Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[François Bissey]

> On 9/11/2017, at 01:28, Clay Thompson  wrote:
> 
> Not sure why git would be using a tarball... 

That takes some explaining. When you run make the first time in sage,
it runs configure. If configure cannot be found - which will be the case
for a GitHub pull - it will first look for a pre-made tarball of configuration
scripts on the internet and install it in place.
Only if that fails will autoreconf and friends need to be called.
So that particular tarball must have been installed as root and that is why
configure doesn’t belong to your regular user.

François

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Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[Clay Thompson]

Thanks.  Come to think of it, I started using "sudo make" exactly for the 
reason you say, but it never actually occurred to me to draw a clear 
distinction for when I should/shouldn't elevate.

On Tuesday, November 7, 2017 at 9:01:53 AM UTC-5, Michael Orlitzky wrote:
>
> On 11/06/2017 09:54 PM, Clay Thompson wrote: 
> > 
> > Usually when I install from source/devel, I install as root ("sudo 
> > make"). But Sage will not allow me to do that. 
>
> General advice, not specific to SageMath: 
>
> Most software should be built as an unprivileged (i.e. non-root) user. 
> It's only when you want to install the result in a location like 
> /usr/local that you would need to escalate to root with "sudo make 
> install ..." 
>
> Root permissions are needed to write to /usr, but they aren't needed to 
> read any of the system libraries, or to write the build junk to the 
> project directory, or to execute the compiler, etc. By running "sudo 
> make", you run the risk of executing any bad code in the project's build 
> system as root. (The "make install" could do something bad, too -- but 
> that one thing is a lot easier to audit than the entire build system of 
> SageMath and its dependencies.) 
>
>

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Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[Clay Thompson]

Not sure why git would be using a tarball... 

As you suspected, the solution was to change ownership"

> sudo chown clay configure

Now I'm tackling all the OpenBLAS issues...



On Monday, November 6, 2017 at 10:08:13 PM UTC-5, François Bissey wrote:
>
> Since you used git clone, “configure” was installed from a tarball 
> probably as root. sudo make doesn’t really work with sage as far as I 
> know. 
>
> François 
>
> > On 7/11/2017, at 15:54, Clay Thompson  
> wrote: 
> > 
> > [clay@localhost sage]$ ls -la | grep configure 
> > -rwxr-xr-x.  1 root root 265065 Nov  5 22:18 configure 
> > -rw-rw-r--.  1 clay clay  36509 Nov  5 21:26 configure.ac 
> > 
> > Usually when I install from source/devel, I install as root ("sudo 
> make"). But Sage will not allow me to do that.  That caveat aside, "clay" 
> is the only user and can be elevated to root. I assume the install process 
> generates the configure file; I have not changed its permissions manually. 
> > 
> > 
> > On Monday, November 6, 2017 at 9:44:03 PM UTC-5, François Bissey wrote: 
> > Hum… Does the file /home/clay/sage/configure belong to the user “clay”? 
> > And what are its permission? 
> > 
> > François 
> > 
> > > On 7/11/2017, at 15:32, Clay Thompson  wrote: 
> > > 
> > > Fresh install of Fedora 26 on an ASUS notebook.  Source code pulled 
> via git on 11/5/2017. Install fails after several hours.  Relevant output 
> from the log file is below. 
> > > 
> > > [clay@localhost sage]$ tail -n 25 
> /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> > > make[7]: Nothing to be done for 'install-data-am'. 
> > > make[7]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
>  
>
> > > make[6]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
>  
>
> > > make[5]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
>  
>
> > > make[4]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build' 
> > > make[3]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build' 
> > > touch: cannot touch '/home/clay/sage/configure': Permission denied 
> > > 
> > > real211m11.667s 
> > > user193m35.547s 
> > > sys11m54.239s 
> > > 
>  
> > > Error installing package gcc-5.4.0 
> > > 
>  
> > > Please email sage-devel (http://groups.google.com/group/sage-devel) 
> > > explaining the problem and including the log file 
> > >   /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> > > Describe your computer, operating system, etc. 
> > > If you want to try to fix the problem yourself, *don't* just cd to 
> > > /home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0 and type 'make' or 
> whatever is appropriate. 
> > > Instead, the following commands setup all environment variables 
> > > correctly and load a subshell for you to debug the error: 
> > >   (cd '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0' && 
> '/home/clay/sage/sage' --sh) 
> > > When you are done debugging, you can type "exit" to leave the 
> subshell. 
> > > 
>  
> > > 
> > > 
> > > -- 
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> Groups "sage-devel" group. 
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> > 
> > 
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>
>

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Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[Michael Orlitzky]

On 11/06/2017 09:54 PM, Clay Thompson wrote:
> 
> Usually when I install from source/devel, I install as root ("sudo
> make"). But Sage will not allow me to do that.

General advice, not specific to SageMath:

Most software should be built as an unprivileged (i.e. non-root) user.
It's only when you want to install the result in a location like
/usr/local that you would need to escalate to root with "sudo make
install ..."

Root permissions are needed to write to /usr, but they aren't needed to
read any of the system libraries, or to write the build junk to the
project directory, or to execute the compiler, etc. By running "sudo
make", you run the risk of executing any bad code in the project's build
system as root. (The "make install" could do something bad, too -- but
that one thing is a lot easier to audit than the entire build system of
SageMath and its dependencies.)

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Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[François Bissey]

Since you used git clone, “configure” was installed from a tarball
probably as root. sudo make doesn’t really work with sage as far as I
know.

François

> On 7/11/2017, at 15:54, Clay Thompson  wrote:
> 
> [clay@localhost sage]$ ls -la | grep configure
> -rwxr-xr-x.  1 root root 265065 Nov  5 22:18 configure
> -rw-rw-r--.  1 clay clay  36509 Nov  5 21:26 configure.ac
> 
> Usually when I install from source/devel, I install as root ("sudo make"). 
> But Sage will not allow me to do that.  That caveat aside, "clay" is the only 
> user and can be elevated to root. I assume the install process generates the 
> configure file; I have not changed its permissions manually.
> 
> 
> On Monday, November 6, 2017 at 9:44:03 PM UTC-5, François Bissey wrote:
> Hum… Does the file /home/clay/sage/configure belong to the user “clay”? 
> And what are its permission? 
> 
> François 
> 
> > On 7/11/2017, at 15:32, Clay Thompson  wrote: 
> > 
> > Fresh install of Fedora 26 on an ASUS notebook.  Source code pulled via git 
> > on 11/5/2017. Install fails after several hours.  Relevant output from the 
> > log file is below. 
> > 
> > [clay@localhost sage]$ tail -n 25 /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> > make[7]: Nothing to be done for 'install-data-am'. 
> > make[7]: Leaving directory 
> > '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
> >  
> > make[6]: Leaving directory 
> > '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
> >  
> > make[5]: Leaving directory 
> > '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
> >  
> > make[4]: Leaving directory 
> > '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build' 
> > make[3]: Leaving directory 
> > '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build' 
> > touch: cannot touch '/home/clay/sage/configure': Permission denied 
> > 
> > real211m11.667s 
> > user193m35.547s 
> > sys11m54.239s 
> >  
> > Error installing package gcc-5.4.0 
> >  
> > Please email sage-devel (http://groups.google.com/group/sage-devel) 
> > explaining the problem and including the log file 
> >   /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> > Describe your computer, operating system, etc. 
> > If you want to try to fix the problem yourself, *don't* just cd to 
> > /home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0 and type 'make' or 
> > whatever is appropriate. 
> > Instead, the following commands setup all environment variables 
> > correctly and load a subshell for you to debug the error: 
> >   (cd '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0' && 
> > '/home/clay/sage/sage' --sh) 
> > When you are done debugging, you can type "exit" to leave the subshell. 
> >  
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google Groups 
> > "sage-devel" group. 
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> > For more options, visit https://groups.google.com/d/optout. 
> 
> 
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Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[Clay Thompson]

[clay@localhost sage]$ ls -la | grep configure
-rwxr-xr-x.  1 root root 265065 Nov  5 22:18 configure
-rw-rw-r--.  1 clay clay  36509 Nov  5 21:26 configure.ac

Usually when I install from source/devel, I install as root ("sudo make"). 
But Sage will not allow me to do that.  That caveat aside, "clay" is the 
only user and can be elevated to root. I assume the install process 
generates the configure file; I have not changed its permissions manually.


On Monday, November 6, 2017 at 9:44:03 PM UTC-5, François Bissey wrote:
>
> Hum… Does the file /home/clay/sage/configure belong to the user “clay”? 
> And what are its permission? 
>
> François 
>
> > On 7/11/2017, at 15:32, Clay Thompson  
> wrote: 
> > 
> > Fresh install of Fedora 26 on an ASUS notebook.  Source code pulled via 
> git on 11/5/2017. Install fails after several hours.  Relevant output from 
> the log file is below. 
> > 
> > [clay@localhost sage]$ tail -n 25 
> /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> > make[7]: Nothing to be done for 'install-data-am'. 
> > make[7]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
>  
>
> > make[6]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
>  
>
> > make[5]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
>  
>
> > make[4]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build' 
> > make[3]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build' 
> > touch: cannot touch '/home/clay/sage/configure': Permission denied 
> > 
> > real211m11.667s 
> > user193m35.547s 
> > sys11m54.239s 
> >  
> > Error installing package gcc-5.4.0 
> >  
> > Please email sage-devel (http://groups.google.com/group/sage-devel) 
> > explaining the problem and including the log file 
> >   /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> > Describe your computer, operating system, etc. 
> > If you want to try to fix the problem yourself, *don't* just cd to 
> > /home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0 and type 'make' or 
> whatever is appropriate. 
> > Instead, the following commands setup all environment variables 
> > correctly and load a subshell for you to debug the error: 
> >   (cd '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0' && 
> '/home/clay/sage/sage' --sh) 
> > When you are done debugging, you can type "exit" to leave the subshell. 
> >  
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com . 
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> . 
> > Visit this group at https://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>

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Re: [sage-devel] build fail on Fedora 26: cannot touch...: Permission denied

[François Bissey]

Hum… Does the file /home/clay/sage/configure belong to the user “clay”?
And what are its permission?

François

> On 7/11/2017, at 15:32, Clay Thompson  wrote:
> 
> Fresh install of Fedora 26 on an ASUS notebook.  Source code pulled via git 
> on 11/5/2017. Install fails after several hours.  Relevant output from the 
> log file is below.
> 
> [clay@localhost sage]$ tail -n 25 /home/clay/sage/logs/pkgs/gcc-5.4.0.log 
> make[7]: Nothing to be done for 'install-data-am'.
> make[7]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
> make[6]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
> make[5]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build/x86_64-unknown-linux-gnu/libatomic'
> make[4]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build'
> make[3]: Leaving directory 
> '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0/gcc-build'
> touch: cannot touch '/home/clay/sage/configure': Permission denied
> 
> real  211m11.667s
> user  193m35.547s
> sys   11m54.239s
> 
> Error installing package gcc-5.4.0
> 
> Please email sage-devel (http://groups.google.com/group/sage-devel)
> explaining the problem and including the log file
>   /home/clay/sage/logs/pkgs/gcc-5.4.0.log
> Describe your computer, operating system, etc.
> If you want to try to fix the problem yourself, *don't* just cd to
> /home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0 and type 'make' or 
> whatever is appropriate.
> Instead, the following commands setup all environment variables
> correctly and load a subshell for you to debug the error:
>   (cd '/home/clay/sage/local/var/tmp/sage/build/gcc-5.4.0' && 
> '/home/clay/sage/sage' --sh)
> When you are done debugging, you can type "exit" to leave the subshell.
> 
> 
> 
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