#583 Make install cannot find libavogadro.so.1.0.3
Hi,
Sorry to bother you but I have been looking in the bugs/docs and cannot find my trouble. I am on RedHat 4 on a X86_64 machine. Everything builds (or seems to build fine. Below is my output from "make all" and "make install" It looks like I could almost just harvest the binaries into the library if I knew what the right string is. Any suggestions of other information I could provide, I would be happy to oblige. I am logged into Source Forge, but I see no field for my contact info. My e-mail address, if needed, is rsheppar@iu.edu Thanks.
Ray
rsheppar@Quarry: /N/dc/projects/ray/pharma/avogadro> make all
Linking CXX shared library ../../lib/libavogadro.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc5uJKXVas_.s
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/SelfAdjointEigenSolver.h(385): (col. 7) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/SelfAdjointEigenSolver.h(385): (col. 7) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/Tridiagonalization.h(284): (col. 66) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/Tridiagonalization.h(287): (col. 72) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/Block.h(227): (col. 5) remark: LOOP WAS VECTORIZED.
[ 20%] Built target avogadro
Linking CXX shared module ../../../lib/axesengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcusdLDjas_.s
[ 21%] Built target axesengine
Linking CXX shared module ../../../lib/cartoonengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc0Ie0gcas_.s
[ 22%] Built target cartoonengine
Linking CXX shared module ../../../lib/dipoleengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcCi5E8xas_.s
[ 23%] Built target dipoleengine
Linking CXX shared module ../../../lib/forceengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc8tMb4Has_.s
[ 23%] Built target forceengine
Linking CXX shared module ../../../lib/hbondengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcHiDiQFas_.s
[ 24%] Built target hbondengine
Linking CXX shared module ../../../lib/labelengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcPo9P2yas_.s
[ 25%] Built target labelengine
Linking CXX shared module ../../../lib/overlayengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcI9bipias_.s
[ 25%] Built target overlayengine
Linking CXX shared module ../../../lib/polygonengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcht3R65as_.s
[ 26%] Built target polygonengine
Linking CXX shared module ../../../lib/ribbonengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcDSHeeOas_.s
[ 26%] Built target ribbonengine
Linking CXX shared module ../../../lib/ringengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc7rkJobas_.s
[ 27%] Built target ringengine
Linking CXX shared module ../../../lib/simplewireengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcB6o6SBas_.s
[ 28%] Built target simplewireengine
Linking CXX shared module ../../../lib/sphereengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc180xTjas_.s
[ 28%] Built target sphereengine
Linking CXX shared module ../../../lib/stickengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcuq34mNas_.s
[ 29%] Built target stickengine
Linking CXX shared module ../../../lib/surfaceengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcIcsj5das_.s
[ 30%] Built target surfaceengine
Linking CXX shared module ../../../lib/wireengine.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcStpxAcas_.s
[ 31%] Built target wireengine
Linking CXX shared module ../../../lib/aligntool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcIW8VdPas_.s
[ 31%] Built target aligntool
Linking CXX shared module ../../../lib/autoopttool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcoAXgeFas_.s
[ 32%] Built target autoopttool
Linking CXX shared module ../../../lib/autorotatetool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcrFqNtCas_.s
[ 33%] Built target autorotatetool
Linking CXX shared module ../../../lib/bondcentrictool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcCaO7wSas_.s
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Geometry/Transform.h(587): (col. 17) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Geometry/Transform.h(587): (col. 17) remark: LOOP WAS VECTORIZED.
[ 35%] Built target bondcentrictool
Linking CXX shared module ../../../lib/clickmeasuretool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcFxyWvNas_.s
[ 36%] Built target clickmeasuretool
Linking CXX shared module ../../../lib/drawtool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcMzT1hYas_.s
[ 37%] Built target drawtool
Linking CXX shared module ../../../lib/manipulatetool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpciqg33kas_.s
[ 38%] Built target manipulatetool
Linking CXX shared module ../../../lib/navigatetool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpchzqUlKas_.s
[ 40%] Built target navigatetool
Linking CXX shared module ../../../lib/selectrotatetool.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcC2EIFIas_.s
[ 41%] Built target selectrotatetool
Linking CXX shared module ../../../lib/animationextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpciaWEV8as_.s
[ 44%] Built target animationextension
Linking CXX shared module ../../../lib/fileimportextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcdEsSXMas_.s
[ 44%] Built target fileimportextension
Linking CXX shared module ../../../lib/forcefieldextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcJwgicras_.s
[ 48%] Built target forcefieldextension
Linking CXX shared module ../../../lib/gamessextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcTletxDas_.s
/N/dc/projects/ray/pharma/avogadro-1.0.3/libavogadro/src/extensions/gamessinputdata.cpp(55): (col. 5) remark: LOOP WAS VECTORIZED.
[ 51%] Built target gamessextension
Linking CXX shared module ../../../lib/h2methylextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcP99g65as_.s
[ 51%] Built target h2methylextension
Linking CXX shared module ../../../lib/hydrogenextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcl7VXU7as_.s
[ 52%] Built target hydrogenextension
Linking CXX shared module ../../../lib/inputfileextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcXszhPUas_.s
[ 56%] Built target inputfileextension
Linking CXX shared module ../../../lib/insertfragmentextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcinSTUfas_.s
[ 58%] Built target insertfragmentextension
Linking CXX shared module ../../../lib/insertpeptideextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpciGJ6kAas_.s
[ 59%] Built target insertpeptideextension
Linking CXX shared module ../../../lib/molecularpropextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcXOAwI6as_.s
[ 60%] Built target molecularpropextension
Linking CXX shared module ../../../lib/networkfetchextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcsiiW4qas_.s
[ 60%] Built target networkfetchextension
Linking CXX shared module ../../../lib/povrayextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcMeqTHpas_.s
[ 62%] Built target povrayextension
Linking CXX shared module ../../../lib/propextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcxTNGnzas_.s
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Geometry/Transform.h(587): (col. 17) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Geometry/Transform.h(587): (col. 17) remark: LOOP WAS VECTORIZED.
[ 63%] Built target propextension
Linking CXX shared module ../../../lib/selectextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcrYk597as_.s
[ 64%] Built target selectextension
Linking CXX shared module ../../../lib/spectraextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcT2azckas_.s
[ 67%] Built target spectraextension
Linking CXX shared module ../../../lib/supercellextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpclVcvURas_.s
[ 68%] Built target supercellextension
Linking CXX shared module ../../../lib/surfaceextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpck9w5UGas_.s
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/SolveTriangular.h(175): (col. 89) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/SolveTriangular.h(175): (col. 89) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/SolveTriangular.h(215): (col. 33) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/SolveTriangular.h(215): (col. 33) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/SolveTriangular.h(175): (col. 89) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/SolveTriangular.h(175): (col. 89) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/Dot.h(279): (col. 41) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/SelfAdjointEigenSolver.h(385): (col. 7) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/SelfAdjointEigenSolver.h(385): (col. 7) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/Tridiagonalization.h(287): (col. 72) remark: LOOP WAS VECTORIZED.
[ 73%] Built target surfaceextension
Linking CXX shared module ../../../lib/unitcellextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcN3GceUas_.s
[ 75%] Built target unitcellextension
Linking CXX shared module ../../../lib/vibrationextension.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc4yx7ePas_.s
[ 76%] Built target vibrationextension
Linking CXX shared module ../../../lib/atomindexcolor.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcIbX8EPas_.s
[ 76%] Built target atomindexcolor
Linking CXX shared module ../../../lib/chargecolor.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcXAS9Y9as_.s
[ 77%] Built target chargecolor
Linking CXX shared module ../../../lib/customcolor.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcw7rcxqas_.s
[ 78%] Built target customcolor
Linking CXX shared module ../../../lib/distancecolor.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcdKrHKSas_.s
[ 78%] Built target distancecolor
Linking CXX shared module ../../../lib/residuecolor.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcyFAbCjas_.s
[ 79%] Built target residuecolor
Linking CXX executable ../../bin/avogadro
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpcA7F7r2as_.s
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(3682): (col. 7) remark: FUSED LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(3683): (col. 7) remark: FUSED LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(3690): (col. 11) remark: FUSED LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(3710): (col. 11) remark: FUSED LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(3733): (col. 11) remark: FUSED LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(5054): (col. 3) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(4935): (col. 5) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(4946): (col. 5) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(4957): (col. 5) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(4968): (col. 5) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/avogadro-1.0.3/avogadro/gl2ps/gl2ps.c(3529): (col. 7) remark: FUSED LOOP WAS VECTORIZED.
[100%] Built target avogadro-app
rsheppar@Quarry: /N/dc/projects/ray/pharma/avogadro> make install
[ 20%] Built target avogadro
[ 21%] Built target axesengine
[ 22%] Built target cartoonengine
[ 23%] Built target dipoleengine
[ 23%] Built target forceengine
[ 24%] Built target hbondengine
[ 25%] Built target labelengine
[ 25%] Built target overlayengine
[ 26%] Built target polygonengine
[ 26%] Built target ribbonengine
[ 27%] Built target ringengine
[ 28%] Built target simplewireengine
[ 28%] Built target sphereengine
[ 29%] Built target stickengine
[ 30%] Built target surfaceengine
[ 31%] Built target wireengine
[ 31%] Built target aligntool
[ 32%] Built target autoopttool
[ 33%] Built target autorotatetool
[ 35%] Built target bondcentrictool
[ 36%] Built target clickmeasuretool
[ 37%] Built target drawtool
[ 38%] Built target manipulatetool
[ 40%] Built target navigatetool
[ 41%] Built target selectrotatetool
[ 44%] Built target animationextension
[ 44%] Built target fileimportextension
[ 48%] Built target forcefieldextension
[ 51%] Built target gamessextension
[ 51%] Built target h2methylextension
[ 52%] Built target hydrogenextension
[ 56%] Built target inputfileextension
[ 58%] Built target insertfragmentextension
[ 59%] Built target insertpeptideextension
[ 60%] Built target molecularpropextension
[ 60%] Built target networkfetchextension
[ 62%] Built target povrayextension
[ 63%] Built target propextension
[ 64%] Built target selectextension
[ 67%] Built target spectraextension
[ 68%] Built target supercellextension
[ 73%] Built target surfaceextension
[ 75%] Built target unitcellextension
[ 76%] Built target vibrationextension
[ 76%] Built target atomindexcolor
[ 77%] Built target chargecolor
[ 78%] Built target customcolor
[ 78%] Built target distancecolor
[ 79%] Built target residuecolor
[100%] Built target avogadro-app
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/AvogadroConfig.cmake
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/AvogadroConfigVersion.cmake
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/1_0/AvogadroUse.cmake
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/1_0/AvogadroBuildSettings.cmake
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/1_0/AvogadroLibraryDeps.cmake
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/1_0/cmake/FindEigen2.cmake
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/lib/avogadro/1_0/cmake/FindGLEW.cmake
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alcohols
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alcohols/ethanol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alcohols/methanol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alcohols/propan-1-ol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alcohols/propan-2-ol.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aldehydes
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aldehydes/acetaldehyde.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aldehydes/formaldehyde.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkanes
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkanes/2-methylpropane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkanes/ethane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkanes/methane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkanes/propane.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkenes
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkenes/but-1-ene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkenes/ethene.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkynes
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkynes/acetylene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/alkynes/propyne.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amides
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amides/N_N-dimethylacetamide.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amides/N_N-dimethylformamide.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amides/acetamide.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amides/ethyl_carbamate.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amides/oxamide.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amines
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amines/ammonia.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amines/azepane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amines/ethylamine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amines/methylamine.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-alanine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-allo-threonine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-arginine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-asparagine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-aspartic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-cysteine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-glutamic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-glutamine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-histidine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-isoleucine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-leucine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-lysine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-methionine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-phenylalanine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-proline.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-serine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-threonine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-tryptophan.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-tyrosine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/D-valine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-4-nitrophenylalanine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-alanine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-allo-isoleucine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-arginine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-asparagine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-aspartic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-cysteine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-glutamic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-glutamine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-histidine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-isoleucine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-leucine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-lysine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-methionine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-phenylalanine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-proline.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-serine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-threonine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-tryptophan.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-tyrosine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/L-valine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/amino_acids/glycine.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/1H-indene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/aniline.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/anisole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/anthracene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/benzaldehyde.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/benzene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/benzoic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/benzoyl_chloride.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/caffeine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/naphthalene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/nitrobenzene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/phenol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/aromatics/toluene.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbamides
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbamides/urea.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-allose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-altrose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-arabinose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-erythrose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-erythrulose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-fructose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-galactose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-glucose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-glyceraldehyde.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-gulose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-idose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-lyxose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-mannose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-psicose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-ribose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-ribulose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-sorbose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-tagatose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-talose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-threose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-xylose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/d-xylulose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carbohydrates/dihydroxyacetone.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/2_2-dichloroacetic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/2_2_2-trichloroacetic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/2_2_2-trifluoroacetic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/D-lactic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/D-malic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/D-tartaric_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/L-ascorbic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/L-lactic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/L-malic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/L-tartaric_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/acetic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/butanoic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/citric_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/formic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/isobutyric_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/oxalic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/carboxylic_acids/propanoic_acid.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/3-trigonal-planar.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/3-trigonal-pyramidal.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/4-planar.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/4-tetrahedral.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/5-square-pyramidal.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/5-trigonal-bipyramidal.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/coordination/6-octahedral.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/adamantane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/cubane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/cyclobutane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/cycloheptane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/cyclopentane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/cyclopropane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/norbornane.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic alkanes/cyclohexane.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-allopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-arabinopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-fucopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-galactopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-galacturonopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-glucopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-glucuronopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-gulopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-idopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-lyxopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-mannopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-psicopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-rhamnopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-ribopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-tagatopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-talopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-D-xylopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-arabinopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-fucopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-galactopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-lyxopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-rhamnopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-ribopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-sorbopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/alpha-L-xylopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-allopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-arabinopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-fructopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-fucopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-galactopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-glucopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-gulopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-idopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-lyxopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-mannopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-rhamnopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-ribopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-tagatopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-talopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-D-xylopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-L-arabinopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-L-lyxopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-L-ribopyranose.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/cyclic sugars/beta-L-xylopyranose.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/di-tert-butylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/dibutylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/diethylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/diisopropylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/dimethylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/dipropylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/ethylmethylether.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ethers/tetrahydrofuran.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/decanoic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/hexanoic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/lauric_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/linoleic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/octanoic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/oleic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/palmitic_acid.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/fatty acids/stearic_acid.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1H-indole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1H-pyrazole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1H-pyrrole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1_2-oxazole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1_2-thiazole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1_3-oxazole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/1_3-thiazole.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/benzofuran.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/benzothiophene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/furan.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/pyridine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/heteroaromatics/thiophene.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ketones
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ketones/acetone.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/ketones/butanone.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/macrocycles
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/macrocycles/porphin.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/nucleobases
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/nucleobases/adenine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/nucleobases/cytosine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/nucleobases/guanine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/nucleobases/thymine.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/nucleobases/uracil.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/steroids
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/steroids/cholesterol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/steroids/estradiol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/steroids/testosterone.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/sulfoxides
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/sulfoxides/dimethyl_sulfoxide.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/thiols
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/thiols/ethanethiol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/thiols/methanethiol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/thiols/pentane-1-thiol.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/buckminsterfullerene.cml
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/fragments/water.cml
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder
-- Installing: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-ala.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-arg.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-asn.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-asp.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-cys.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-gln.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-glu.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-his.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-ile.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-leu.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-lys.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-met.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-phe.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-pro.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-ser.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-thr.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-trp.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-tyr.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/d-val.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/gly.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-ala.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-arg.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-asn.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-asp.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-cys.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-gln.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-glu.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-his.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-ile.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-leu.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-lys.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-met.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-phe.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-pro.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-pyl.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-sec.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-ser.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-thr.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-trp.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-tyr.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/share/avogadro/builder/amino/l-val.zmat
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/bin/avopkg
-- Up-to-date: /N/dc/projects/ray/pharma/avogadro/features/avogadro.prf
CMake Error at libavogadro/src/cmake_install.cmake:42 (FILE):
file INSTALL cannot find file
"/N/dc/projects/ray/pharma/avogadro/lib/libavogadro.so.1.0.3" to install.
Call Stack (most recent call first):
libavogadro/cmake_install.cmake:37 (INCLUDE)
cmake_install.cmake:75 (INCLUDE)
This looks like a CMake problem. Marcus, do you know what could be causing this? My first thought was that it might be because the intel compiler was being used, but that shouldn't cause the symlinks to not be generated...
In the meantime, try creating a link from the existing libavogadro.so to libavogadro.so.1.0.3 manually:
cd /N/dc/projects/ray/pharma/avogadro/lib
ln -s libavogadro.so libavogadro.so.1.0.3
and re-run make install.
Hi again,
Thans for getting back to me. When I tired the soft link, it complained of too many links. The linking seems to start off by linking with CXX libs and doesn't like someone being there already:
/N/dc/projects/ray/pharma> cd avogadro/lib
rsheppar@Quarry: /N/dc/projects/ray/pharma/avogadro/lib> ln -s libavogadro.so libavogadro.so.1.0.3
rsheppar@Quarry: /N/dc/projects/ray/pharma/avogadro/lib> cd ..
rsheppar@Quarry: /N/dc/projects/ray/pharma/avogadro> make install
make[2]: stat:lib/libavogadro.so: Too many levels of symbolic links
make[2]: stat:lib/libavogadro.so.1.0.3: Too many levels of symbolic links
Linking CXX shared library ../../lib/libavogadro.so
icpc: command line remark #10148: option '-msse2' not supported
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11006: generating assembly file /tmp/icpc6vng7Nas_.s
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/SelfAdjointEigenSolver.h(385): (col. 7) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/SelfAdjointEigenSolver.h(385): (col. 7) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/Tridiagonalization.h(284): (col. 66) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/QR/Tridiagonalization.h(287): (col. 72) remark: LOOP WAS VECTORIZED.
/N/dc/projects/ray/pharma/eigen2/include/eigen2/Eigen/src/Core/Block.h(227): (col. 5) remark: LOOP WAS VECTORIZED.
ld: cannot open output file ../../lib/libavogadro.so.1.0.3: Too many levels of symbolic links
make[2]: [lib/libavogadro.so.1.0.3] Error 1
make[1]: [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
make: *** [all] Error 2
Hi All,
I did several things. The biggest was to move from a Lustre mount to the supercomputer to a more traditional NFS mount and I installed CMake-2.8.7. That found a few bugs like not declaring #include <typeinfo> in OpenBabel during Avogadro's build. Except for some unknown "class xxx lacks Q_OBJECT macro" warnings, everything built and installed. Next up is to actually test it. My fingers are crossed. Thanks.
Ray
I'm revisiting for the 1.1 release. Is this still a problem?
Thanks!
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