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From: Hanspeter N. <fi...@sn...> - 2020-11-01 16:31:04
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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 <fin...@li...> > The Fink Beginners List <fin...@li...>. > > 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 |