Re: installation of fink: error with finkmirrors and pymol

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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