) and then apktool b foo(recompile failed with similar error).
The apktool tool above was installed via sudo apt-get install apktool on Kali Linux.
So, the solution was visits apktool's official site, e.g. https://connortumbleson.com/2017/01/23/apktool-v2-2-2-released/ (it's latest version at this time of writing), download it, md5sum it, e.g. md5sum apktool_2.2.2.jar to verify, then rename that apktool_2.2.2.jar to apktool.jar.
Then do java -jar ./apktool.jar b foo to recompile, it success without error (the generated apk located at ./foo/dist/foo.apk).
The main issue is apktool version you need 2.4.0
You must manually install it from ibotpeaches git hub
here some good info
https://www.youtube.com/watch?v=kB6s10Uwpcs
and a automated script for kali
https://github.com/catenatedgoose?tab=repositories
In my mind the problem is how you install apktool...
I had the same problem and I did this and it worked very well:
For installation you first have to remove any installed apktool by the command:
sudo apt purge apktool
Then you'll have to install apktool but in a different way.
To continue save the link bellow as apktool in a directory.
[https://raw.githubusercontent.com/iBotPeaches/Apktool/master/scripts/linux/apktool]
Then open this link below and download the latest apktool.jar file: https://bitbucket.org/iBotPeaches/apktool/downloads/
Then rename the file as apktool.jar
After that give both files the permission by the command:
Sudo chmod -x apktool.jar
And for the saved script:
Sudo chmod -x apktool
At the end copy both files in the directory:
/usr/local/bin
By the command:
Sudo cp apktool.jar /usr/local/bin
And the script file:
Sudo cp apktool /usr/local/bin
After that try running apktoolin the terminal.
The solution is to include your apktool directory into your system PATH.