Linux help
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You are currently reading a thread in /g/ - Technology
Why isn't this working?
>>51289597
Why does Linux NEVER work for me? Fuck.
>>51289597
Bump. Help me /g/. You're my only hope.
>>51289597
Because CentOS.
>inb4 install gentoo
install FreeBSD or Debian
>>51289597
Mark as executable. (Using the WM or the console)
>>51289661
I can't, it's a distro made for FreeSurfer and I've spent a shit ton of time getting that set up. Surely it's possible to get this to work on CentOS?
chmod +x it?
try sh before the command?
fuck if i know
install.sh is probably not executable.
Either:
source install.sh
or:
chmod +x install.sh && ./install.sh
>>51289683
Thanks, that seems to have done something. How do I fix this permission denied error though?
>>51289597
I've had cases where my drive was not mounted with the exec flag, try what others told you to do and then if all else fail try
bash install.sh
>>51289706
>>51289710
>>51289683
this
post ls -l
>>51289726
Same problem, mark that file as executable.
>>51289740
>post ls -l
try
dd if=/dev/urandom of=/dev/sda bs=1m seek=$RANDOM
>>51289763
My hero! Thanks!
But desu, having to do all this just to start an installer is absolutely ridiculous. In Windows I can just double click the .exe file.
>>51289710
>>51289706
>>51289683
This
Chmod 777 or 555...duck it
>>51289797
A small price to pay for complete freedom don't you think?
>>51289797
Sure, blame the OS for the developer's fault
>>51289804
Okay so I was hoping installing this garbage would let me run a program called SurfRelax. But alas, I'm stuck again.
I've followed this installation guide, and pic related is what I've got.
http://www.pc.rhul.ac.uk/staff/J.Larsson/software/surfrelax/doc/SurfRelax-HOWTO-2.html#ss2.1
Anyone got an idea how I can start this program?
>>51289867
Run 'surfrelax' on your terminal?
>>51289827
I dunno man, I've spent so much time trying to MacGyver this thing into working that I don't have time to be free anymore.
>>51289797
>In Windows I can just double click the .exe file.
That's a pretty basic security measure that windows omits without any good reason IMO
>>51289885
Doesn't seem to work. Tried to make it an executable, no luck
>>51289921
>chmod -x surfrelax
>./surfrelax
You have no idea what are you doing don't you?
You just unremark that binary as non-executable and try to run it as bash script
>>51289895
But you need admin rights to run them, seems safe enough to me? Click "allow" on the popup that comes up vs typing lots of shit into the terminal. I mean sure, when you know all the commands by heart it's trivial to give the permissions and make the files an executable, but it's very inefficient and a waste of time
>>51289890
There's always a learning curve for a piece of software that you don't know well, i think it's a bit unfair to say that linux is hard when most people started using windows and they even studied how things are done on windows as obligatory subjects.
>>51289957
Not if your software is in your distro repository
What distro are you on?
And what is this surfrelax program do?
>>51289947
No, I just tried to see if it would work. I'm a Linux babby, but I'm really trying to get it to work here. So far the learning curve seems rather high, but at least I've learned to navigate folders using the terminal.. I've also managed to install and run FreeSurfer so far, which was quite a challenge to me. The irony is that I'm gonna use the software to some some brain scan analyses, and I can't even get past installing the software..
>>51289978
not op but maybe is this one
http://ftp.kyb.mpg.de/kyb/chaimow/For%20Me/TFI/doc/SurfRelax-HOWTO-1.html
>>51289797
Use your distro's package manager fucking retard.
this thread probably should have been in the SQT but whatever
>>51289921
>chmod -x
>./ surfrelax
should bechmod +x ./surfrelax
./surfrelax
note the lack of space between ./ and surfrelax
also, the +x instead of -x
if you can't into terminal, you can right click it and mark it as executable too in the file properties and then just double click
>>51289957
most shit is installed with the package manager, so you don't need to do that shit yourself most of the time, you just doubleclick the RPM or select it from the repository and bam, shit's installed, no fuss, no muss
>>51289999
Is this one?
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>51289999
>>51290000
>>51290008
No need to be so rude
Opee clearly said he's linux baby
Also it seems like this is specialized software not available in repositories
>>51289597
Hmm, there's actually installation instructions, op.
Are you following them?
https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall
>>51289597
What do you think about this?
http://pkgs.org/centos-6/puias-computational-x86_64/
This repo seems to contain freesurfer:
http://pkgs.org/centos-6/puias-computational-x86_64/freesurfer-5.3.0-1.el6.x86_64.rpm.html
More info:
http://pkgs.org/search/?query=freesurfer&type=smart
>>51289978
>And what is this surfrelax program do?
Basically, this anon is correct:
>>51290000
"SurfRelax is a set of programs and Tk/Tcl scripts, with a GUI wrapper, for extracting cortical surface models from anatomical MR images of the brain. SurfRelax is based on the TFI C++ library and is written for a Unix-based environment."
http://www.pc.rhul.ac.uk/staff/J.Larsson/software/surfrelax/doc/SurfRelax-HOWTO-1.html#ss1.1
I'm trying to get it to work on my CentOS installation.
>>51290097
forgot image
>>51289804
thats probably the worst advice to give to any newbie
>>51290018
That worked, thank you! But now, how do I get the GUI working?
>>51290022
That's FreeSurfer, yes. It's similar to SurfRelax, but a totally different program none the less.
>>51290097
That looks great, but I downloaded a CentOS VM from the freesurfer wiki page. It comes with a install.py script that downloads everything. The issue then was figuring out how to tell the system where I store the data and where the fsl.csh is etc. With some help this worked:
setenv FSLDIR /usr/local/fsl
source $FSLDIR/etc/fslconf/fsl.csh
"/usr/local/fsl/bin/fsl"
then
setenv SUBJECTS_DIR "/home/fsl/Public/2/"
echo $SUBJECTS_DIR
>>51290216
cent OS is babby level easy to install. ignore the vm they gave you and install your own, you'll be more happy with a vm you tweaked during the install to your liking.
>>51290162
The pic in this post is what I'm trying to start. Any ideas how to do that? Pic related is all the files in the bin folder.
>>51290111
>>51290246
For sure if I can get this software to work I will eventually try to install CentOS natively on a machine and use it actively. FreeSurfer is working though, now I'm trying to get
>>51290162
working.
Okay, so when I start SurfaceViewer, this pops up. But if I do the same with "SurfRelax.tcl" I get the message "./SurfRelax.tcl: line 3: exec: wish: not found"
>>51289794
I just ran this and now my system is running so much faster.
Anyone got any idea what this is all about?
>>51290441
This is line 3 of the file.
>>51290470
A google tells me:
"Do you have the tcl and tk libraries installed? They supply "wish" which is the tcl interpreter which is required for tcltkgrass..."
Is there an easy way to get the tcl and tk libraries? I thought that was what I did here:
>>51289797
?
Please don't give up on me /g/
>>51290441
>>51290470
It's looking for the wish package from the same software provider, and it looks like it wasn't installed alongside the software.
Whoever supplied this software package is an absolute madman.
>>51290529
So this isn't representative of the average Linux program?
>>51290555
Most linux software you just install in the repos and it handles the dependencies and shit for you.
>>51290555
No. Typically when software is provided either through your package manager or a .deb (for Debian based distros) or .rpm (for RHEL based distros like CentOS) files it can flag dependant packages that are needed. When it comes in a standalone archive that requires manual installation, most providers make sure that everything is bundled together to prevent this exact thing from happening.
>>51290555
not in the slightest
that's really weird too, activetcl should come with wish afaik
Okay so I found this:
"The software uses Qt (currently version 3.x) for visualization (www.trolltech.com), as well as Tk/Tcl (www.tcl.tk) and the Tk extension Tix (tix.sourceforge.net). Tk/Tcl and tix are included with FSL. The Qt library must be installed to compile the source code, but is otherwise not required. Qt is available for almost all Unix versions and is relatively easy to install."
I already have FSL though, so I don't understand why it doesn't work?
Quoted from here:
http://www.pc.rhul.ac.uk/staff/J.Larsson/software/surfrelax/doc/SurfRelax-HOWTO-1.html#ss1.1
>>51290602
>www.trolltech.com
>>51290602
Qt is just a library. KDE (your desktop environment) should have installed it already.
>>51290633
>The Qt library must be installed to compile the source code, but is otherwise not required.
>The Qt library must be installed to compile the source code, but is otherwise not required.
So ""wish" is "the tcl interpreter", ergo I need Tcl, right?
>>51289597sudo chmod +x ./install.sh
>>51290658
I don't know man, it might be a start. I personally try installing wish by itself first. Can you run this in the terminal and see if it installs it?yum install wish
Try
sudo bash install.sh
or give it the full path to the script instead of using "."
>>51290681
I got this.
>>51290667
>>51290682
Thanks, but I already installed it.
This is the install location. Could that be the issue? Or perhaps that I'm using a new version of ActiveTcl when the program is rather old?
>>51289597
>MATE desktop
found your problem
>>51290746
The fact that each folder opens up in a new window is slowly draining the will to live out of me.
>>51289794
Is this like the system32 joke for *nix noobs? Why not go like bs=128m or even higher?
Either I haven't been g for a while or is gets my nomination to spread this helpful tip everywhere!
>>51290008
/thread
Even if its not in the dustros package manager, still use it to install. He's just typing the file name not saying what to do with it.
This has got to be it, right? Perhaps it's in the wrong directory??
>>51290555
makeinstall people, install depencies automatically...
>>51290858
Install what? TFI SurfRelax?
>>51290772
>not liking spatial file management
also, it's configurable to browser style single-window mode like any recent file manager
>>51290938
>also, it's configurable to browser style single-window mode like any recent file manager
Oh I know, I have a friend who is getting his PhD doing just that..
After reading this thread I really wonder how PC users can cope with this kind of shit every time they would like to install any software application
Cp trucyp
That kind of support by LINUX BROTHERS is one thing i love you all and all FOSS comunnity
That wouldnt happed if op was using win ors osx
>>51290587
HOW about run files? How does dependences work in those?
>>51291019
It's okay, everything is fine. Things will be okay. I'm sure it's just a few commands left until this whole thing is sorted out. Just a few more commands in the terminal now.
>>51290840
1m makes it like russian roulette.
dd if=/dev/zero of=/dev/sda bs=446 count=1
>>51290861
either reinstall tcl
or maybe it's not in your PATH (can't remember how to add things to it on Linux off the top of my head)
like, typewhich tclsh
which wish
in your terminal and post results
>>51291116
I've tried to reinstall tcl, same error. (wish: not found)
Okay /g/, I copied wish to /usr/bin/wish, and now I get this permission error. How can I fix that?
>>51291353
chmod +x $(which wish)
>>51291448
Tells me: "Illegal variable name."
>>51289597
try
>>51291353
Anyone?
>>51291353
>>51291458
Okay so I ran chmod +x wish and it worked!
Now I get pic related (thetideneverends.png)
>>51289804
>chmod 777
b-but anon, thats insecure
just use chmod +x
>>51291558
>b-but anon, thats insecure
I'm way, way past giving even a thought about security, anon.
I have to fucking BUILD Tix.
I'm almost shitty my self with rage.
>>51291353
chmod +x SurfRelax.tcl && sudo ./SurfRelax.tcl
>>51291683
Thanks but I fixed it with >>51291540
Now my problem is >>51291540
I need the Tix package.
http://tix.sourceforge.net/
Can anyone build it for me and upload it? I'm too stupid for this.
>>51289597
without ls -la print out you're a worthless fuck.
Someone should archive this thread and send it around to every freetard next time they get uppity and start shitting on everything while proclaiming that loonix is best muh freedumbs
I'm trying to build Tix but OFCOURSE I run into snags. It seems like this is gonna fight me every step on the way. Any help /g/?
>>51289597
>Linux
>ever working
>he fell for the meme
>>51291884
Wtf is tix and why do you need it, and why isn't it in your package manager?
>>51292167
See this:
>>51291540
When I try to start "SurfRelax.tcl", which as far as I understand is the main program, I get the error "can't find package Tix"
So I need Tix to start the program.
>>51292167
>>51292184
Also, Tix is only available as source. If you can help me I'd be eternally grateful anon.
>>51292191
If you then promise me to not give up on Linux, and also start using your package manager, I'll go find my computer (need a reason to get out of bed anyways)
>>51292219
I promise, anon. Thank you.
>>51292232
Jeg vet hvor du bor, så du kommer ikke unna å installere Windows.
>>51292248
Hehe. Jeg lover;)
>>51289597
have you already chmod +X ?
>>51291884
you have to specify the path to the tix makefile, that or try cmake or sudo before hand. also KDE is bollocks install gnome metacity and get a nice theme like numix
>>51292280
>SurfRelax
Waaait, you're doing MR analysis?
>>51292370
If so, you might want to try to install `fsl` instead if its in your package manager.
>>51292318
I reinstalled tcl into the correct dir and now I get:
[fsl@fslvm6 ~]$ cd /home/fsl/Desktop/Tix8.4.3
[fsl@fslvm6 Tix8.4.3]$ sudo ./configure
[sudo] password for fsl:
checking for correct TEA configuration... ok (TEA 3.6)
checking for Tcl configuration... found /usr/local/lib/tclConfig.sh
checking for existence of /usr/local/lib/tclConfig.sh... loading
checking for Tk configuration... found /usr/local/lib/tkConfig.sh
checking for existence of /usr/local/lib/tkConfig.sh... loading
configure: --prefix defaulting to TCL_PREFIX /usr/local
configure: --exec-prefix defaulting to TCL_EXEC_PREFIX /usr/local
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... yes
checking for ranlib... ranlib
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
>>51292383
checking for unistd.h... yes
checking if the compiler understands -pipe... yes
checking whether byte ordering is bigendian... no
checking for sin... no
checking for main in -lieee... yes
checking for main in -linet... no
checking net/errno.h usability... no
checking net/errno.h presence... no
checking for net/errno.h... no
checking for connect... yes
checking for gethostbyname... yes
checking dirent.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/wait.h usability... yes
checking sys/wait.h presence... yes
checking for sys/wait.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for Tcl private include files... configure: error: Cannot find private header tclInt.h in /home/andreask/dbn/lba/GlobalBuildArena/builds/linux-x86_64/tcl.inst
>>51292370
>Waaait, you're doing MR analysis?
Si senor.
>>51292374
>If so, you might want to try to install `fsl` instead if its in your package manager.
I already have fsl installed. But I need to get SurfRelax going because of reasons.
The thing that puzzles me is that supposedly fsl comes with Tix.
>>51292388
give us `sudo find / -name tclInt.h`
And what did you do to install tcl?
>>51292418
>give us `sudo find / -name tclInt.h`
[fsl@fslvm6 ~]$ sudo find / -name tclInt.h
[sudo] password for fsl:
/home/fsl/Desktop/ActiveTcl8.6.4.1.299124-linux-x86_64-threaded/payload/include/tcl8.6/tclInt.h
/home/fsl/Desktop/ActiveTcl8.6.4.1.299124-linux-x86_64-threaded/payload/include/tclInt.h
/usr/local/include/tcl8.6/tclInt.h
/usr/local/include/tclInt.h
/usr/local/fsl/extras/src/tcl/generic/tclInt.h
/opt/ActiveTcl-8.6/include/tcl8.6/tclInt.h
/opt/ActiveTcl-8.6/include/tclInt.h
[fsl@fslvm6 ~]$
>>51292418
>And what did you do to install tcl?
I did this:
>>51289797
>>51292450
Gotcha, too lazy to read the whole thread.
Did you install tcl or something else with the user `andreask` before starting to use `tsl`?
>>51292481
No, and as far ans I know there is only one user on this machine, "fsluser".
Also, have a look here: http://www.pc.rhul.ac.uk/staff/J.Larsson/software/surfrelax/doc/SurfRelax-HOWTO-2.html#ss2.1
Seems to me it implies that SETUP.sh would install the packages? Yet I have no SETUP.sh in my TFI folder.
>>51292450
Oh, and run './configure' *not* as sudo.
>>51292513
That's weird, cause it complains that tcllnt.h can't be found in /home/andreask/dbn/lba/GlobalBuildArena/builds/linux-x86_64/tcl.inst
>>51292536
>run './configure' *not* as sudo.
"line 982: config.log: Permission denied"
>>51292542
It is weird.. Perhaps a bug?
>>51292563
Absurd. You should also run both configure and make as a normal user, so it seems you've made a proper mess. I have a meeting on the other side of the city in 45 minutes, so I don't have any more time to help you now, but my best general tip is:
You've gone through a lot of steps, and learned a lot about how cli works, so if you now deinstall as much as you can, retrace your steps back to what you originally needed, and then start afresh I'm sure you have it up and running on the better side of an hour.
You know if OP had instead spent the time he wasted here on:
- CLI basics
- learning his distro's package manager
- reading the app's README
- verifying dependencies are present
...then installing this would literally be a 60 second job for him. He would be done by now, and we would have never heard shit from him.
Instead he comes in here not knowing how to chmod +x. OP, if you cant even read, then Linux is not for you.
>>51293070
That's very salty of you anon, but I'm not gonna deny that I'm new to Linux.
If it's a one minute job, could you help me get it going? I've read the readme, and I know one dependency is missing: Tix
>>51293113
Open a terminal, cd into the directory where that file is, then type
sudo chmod u+x install.sh
Linux filesystem has a more rigorous permission structure than windows.
chmod changes permissions, u is for user, x is for executable.
>>51289726
You can't use `./` with `sudo`
>>51293149
And here I thought you had read the thread. That issue was resolved in post 4.
>>51293158
Worked fine on my machine. The problem wasn't using sudo ./ but rather that I had to do it with two different files.
>>51290364
You need a binary called 'wish' as your program needs it do some more stuff. Google wish + centos and find that package. Then use the package name to install it through your package manager.
>>51293227
Resolved here:
>>51291540
Current issue: Need Tix, see same screenshot
>>51293158
yes you can
http://tix.sourceforge.net/docs/UnixInst.html
did u do all this?
>>51293113
"If its so simple to just drive down the block to the liquor store, then tell me how to do it already!"
Alright OP, do you have a car?
A WORKING car?
Do you have keys?
Okay, go out to your car and insert the keys into...oh, you're in Cleveland but your car is in Los Angeles? You didn't mention that. Yes, you're right, I failed to specify you and your car must be in same location. Silly me!
Alright, starting over...does your neighbor have a car? Wait, you say you're not sure what a neighbor is???
OP, do you see how impossible this would be if you were dealing with a person that knows literally nothing?
>>51293579
Wow, what an asshole. You will hereby be ignored.
OP, the problem of yours seem to be that this andreask-user has exported some variables so that configure thinks Tix's files are loated in his home folder that the fsl-user doesn't have access to.
Give us the output of <code> echo $PATH </code> and <code> echo $LD_LIBRARY_PATH </code>
sh install.sh
