Re: installation of fink: error with finkmirrors and pymol

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?

Thanks for your help!

Best, Tobias.


On Tue, Oct 20, 2020 at 11:54 AM Hanspeter Niederstrasser <
[email protected]> wrote:

> On 10/12/20 8:09 AM, miller wrote:
> > Dear all,
> >
> > I have exactly the same problem
> >
> > best
> >
> > Heinz
> >
> > Am 12.10.20 um 14:33 schrieb Tobias Beck:
> >> Dear all,
> >>
> >> Thanks!
> >>
> >> >The “command not found” message probably indicates that you didn’t
> >> open a new terminal window.  pathsetup.sh doesn’t update the
> >> environment for the shell session you run it in.
> >>
> >> Yes, indeed - I tried with typing 'bash' to update, but that does not
> >> update the environment.
> >>
> >> With a new terminal window and 'fink selfupdate-rsync', I get this
> >> warning / error
> >>
> >> snip
> >>
> >> configure: WARNING: stddef.h: present but cannot be compiled
> >> configure: WARNING: stddef.h:     check for missing prerequisite
> headers?
> >> configure: WARNING: stddef.h: see the Autoconf documentation
> >> configure: WARNING: stddef.h:     section "Present But Cannot Be
> >> Compiled"
> >> configure: WARNING: stddef.h: proceeding with the preprocessor's result
> >> configure: WARNING: stddef.h: in the future, the compiler will take
> >> precedence
> >> configure: WARNING:     ## ------------------------------------------ ##
> >> configure: WARNING:     ## Report this to the AC_PACKAGE_NAME lists.  ##
> >> configure: WARNING:     ## ------------------------------------------ ##
> >> checking for stddef.h... yes
> >> checking error.h usability... no
> >> checking error.h presence... no
> >> checking for error.h... no
> >> checking locale.h usability... yes
> >> checking locale.h presence... yes
> >> checking for locale.h... yes
> >> checking whether sys_siglist is declared... yes
> >> checking for ihash_create in -lihash... no
> >> checking for proc_stat_list_create in -lps... no
> >> checking for fmt_past_time in -lshouldbeinlibc... no
> >> checking for kvm_openfiles in -lkvm... no
> >> checking for initscr in -lncurses... yes
> >> checking if TIOCNOTTY is defined in sys/ioctl.h... yes
> >> checking for va_copy... no
> >> checking for va_list assignment copy... configure: error: no
> >> ### execution of /tmp/fink.S1Bv1 failed, exit code 1
> >> Removing runtime build-lock...
> >> Removing build-lock package...
> >> /opt/sw/bin/dpkg-lockwait -r fink-buildlock-dpkg-1.10.21-1250
> >> (Reading database ... 5120 files and directories currently installed.)
> >> Removing fink-buildlock-dpkg-1.10.21-1250 ...
> >> Failed: phase compiling: dpkg-1.10.21-1250 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]
> >> <mailto:[email protected]>>
> >> The Fink Beginners List <[email protected]
> >> <mailto:[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 Mon Oct 12 14:24:57 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
> >> dpkg-1.10.21-1250 is set to build with only one job.
> >>
> >>
> >> I have tried selfupdate now 3 times, same error.
>
> I just fixed this dpkg build error with Xcode 12.
>
> Hanspeter
>
>

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