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List: fink-beginners
Subject: [Fink-beginners] Fink Install Errors (./bootstrap?) causing Package Install Errors.
From: Aric Newton <aricnewton () sbcglobal ! net>
Date: 2021-06-07 20:09:15
Message-ID: 2BB4418D-BCED-4756-BB43-44D085940B3E () sbcglobal ! net
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Hi All,
I am running Mac OSX 10.15.7 (Catalina, Intel-processor) and Xcode 12.4. I have \
installed fink (fink-0.45.3.tar.gz) with the helper script (InstallFink.tgz) \
available on GitHub. The install script bonked because access was denied to the \
hyperlink for the installation of Xquartz 2.7.11. I downloaded and installed Xquartz \
2.7.11 from the Xquartz website (https://www.xquartz.org/releases/Xquartz-2.7.11.html \
<https://www.xquartz.org/releases/Xquartz-2.7.11.html>) and re-ran the InstallFink \
script. The install script failed and provided the following output. 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
Get:1 http://bindist.finkmirrors.net stable/main Release [85B]
Fetched 85B in 0s (215B/s)
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.
ERROR: Bootstrap phase 2 failed!
[Process completed]
I then tried a set of fink commands to try to clean this up (e.g. "fink self-update"; \
"fink scanpackages"; "fink update-rsync") to no effect. I altered line 28 of the \
fink.conf file (UseBinaryDist: false) per a discussion on githubmemory \
(https://githubmemory.com/repo/fink/scripts/issues/55 \
<https://githubmemory.com/repo/fink/scripts/issues/55>) and the issue appeared to be \
resolved. However, I am getting a number of errors when trying to install other Fink \
packages and wonder if they are related to this modification. I installed gcc10 \
without incident. I need to install other packages to build an open source program \
(LAMMPS) for simulations. These additional packages are FFTW3 (fast fourier \
transform) and OpenMPI. The build of FFTW3 was looking for some components of the \
gcc9 (compiler and shared libraries) and reported "404 Not Found" errors for the \
first mirror and an alternate mirror from the same continent (North America). The \
"Search from Source URL" did find what it was looking for and the installation \
completed without further errors. I next attempted to install OpenMPI. The install \
reported errors with attempts to download from the mirrors, but the "Search from \
Source URL" found (some) of the necessary components. The build failed with the final \
error reported being: New package: \
dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb
Failed: phase compiling: libxslt-1.1.29-1 failed
The output advised trying "fink self-update" and then to try to install again. The \
update command turned up no new packages or updates to install. The build error \
message also recommend changing the fink.conf file to limit the maximum number of \
build jobs to 1. That edit of the configuration file had no effect. The error that \
aborts the install is still: checking for xml2-config... /opt/sw/bin/xml2-config
checking for LIBXML... no
configure: error: Could not find libxml2 anywhere, check ftp://xmlsoft.org/.
### execution of ./configure failed, exit code 1
### execution of /tmp/fink.aYvDh failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/opt/sw/bin/dpkg-lockwait -r fink-buildlock-libxslt-1.1.34-1
(Reading database ... 24445 files and directories currently installed.)
Removing fink-buildlock-libxslt-1.1.34-1 ...
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_3.20.0-1_darwin-x86_64.deb
New package: dists/stable/main/binary-darwin-x86_64/utils/libbrotli1-shlibs_1.0.9-1_darwin-x86_64.deb
New package: dists/stable/main/binary-darwin-x86_64/utils/brotli_1.0.9-1_darwin-x86_64.deb
New package: dists/stable/main/binary-darwin-x86_64/utils/libbrotli1_1.0.9-1_darwin-x86_64.deb
New package: dists/stable/main/binary-darwin-x86_64/text/docbook-dtd_4.5.0-1_darwin-x86_64.deb
New package: dists/stable/main/binary-darwin-x86_64/text/docbook-xsl_1.78.1-1_darwin-x86_64.deb
New package: dists/stable/main/binary-darwin-x86_64/text/docbook-dsssl-nwalsh_1.79-4_darwin-x86_64.deb
Failed: phase compiling: libxslt-1.1.34-1 failed
The libxml2 library (and the *-bin and *-shlibs) that it couldn't find seems like it \
could be the culprit, but those libraries do appear to be installed (and the *-bin \
and *-shlibs, too) -- %fink list libxml
...
i libxml2 2.9.12-2 XML parsing library, version 2
So, I am stumped. Are the persistent package errors due to my initial install (Mac OS \
X 10.15 with Xcode 12.4) or is there something else that I am needing to modify to \
get fink to run better? I have previously used fink with much earlier versions of Mac \
OS X (< 10.11) and was pleased with its performance. Not sure if I'm just rusty or \
there is something new that I missed out on. Thank you for taking the time to read \
through my post.
Regards,
Aric
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<html><head><meta http-equiv="Content-Type" content="text/html; \
charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; \
line-break: after-white-space;" class="">
<p style="margin-bottom: 0in; line-height: 100%" class=""><span style="font-style: \
normal;" class="">Hi All,</span></p><p style="margin-bottom: 0in; line-height: 100%" \
class=""><span style="font-style: normal;" class="">I am running Mac OSX 10.15.7 \
(Catalina, Intel-processor) and Xcode 12.4. I have installed fink \
(fink-0.45.3.tar.gz) with the helper script (<font color="#000000" class=""><font \
class="">InstallFink.tgz</font></font><font color="#000000" class=""><font class="">) \
available on GitHub. The install script bonked because access was denied to the \
hyperlink for the installation of Xquartz 2.7.11. I downloaded and installed Xquartz \
2.7.11 from the Xquartz website (</font></font><a \
href="https://www.xquartz.org/releases/Xquartz-2.7.11.html" class=""><font \
color="#000000" class=""><font \
class="">https://www.xquartz.org/releases/Xquartz-2.7.11.html</font></font></a><font \
color="#000000" class=""><font class="">) and re-ran the InstallFink script. The \
install script failed and provided the following output.</font></font></span></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
face="Monaco" class=""><span style="font-style: normal; font-size: 11px;" \
class="">Downloading the indexes of available packages in the binary \
distribution.</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font face="Monaco" class=""><span style="font-style: \
normal; font-size: 11px;" class="">/opt/sw/bin/apt-get-lockwait
-q update</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font face="Monaco" class=""><span style="font-style: \
normal; font-size: 11px;" class="">Err <a href="http://bindist.finkmirrors.net" \
class="">http://bindist.finkmirrors.net</a> stable/main Packages</span></font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><span \
style="font-size: 11px; font-family: Monaco;" class="">404 Not Found</span></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
face="Monaco" class=""><span style="font-style: normal; font-size: 11px;" \
class="">Get:1 <a href="http://bindist.finkmirrors.net" \
class="">http://bindist.finkmirrors.net</a> stable/main Release \
[85B]</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; line-height: \
100%" class=""><font face="Monaco" class=""><span style="font-style: normal; \
font-size: 11px;" class="">Fetched 85B in 0s (215B/s)</span></font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
face="Monaco" class=""><span style="font-style: normal; font-size: 11px;" \
class="">Failed to fetch
<a href="http://bindist.finkmirrors.net/10.15/dists/stable/main/binary-darwin-x86_64/Packages" \
class="">http://bindist.finkmirrors.net/10.15/dists/stable/main/binary-darwin-x86_64/Packages</a>
404 Not Found</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font face="Monaco" class=""><span style="font-style: \
normal; font-size: 11px;" class="">Reading Package Lists...</span></font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
face="Monaco" class=""><span style="font-style: normal; font-size: 11px;" \
class="">Building Dependency Tree...</span></font></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font face="Monaco" class=""><span \
style="font-style: normal; font-size: 11px;" class="">E: Some index files failed to \
download, they have been ignored, or old ones used instead.</span></font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
face="Monaco" class=""><span style="font-style: normal; font-size: 11px;" \
class="">### execution of /opt/sw/bin/apt-get-lockwait failed, exit code \
100</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; line-height: \
100%" class=""><font face="Monaco" class=""><span style="font-style: normal; \
font-size: 11px;" class="">WARNING: Failure while updating \
indexes.</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font face="Monaco" class=""><span style="font-style: \
normal; font-size: 11px;" class="">ERROR: Bootstrap phase 2 \
failed!</span></font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font class=""><font color="#000000" face="Monaco" \
style="font-style: normal; font-size: 11px;" class="">[Process \
completed]</font></font></p><p style="margin-bottom: 0in; line-height: 100%" \
class=""><span style="font-style: normal;" class=""><font color="#000000" \
class=""><font class="">I then </font></font><font color="#000000" class=""><font \
class="">tried a set of fink commands to try to clean this up (e.g. "fink
self-update"; "fink scanpackages"; "fink update-rsync") to
no effect. I altered line 28 of the fink.conf file (</font></font><font \
color="#000000" class=""><font class="">UseBinaryDist: false</font></font><font \
color="#000000" class=""><font class="">)</font></font><font color="#000000" \
class=""><font class=""> per a discussion on githubmemory
</font></font><font color="#000000" class=""><font class="">(<a \
href="https://githubmemory.com/repo/fink/scripts/issues/55" \
class="">https://githubmemory.com/repo/fink/scripts/issues/55</a>) \
</font></font><font color="#000000" class=""><font class="">and the issue appeared to \
be resolved. However, I am getting a number of errors when trying to install other \
Fink packages and wonder if they are related to this \
modification.</font></font></span></p><p style="margin-bottom: 0in; line-height: \
100%" class=""><span style="font-style: normal;" class=""><font color="#000000" \
class=""><font class="">I installed gcc10 without incident. I need to \
</font></font><font color="#000000" class=""><font class="">install \
</font></font><font color="#000000" class=""><font class="">other packages to build \
an open source program (LAMMPS) for </font></font><font color="#000000" \
class=""><font class="">simulations. These additional packages are FFTW3 (fast \
fourier transform) and OpenMPI. The build of FFTW3 was looking for some components \
of </font></font><font color="#000000" class=""><font class="">the \
</font></font><font color="#000000" class=""><font class="">gcc9 (compiler and shared \
libraries) and reported "404 Not Found" errors </font></font><font \
color="#000000" class=""><font class="">for the first mirror and an alternate mirror \
from the same continent (North America). The "Search from Source URL" did find what \
it was looking for </font></font><font color="#000000" class=""><font class="">and
the installation completed without further errors.</font></font></span></p><p \
style="margin-bottom: 0in; line-height: 100%" class="">I next attempted to install \
OpenMPI. The install reported errors with attempts to download from the mirrors, but \
the "Search from Source URL" found (some) of the necessary components. The build \
failed with the final error reported being:</p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%;" class=""> <font color="#000000" face="Monaco" \
style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">Failed: phase \
compiling: libxslt-1.1.29-1 failed</font></p><p style="margin-bottom: 0in; \
line-height: 100%" class="">The output advised trying "fink self-update" and then to \
try to install again. The update command turned up no new packages or updates to \
install. The build error message also recommend changing the fink.conf
file to limit the maximum number of build jobs to 1. That edit of
the configuration file had
no effect. The error that aborts the install is still:</p><p style="margin-left: \
0.5in; margin-bottom: 0in; line-height: 100%;" class=""> <font color="#000000" \
face="Monaco" style="font-style: normal;" class="">checking for xml2-config... \
/opt/sw/bin/xml2-config</font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font color="#000000" face="Monaco" style="font-style: \
normal;" class="">checking for LIBXML... no</font></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" face="Monaco" \
style="font-style: normal;" class="">configure:
error: Could not find libxml2 anywhere, check <a href="ftp://xmlsoft.org/" \
class="">ftp://xmlsoft.org/</a>.</font></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" face="Monaco" \
style="font-style: normal;" class="">### execution of ./configure failed, exit code \
1</font></p><p style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" \
class=""><font color="#000000" face="Monaco" style="font-style: normal;" class="">### \
execution of /tmp/fink.aYvDh failed, exit code 1</font></p><p style="margin-left: \
0.5in; margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" \
face="Monaco" style="font-style: normal;" class="">Removing runtime \
build-lock...</font></p><p style="margin-left: 0.5in; margin-bottom: 0in; \
line-height: 100%" class=""><font color="#000000" face="Monaco" style="font-style: \
normal;" class="">Removing build-lock package...</font></p><p style="margin-left: \
0.5in; margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" \
face="Monaco" style="font-style: normal;" \
class="">/opt/sw/bin/dpkg-lockwait
-r fink-buildlock-libxslt-1.1.34-1</font></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" face="Monaco" \
style="font-style: normal;" class="">(Reading database ... 24445 files and \
directories currently installed.)</font></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" face="Monaco" \
style="font-style: normal;" class="">Removing fink-buildlock-libxslt-1.1.34-1 \
...</font></p><p style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" \
class=""><font color="#000000" face="Monaco" style="font-style: normal;" \
class="">Updating the list of locally available binary packages.</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">Scanning \
dists/stable/main/binary-darwin-x86_64</font></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" face="Monaco" \
style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/devel/cmake_3.20.0-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/utils/libbrotli1-shlibs_1.0.9-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/utils/brotli_1.0.9-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/utils/libbrotli1_1.0.9-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/text/docbook-dtd_4.5.0-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/text/docbook-xsl_1.78.1-1_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">New package:
dists/stable/main/binary-darwin-x86_64/text/docbook-dsssl-nwalsh_1.79-4_darwin-x86_64.deb</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal;" class="">Failed: phase \
compiling: libxslt-1.1.34-1 failed</font></p><p style="margin-bottom: 0in; \
line-height: 100%" class=""><span style="font-style: normal;" class=""><font \
color="#000000" class=""><font class="">The libxml2 </font></font><font \
color="#000000" class=""><font class="">library </font></font><font color="#000000" \
class=""><font class="">(and the *-bin and *-shlibs)</font></font><font \
color="#000000" class=""><font class=""> </font></font><font color="#000000" \
class=""><font class="">that it couldn't find seems like it could be the culprit, but \
those libraries do appear to be installed </font></font><font color="#000000" \
class=""><font class="">(and the *-bin and *-shlibs, too)</font></font><font \
color="#000000" class=""><font class=""> </font></font><font color="#000000" \
class=""><font class="">--</font></font></span></p><p style="margin-left: 0.5in; \
margin-bottom: 0in; line-height: 100%" class=""><font color="#000000" face="Monaco" \
style="font-style: normal; font-size: 11px;" class="">%fink list libxml</font></p><p \
style="margin-left: 0.5in; margin-bottom: 0in; line-height: 100%" class=""><font \
color="#000000" face="Monaco" style="font-style: normal; font-size: 11px;" \
class="">...</font></p><p style="margin-left: 0.5in; margin-bottom: 0in; line-height: \
100%" class=""><font color="#000000" face="Monaco" style="font-style: normal; \
font-size: 11px;" class="">i libxml2 2.9.12-2 XML parsing library, \
version 2</font></p><p style="margin-bottom: 0in; line-height: 100%;" class=""> <font \
color="#000000" class=""><font class="">So, I am stumped. Are the persistent package \
errors due to my initial install (Mac OS X 10.15 with Xcode 12.4) or is there \
something else that I am needing to modify to get fink to run better? I have
previously used fink with much earlier versions of Mac OS X (<
10.11) and was pleased with its performance. Not sure if I'm just rusty or \
there is something new that I missed out on.</font></font></p><p \
style="margin-bottom: 0in; line-height: 100%;" class=""> <font color="#000000" \
class=""><font style="font-style: normal;" class="">Thank you for taking the time to \
read through my post.</font></font></p><p style="margin-bottom: 0in; line-height: \
100%;" class=""><font color="#000000" class=""><font style="font-style: normal;" \
class=""><br class=""></font></font></p><p style="margin-bottom: 0in; line-height: \
100%;" class=""> <font color="#000000" class=""><font style="font-style: normal;" \
class="">Regards,</font></font></p><p style="margin-bottom: 0in; line-height: 100%;" \
class=""> <font color="#000000" class=""><font style="font-style: normal;" \
class="">Aric</font></font></p></body></html>
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