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I hoped to heal the problem by reinstalling the >>>>> installed gnuplot packages. Now I get both the messages. >>>> >>>> If you look in /var7Log/setup.log.full you should be able to see what >>>> error messages, if any, were recorded. >>>> >>>> The gnuplot related script should just set up the current alternative >>>> for "gnuplot" to use, but something on your system seems to prevent >>>> that from happening. You can also run the script in sh (you must tell >>>> the shell to source it) and should get the same error (most likely). >>> >>> When I do that in an elevated shell: >>> >>> $ cd /etc/postinstall/ >>> >>> $ cat gnuplot-base.dash >>> /usr/sbin/alternatives --install /usr/bin/gnuplot gnuplot >>> /usr/bin/gnuplot-base.exe 10 >>> >>> $ . gnuplot-base.dash >>> failed to read link /usr/bin/gnuplot: No such file or directory >>> failed to link /usr/bin/gnuplot -> /etc/alternatives/gnuplot: No such >>> file or directory >> >> Something seems to be confusing 'alternatives'. Can you show a listing of >> /etc/alternatives? > > $ cd /etc/alternatives/ > > $ ls -l > total 2.0K > lrwxrwxrwx 1 Admin None 35 Oct 3 2017 automake-doc -> > /usr/share/info/automake1.9.info.gz > lrwxrwxrwx 1 Admin None 19 Jun 16 17:48 lua -> /usr/bin/lua5.3.exe* > lrwxrwxrwx 1 Admin None 31 Jun 16 17:48 lua.1.gz -> > /usr/share/man/man1/lua5.3.1.gz > lrwxrwxrwx 1 Admin None 20 Jun 16 17:48 luac -> /usr/bin/luac5.3.exe* > lrwxrwxrwx 1 Admin None 32 Jun 16 17:48 luac.1.gz -> > /usr/share/man/man1/luac5.3.1.gz > lrwxrwxrwx 1 Admin None 15 Jun 5 08:46 pip3 -> /usr/bin/pip3.8* > lrwxrwxrwx 1 Admin None 22 Jun 16 07:34 python -> /usr/bin/python3.8.exe* > -rw-r--r-- 1 Admin None 163 Apr 4 2013 README This shows that alternatives worked in June. Have you changed anything since then that might be related to symlinks (e.g., the CYGWIN environment variable)? Here are a few other things you could try: 1. Attach cygcheck output as requested in https://cygwin.com/problems.html 2. Add --verbose to the alternatives call. 3. Run the alternatives call under strace and look for errors involving symlinks. Or post the output somewhere so that we can look at it. Ken