Re: installation of fink: error with finkmirrors and pymol

Dear Hanspeter,

Thanks a lot for looking into this!

I carried out
fink selfupdate
fink update-all

but with
bash-3.2$ fink install pymol-py27

I get this error:

bash-3.2$ fink install pymol-py27
Information about 10356 packages read in 1 seconds.
W: Couldn't stat source package list http://bindist.finkmirrors.net
stable/main Packages
(/opt/sw/var/lib/apt/lists/bindist.finkmirrors.net_10.15_dists_stable_main_binary-darwin-x86%5f64_Packages)
- stat (2 No such file or directory)
W: Couldn't stat source package list http://bindist.finkmirrors.net
stable/main Packages
(/opt/sw/var/lib/apt/lists/bindist.finkmirrors.net_10.15_dists_stable_main_binary-darwin-x86%5f64_Packages)
- stat (2 No such file or directory)
Can't resolve dependency "xcode (>= 6.2)" for package "gcc9-9.3.0-1" (no
matching packages/versions found)
Exiting with failure.


Not sure what this means?

To find out which xcode I have (I am pretty sure I downloaded xcode 12)

xcodebuild -version gives this output:

xcode-select: error: tool 'xcodebuild' requires Xcode, but active developer
directory '/Library/Developer/CommandLineTools' is a command line tools
instance

but gcc --version gives this:

Apple clang version 12.0.0 (clang-1200.0.32.21)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

My system: 10.15.7 (updated this morning)
apparently Xcode 12 (see gcc)

Thanks for help regarding the error from the finkmirrors and the gcc
dependency!

Best, Tobias.

On Sun, Nov 1, 2020 at 5:30 PM Hanspeter Niederstrasser <
[email protected]> wrote:

>
> On 10/30/20 9:09 AM, Tobias Beck wrote:
>  > Dear all,
>  >
>  > Thanks for fixing!
>  >
>  > With fink selfupdate, I now get this error message, which I think is
> just a
>  > warning:
>  >
>  > snip
>  > /usr/bin/rsync -az -q  rsync://
>  > distfiles.master.finkmirrors.net/finkinfo//TIMESTAMP
>  > /opt/sw/fink/TIMESTAMP.tmp
>  > I will now run the rsync command to retrieve the latest package
>  > descriptions.
>  > /usr/bin/rsync -rtz --delete-after --delete -q
>  --include='10.9-libcxx/'
>  > --include='10.9-libcxx/stable/' --include='10.9-libcxx/stable/main/'
>  > --include='10.9-libcxx/stable/main/finkinfo/'
>  > --include='10.9-libcxx/stable/main/finkinfo/*/'
>  > --include='10.9-libcxx/stable/main/finkinfo/*'
>  > --include='10.9-libcxx/stable/main/finkinfo/**/*' --include='VERSION'
>  > --include='DISTRIBUTION' --include='README' --exclude='**' 'rsync://
>  > distfiles.master.finkmirrors.net/finkinfo' '/opt/sw/fink/'
>  > Downloading the indexes of available packages in the binary
> distribution.
>  > /opt/sw/bin/apt-get-lockwait -q update
>  > Err http://bindist.finkmirrors.net stable/main Packages
>  >    404 Not Found
>  > Ign http://bindist.finkmirrors.net stable/main Release
>  > Failed to fetch
>  >
>
> http://bindist.finkmirrors.net/10.15/dists/stable/main/binary-darwin-x86_64/Packages
>  >   404 Not Found
>  > Reading Package Lists...
>  > Building Dependency Tree...
>  > W: Couldn't stat source package list http://bindist.finkmirrors.net
>  > stable/main Packages
>  >
>
> (/opt/sw/var/lib/apt/lists/bindist.finkmirrors.net_10.15_dists_stable_main_binary-darwin-x86%5f64_Packages)
>  > - stat (2 No such file or directory)
>  > W: Couldn't stat source package list http://bindist.finkmirrors.net
>  > stable/main Packages
>  >
>
> (/opt/sw/var/lib/apt/lists/bindist.finkmirrors.net_10.15_dists_stable_main_binary-darwin-x86%5f64_Packages)
>  > - stat (2 No such file or directory)
>  > W: You may want to run apt-get update to correct these problems
>  > E: Some index files failed to download, they have been ignored, or
> old ones
>  > used instead.
>  > ### execution of /opt/sw/bin/apt-get-lockwait failed, exit code 100
>  > WARNING: Failure while updating indexes.
>  > Running 'fink scanpackages' may fix indexing problems.
>  >
>  >
>  > The core packages have been updated. You should now update the other
>  > packages using commands like 'fink update-all'.
>  >
>  > /snip
>  >
>  >
>  > fink update-all
>  > gives no packages to install
>  >
>  > However, when I try to install pymol-py27, I get this error:
>  >
>  > snip
>  >
>  > gcc -c -DHAVE_CONFIG_H   -I. -I. -MD -I/opt/sw/include
>  > -DRL_LIBRARY_VERSION='"6.3"' -g -O rltty.c
>  > rltty.c:83:7: error: implicit declaration of function 'ioctl' is
> invalid in
>  > C99 [-Werror,-Wimplicit-function-declaration]
>  >    if (ioctl (tty, TIOCGWINSZ, &w) == 0)
>  >        ^
>  > rltty.c:720:3: error: implicit declaration of function 'ioctl' is
> invalid
>  > in C99 [-Werror,-Wimplicit-function-declaration]
>  >    ioctl (fildes, TIOCSTART, 0);
>  >    ^
>  > rltty.c:759:3: error: implicit declaration of function 'ioctl' is
> invalid
>  > in C99 [-Werror,-Wimplicit-function-declaration]
>  >    ioctl (fildes, TIOCSTOP, 0);
>  >    ^
>  > 3 errors generated.
>  > make: *** [rltty.o] Error 1
>  > ### execution of /tmp/fink.hU400 failed, exit code 2
>  > ### execution of /tmp/fink.5PYbZ failed, exit code 2
>  > Removing runtime build-lock...
>  > Removing build-lock package...
>  > /opt/sw/bin/dpkg-lockwait -r fink-buildlock-readline6-6.3.8-2
>  > (Reading database ... 13765 files and directories currently installed.)
>  > Removing fink-buildlock-readline6-6.3.8-2 ...
>  > Updating the list of locally available binary packages.
>  > Scanning dists/stable/main/binary-darwin-x86_64
>  > New package:
>  >
>
> dists/stable/main/binary-darwin-x86_64/devel/cmake_3.16.2-1_darwin-x86_64.deb
>  > New package:
>  >
>
> dists/stable/main/binary-darwin-x86_64/sci/openblas_0.3.10-1_darwin-x86_64.deb
>  > New package:
>  >
>
> dists/stable/main/binary-darwin-x86_64/sci/openblas-shlibs_0.3.10-1_darwin-x86_64.deb
>  > New package:
>  >
>
> dists/stable/main/binary-darwin-x86_64/languages/gcc10-shlibs_10.2.0-1_darwin-x86_64.deb
>  > New package:
>  >
>
> dists/stable/main/binary-darwin-x86_64/languages/gcc10-compiler_10.2.0-1_darwin-x86_64.deb
>  > New package:
>  >
>
> dists/stable/main/binary-darwin-x86_64/languages/gcc10_10.2.0-1_darwin-x86_64.deb
>  > Downloading the indexes of available packages in the binary
> distribution.
>  > /opt/sw/bin/apt-get-lockwait -q update
>  > Err http://bindist.finkmirrors.net stable/main Packages
>  >    404 Not Found
>  > Ign http://bindist.finkmirrors.net stable/main Release
>  > Failed to fetch
>  >
>
> http://bindist.finkmirrors.net/10.15/dists/stable/main/binary-darwin-x86_64/Packages
>  >   404 Not Found
>  > Reading Package Lists...
>  > Building Dependency Tree...
>  > E: Some index files failed to download, they have been ignored, or
> old ones
>  > used instead.
>  > ### execution of /opt/sw/bin/apt-get-lockwait failed, exit code 100
>  > WARNING: Failure while updating indexes.
>  > Failed: phase compiling: readline6-6.3.8-2 failed
>  >
>  > Before reporting any errors, please run "fink selfupdate" and try again.
>  >
>  > If you continue to have issues, please check to see if the FAQ on Fink's
>  > website solves the problem.  If not, ask on one (not both, please) of
>  > these mailing lists:
>  >
>  > The Fink Users List <[email protected]>
>  > The Fink Beginners List <[email protected]>.
>  >
>  > Please try to include the complete error message in your report.  This
>  > generally consists of a compiler line starting with e.g. "gcc" or "g++"
>  > followed by the actual error output from the compiler.
>  >
>  > Also include the following system information:
>  > Package manager version: 0.45.2
>  > Distribution version: selfupdate-rsync Fri Oct 30 09:30:43 2020, 10.15,
>  > x86_64
>  > Trees: local/main stable/main
>  > No recognized Xcode.app installed
>  > Xcode command-line tools: 12.0.0.0.1.1599194153
>  > Max. Fink build jobs:  1
>  >
>  > snip
>  >
>  > I have done fink selfupdate and tried again, same error
>  > I have reconfigured fink to one build job, same error
>  >
>  > Two questions:
>  > 1.) Is my fink installation fine?
>  > 2.) How can I fix the error for the pymol installation?
>
>
> The problem was in readline6, which is an intermediate to getting pymol.
> That's now been fixed, and I was able to build pymol myself on
> 10.15/Xcode12.
>
> Hanspeter
>
> --
> Organic chemistry is the study of carbon compounds.
> Biochemistry is the study of carbon compounds that crawl.
>    --Mike Adams
>

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