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jayponderjayponder
committed
convert to Tinker-FFE 8.7.2 based on Tinker update
1 parent f42c904 commit 653efb8

13 files changed

+68
-66
lines changed

‎build/build.log-linux‎

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -40,10 +40,10 @@ init:
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[mkdir] Created dir: /home/ponder/ffe/build/apbs/include
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[mkdir] Created dir: /home/ponder/ffe/build/apbs/include/maloc
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[echoproperties] #Ant properties
43-
[echoproperties] #Thu Jul 11 18:42:12 CDT 2019
44-
[echoproperties] DSTAMP=20190711
45-
[echoproperties] TODAY=July 11 2019
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[echoproperties] TSTAMP=1842
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[echoproperties] #Wed Nov 27 21:05:31 CST 2019
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[echoproperties] DSTAMP=20191127
45+
[echoproperties] TODAY=November 27 2019
46+
[echoproperties] TSTAMP=2105
4747
[echoproperties] ant.core.lib=/home/ponder/ffe/build/buildtools/ant/lib/ant.jar
4848
[echoproperties] ant.file=/home/ponder/ffe/build/linux.ant.xml
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[echoproperties] ant.file.Force\ Field\ Explorer\ for\ Linux=/home/ponder/ffe/build/linux.ant.xml
@@ -75,13 +75,13 @@ init:
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[echoproperties] env.BLD=/home/ponder/ffe/build
7676
[echoproperties] env.COLORTERM=
7777
[echoproperties] env.CVS_RSH=ssh
78-
[echoproperties] env.DBUS_SESSION_BUS_ADDRESS=unix\:abstract\=/tmp/dbus-TAxCwKXQ9U,guid\=94f7a2677b4cc7c9525988005d27c729
78+
[echoproperties] env.DBUS_SESSION_BUS_ADDRESS=unix\:abstract\=/tmp/dbus-z3XDMYNE5c,guid\=195e157e4289b46dbf980f005ddf35b0
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[echoproperties] env.DESKTOP_SESSION=default
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[echoproperties] env.DISPLAY=\:0.0
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[echoproperties] env.GDMSESSION=default
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[echoproperties] env.GDM_XSERVER_LOCATION=local
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[echoproperties] env.GNOME_DESKTOP_SESSION_ID=Default
84-
[echoproperties] env.GNOME_KEYRING_SOCKET=/tmp/keyring-IXUVkk/socket
84+
[echoproperties] env.GNOME_KEYRING_SOCKET=/tmp/keyring-J6FY6g/socket
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[echoproperties] env.GROUP=users
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[echoproperties] env.GTK_RC_FILES=/etc/gtk/gtkrc\:/home/ponder/.gtkrc-1.2-gnome2
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[echoproperties] env.G_BROKEN_FILENAMES=1
@@ -92,8 +92,8 @@ init:
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[echoproperties] env.INPUTRC=/etc/inputrc
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[echoproperties] env.KDEDIR=/usr
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[echoproperties] env.KDE_IS_PRELINKED=1
95-
[echoproperties] env.KONSOLE_DCOP=DCOPRef(konsole-4456,konsole)
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[echoproperties] env.KONSOLE_DCOP_SESSION=DCOPRef(konsole-4456,session-1)
95+
[echoproperties] env.KONSOLE_DCOP=DCOPRef(konsole-4115,konsole)
96+
[echoproperties] env.KONSOLE_DCOP_SESSION=DCOPRef(konsole-4115,session-1)
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[echoproperties] env.LANG=en_US.UTF-8
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[echoproperties] env.LD_LIBRARY_PATH=/opt/gcc-4.9.2/lib64\:/opt/gcc-4.9.2/lib\:
9999
[echoproperties] env.LESSOPEN=|/usr/bin/lesspipe.sh %s
@@ -105,19 +105,19 @@ init:
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[echoproperties] env.OSTYPE=linux
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[echoproperties] env.PATH=/home/ponder/ffe/build/buildtools/ant/bin\:.\:..\:/opt/gcc-4.9.2/bin\:/opt/gcc-4.9.2/bin\:/usr/kerberos/bin\:/usr/local/bin\:/usr/bin\:/bin\:/usr/X11R6/bin\:.\:/home/ponder/tinker/bin\:/opt/install4j6/bin\:.\:/home/ponder/tinker/bin\:/opt/install4j6/bin
107107
[echoproperties] env.PWD=/home/ponder/ffe/build
108-
[echoproperties] env.SESSION_MANAGER=local/CentOS\:/tmp/.ICE-unix/4215
108+
[echoproperties] env.SESSION_MANAGER=local/CentOS\:/tmp/.ICE-unix/3863
109109
[echoproperties] env.SHELL=/bin/tcsh
110110
[echoproperties] env.SHLVL=2
111-
[echoproperties] env.SSH_AGENT_PID=4203
111+
[echoproperties] env.SSH_AGENT_PID=3851
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[echoproperties] env.SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
113-
[echoproperties] env.SSH_AUTH_SOCK=/tmp/ssh-iwVwvs4167/agent.4167
113+
[echoproperties] env.SSH_AUTH_SOCK=/tmp/ssh-eKNbYO3815/agent.3815
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[echoproperties] env.TERM=xterm
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[echoproperties] env.TLS=/home/ponder/ffe/build/buildtools
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[echoproperties] env.USER=ponder
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[echoproperties] env.USERNAME=ponder
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[echoproperties] env.VENDOR=unknown
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[echoproperties] env.WINDOWID=27262983
120-
[echoproperties] env.XAUTHORITY=/tmp/.gdmQ14P4Z
120+
[echoproperties] env.XAUTHORITY=/tmp/.gdmRE9FB0
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[echoproperties] env.XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt
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[echoproperties] env.XMODIFIERS=@im\=none
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[echoproperties] error.log=kits/error_8.7.21.log
@@ -1902,19 +1902,19 @@ compile:
19021902
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/macos/OSXAdapter.java:19: warning: [deprecation] ApplicationEvent in com.apple.eawt has been deprecated
19031903
[javac] import com.apple.eawt.ApplicationEvent;
19041904
[javac] ^
1905-
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:146: warning: SignalHandler is internal proprietary API and may be removed in a future release
1905+
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:144: warning: SignalHandler is internal proprietary API and may be removed in a future release
19061906
[javac] SignalHandler handler = new SignalHandler() {
19071907
[javac] ^
1908-
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:146: warning: SignalHandler is internal proprietary API and may be removed in a future release
1908+
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:144: warning: SignalHandler is internal proprietary API and may be removed in a future release
19091909
[javac] SignalHandler handler = new SignalHandler() {
19101910
[javac] ^
1911-
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:147: warning: Signal is internal proprietary API and may be removed in a future release
1911+
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:145: warning: Signal is internal proprietary API and may be removed in a future release
19121912
[javac] public void handle(Signal sig) {
19131913
[javac] ^
1914-
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:161: warning: Signal is internal proprietary API and may be removed in a future release
1914+
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:159: warning: Signal is internal proprietary API and may be removed in a future release
19151915
[javac] Signal.handle(new Signal("INT"), handler);
19161916
[javac] ^
1917-
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:161: warning: Signal is internal proprietary API and may be removed in a future release
1917+
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:159: warning: Signal is internal proprietary API and may be removed in a future release
19181918
[javac] Signal.handle(new Signal("INT"), handler);
19191919
[javac] ^
19201920
[javac] /home/ponder/ffe/build/ffe/src/main/java/ffe/macos/OSXAdapter.java:28: warning: [deprecation] ApplicationAdapter in com.apple.eawt has been deprecated
@@ -2037,20 +2037,20 @@ kits:
20372037
[install4j] Compressing files
20382038
[install4j] Moving media files to media directory /home/ponder/ffe/build/kits
20392039
[install4j] The name of the media file is Tinker-FFE_unix_8.7.21.sh.
2040-
[install4j] The size of the media file is 275.5 MB
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[install4j] The size of the media file is 276.0 MB
20412041
[install4j]
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[install4j] Compressed media file 'Unix Archive':
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[install4j] Moving media files to media directory /home/ponder/ffe/build/kits
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[install4j] The name of the media file is Tinker-FFE_unix_8.7.21.tar.gz.
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[install4j] The size of the media file is 260.8 MB
2045+
[install4j] The size of the media file is 261.3 MB
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[install4j]
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[install4j] Compressed media file 'Linux RPM':
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[install4j] Moving media files to media directory /home/ponder/ffe/build/kits
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[install4j] The name of the media file is Tinker-FFE_linux_8.7.21.rpm.
2050-
[install4j] The size of the media file is 261.5 MB
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[install4j] The size of the media file is 262.0 MB
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[install4j] Writing md5sums.
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[install4j] Writing updates.xml.
2053-
[install4j] Build completed in 77.4 seconds.
2053+
[install4j] Build completed in 64.5 seconds.
20542054
[gzip] Building: /home/ponder/ffe/build/kits/build_8.7.21.log.gz
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[gzip] Building: /home/ponder/ffe/build/kits/error_8.7.21.log.gz
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[delete] Deleting: /home/ponder/ffe/build/kits/build_8.7.21.log
@@ -2059,4 +2059,4 @@ kits:
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make:
20602060

20612061
BUILD SUCCESSFUL
2062-
Total time: 5 minutes 34 seconds
2062+
Total time: 5 minutes 22 seconds

‎build/build.log-macos‎

Lines changed: 26 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -40,10 +40,10 @@ init:
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[mkdir] Created dir: /Users/ponder/ffe/build/apbs/include
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[mkdir] Created dir: /Users/ponder/ffe/build/apbs/include/maloc
4242
[echoproperties] #Ant properties
43-
[echoproperties] #Thu Jul 11 18:11:46 CDT 2019
44-
[echoproperties] DSTAMP=20190711
45-
[echoproperties] TODAY=July 11 2019
46-
[echoproperties] TSTAMP=1811
43+
[echoproperties] #Wed Nov 27 20:25:37 CST 2019
44+
[echoproperties] DSTAMP=20191127
45+
[echoproperties] TODAY=November 27 2019
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[echoproperties] TSTAMP=2025
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[echoproperties] ant.core.lib=/Users/ponder/ffe/build/buildtools/ant/lib/ant.jar
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[echoproperties] ant.file=/Users/ponder/ffe/build/macos.ant.xml
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[echoproperties] ant.file.Force\ Field\ Explorer\ for\ MacOS=/Users/ponder/ffe/build/macos.ant.xml
@@ -72,13 +72,15 @@ init:
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[echoproperties] env.ANT_ARGS=
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[echoproperties] env.ANT_HOME=/Users/ponder/ffe/build/buildtools/ant
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[echoproperties] env.ANT_OPTS=-Xms512M -Xmx1G
75-
[echoproperties] env.Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.ofeg7weSEl/Render
75+
[echoproperties] env.Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.NEMKYRdU5X/Render
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[echoproperties] env.BLD=/Users/ponder/ffe/build
77+
[echoproperties] env.CC=gcc
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[echoproperties] env.CMAKE_OSX_DEPLOYMENT_TARGET=
7879
[echoproperties] env.COPYFILES_DISABLE=true
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[echoproperties] env.CPATH=/opt/intel/composer_xe_2015.3.187/mkl/include
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[echoproperties] env.DISPLAY=0\:
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[echoproperties] env.DYLD_LIBRARY_PATH=/opt/intel/composer_xe_2015.3.187/compiler/lib\:/opt/intel/composer_xe_2015.3.187/compiler/lib/intel64\:/opt/intel/composer_xe_2015.3.187/compiler/lib\:/opt/intel/composer_xe_2015.3.187/mkl/lib\:\:/opt/intel/lib\:/usr/local/cuda/lib\:/usr/local/openmm/lib
83+
[echoproperties] env.F77=gfortran
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[echoproperties] env.G09BASIS=/Applications/gaussian/g09/basis
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[echoproperties] env.GAUSS_ARCHDIR=/Applications/gaussian/g09/arch
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[echoproperties] env.GAUSS_EXEDIR=/Applications/gaussian/g09/bin\:/Applications/gaussian/g09/bsd\:/Applications/gaussian/g09
@@ -94,7 +96,7 @@ init:
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[echoproperties] env.INTEL_LICENSE_FILE=/opt/intel/composer_xe_2015.3.187/licenses\:/opt/intel/licenses\:/Users/ponder/intel/licenses\:/Users/Shared/Library/Application Support/Intel/Licenses
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[echoproperties] env.INTEL_PYTHONHOME=/opt/intel/composer_xe_2015.3.187/debugger/python/intel64/
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[echoproperties] env.JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home
97-
[echoproperties] env.JAVA_MAIN_CLASS_28247=org.apache.tools.ant.launch.Launcher
99+
[echoproperties] env.JAVA_MAIN_CLASS_97822=org.apache.tools.ant.launch.Launcher
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[echoproperties] env.LANG=en_US.UTF-8
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[echoproperties] env.LD_LIBRARY_PATH=/Applications/gaussian/g09/bin\:/Applications/gaussian/g09/bsd\:/Applications/gaussian/g09\:/Applications/gaussian/gv/lib
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[echoproperties] env.LIBRARY_PATH=/opt/intel/composer_xe_2015.3.187/compiler/lib\:/opt/intel/composer_xe_2015.3.187/compiler/lib\:/opt/intel/composer_xe_2015.3.187/mkl/lib
@@ -113,11 +115,11 @@ init:
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[echoproperties] env.PWD=/Users/ponder/ffe/build
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[echoproperties] env.SHELL=/bin/tcsh
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[echoproperties] env.SHLVL=1
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[echoproperties] env.SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.9YcnTZ1MOr/Listeners
118+
[echoproperties] env.SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.UdGop7lJTC/Listeners
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[echoproperties] env.TERM=xterm
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[echoproperties] env.TERM_PROGRAM=Apple_Terminal
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[echoproperties] env.TERM_PROGRAM_VERSION=404.1
120-
[echoproperties] env.TERM_SESSION_ID=F424714F-387A-4FD7-8754-1C89584E6261
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[echoproperties] env.TERM_SESSION_ID=371993CB-B317-4001-BE0A-47A2D2672052
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[echoproperties] env.TLS=/Users/ponder/ffe/build/buildtools
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[echoproperties] env.TMPDIR=/var/folders/2p/kc8wx8rj6555t37q5f2tklfh0000z8/T/
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[echoproperties] env.USER=ponder
@@ -1704,9 +1706,8 @@ maketinker:
17041706
[exec] a - polpot.o
17051707
[exec] a - poltcg.o
17061708
[exec] a - polymer.o
1707-
[exec] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(ascii.o) has no symbolsa - potent.o
1708-
[exec]
1709-
[exec] a - potfit.o/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(math.o) has no symbols
1709+
[exec] a - potent.o
1710+
[exec] a - potfit.o
17101711
[exec] a - pressure.o
17111712
[exec] a - prmkey.o
17121713
[exec] a - promo.o
@@ -1715,18 +1716,16 @@ maketinker:
17151716
[exec] a - prtint.o
17161717
[exec] a - prtmol2.o
17171718
[exec] a - prtpdb.o
1718-
[exec]
17191719
[exec] a - prtprm.o
17201720
[exec] a - prtseq.o
17211721
[exec] a - prtxyz.o
1722-
[exec] a - ptable.o/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(sizes.o) has no symbols
1722+
[exec] a - ptable.o
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[exec] a - qmstuf.o
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[exec] a - qrfact.o
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[exec] a - quatfit.o
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[exec] a - random.o
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[exec] a - rattle.o
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[exec] a - readdyn.o
1729-
[exec]
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[exec] a - readgau.o
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[exec] a - readgdma.o
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[exec] a - readint.o
@@ -1736,7 +1735,6 @@ maketinker:
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[exec] a - readprm.o
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[exec] a - readseq.o
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[exec] a - readxyz.o
1739-
[exec] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(units.o) has no symbols
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[exec] a - refer.o
17411739
[exec] a - repel.o
17421740
[exec] a - replica.o
@@ -1812,6 +1810,10 @@ maketinker:
18121810
[exec] a - zclose.o
18131811
[exec] a - zcoord.o
18141812
[exec] ranlib -c libtinker.a
1813+
[exec] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(ascii.o) has no symbols
1814+
[exec] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(math.o) has no symbols
1815+
[exec] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(sizes.o) has no symbols
1816+
[exec] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libtinker.a(units.o) has no symbols
18151817
[exec] gfortran -Ofast -mssse3 -fopenmp -static-libgcc -framework JavaVM -framework CoreFoundation -o alchemy.x -L. -L/Users/ponder/ffe/build/tinker/lib/macos -L/Users/ponder/ffe/build/fftw/lib -L/Users/ponder/ffe/build/apbs/lib alchemy.o libtinker.a -lfftw3_threads -lfftw3 -lapbsmainroutines -lapbs -lmaloc -lapbsblas -lstdc++; strip alchemy.x
18161818
[exec] gfortran -Ofast -mssse3 -fopenmp -static-libgcc -framework JavaVM -framework CoreFoundation -o analyze.x -L. -L/Users/ponder/ffe/build/tinker/lib/macos -L/Users/ponder/ffe/build/fftw/lib -L/Users/ponder/ffe/build/apbs/lib analyze.o libtinker.a -lfftw3_threads -lfftw3 -lapbsmainroutines -lapbs -lmaloc -lapbsblas -lstdc++; strip analyze.x
18171819
[exec] gfortran -Ofast -mssse3 -fopenmp -static-libgcc -framework JavaVM -framework CoreFoundation -o anneal.x -L. -L/Users/ponder/ffe/build/tinker/lib/macos -L/Users/ponder/ffe/build/fftw/lib -L/Users/ponder/ffe/build/apbs/lib anneal.o libtinker.a -lfftw3_threads -lfftw3 -lapbsmainroutines -lapbs -lmaloc -lapbsblas -lstdc++; strip anneal.x
@@ -1921,19 +1923,19 @@ compile:
19211923
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/macos/OSXAdapter.java:19: warning: [deprecation] ApplicationEvent in com.apple.eawt has been deprecated
19221924
[javac] import com.apple.eawt.ApplicationEvent;
19231925
[javac] ^
1924-
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:146: warning: SignalHandler is internal proprietary API and may be removed in a future release
1926+
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:144: warning: SignalHandler is internal proprietary API and may be removed in a future release
19251927
[javac] SignalHandler handler = new SignalHandler() {
19261928
[javac] ^
1927-
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:146: warning: SignalHandler is internal proprietary API and may be removed in a future release
1929+
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:144: warning: SignalHandler is internal proprietary API and may be removed in a future release
19281930
[javac] SignalHandler handler = new SignalHandler() {
19291931
[javac] ^
1930-
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:147: warning: Signal is internal proprietary API and may be removed in a future release
1932+
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:145: warning: Signal is internal proprietary API and may be removed in a future release
19311933
[javac] public void handle(Signal sig) {
19321934
[javac] ^
1933-
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:161: warning: Signal is internal proprietary API and may be removed in a future release
1935+
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:159: warning: Signal is internal proprietary API and may be removed in a future release
19341936
[javac] Signal.handle(new Signal("INT"), handler);
19351937
[javac] ^
1936-
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:161: warning: Signal is internal proprietary API and may be removed in a future release
1938+
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/Main.java:159: warning: Signal is internal proprietary API and may be removed in a future release
19371939
[javac] Signal.handle(new Signal("INT"), handler);
19381940
[javac] ^
19391941
[javac] /Users/ponder/ffe/build/ffe/src/main/java/ffe/macos/OSXAdapter.java:28: warning: [deprecation] ApplicationAdapter in com.apple.eawt has been deprecated
@@ -2044,15 +2046,15 @@ kits:
20442046
[install4j] Generating VM options file vmoptions.txt.
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[install4j] Moving media files to media directory /Users/ponder/ffe/build/kits
20462048
[install4j] The name of the media file is Tinker-FFE_macos_8.7.11.dmg.
2047-
[install4j] The size of the media file is 262.6 MB
2049+
[install4j] The size of the media file is 263.2 MB
20482050
[install4j]
20492051
[install4j] Compressed media file 'MacOS Archive':
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[install4j] Moving media files to media directory /Users/ponder/ffe/build/kits
20512053
[install4j] The name of the media file is Tinker-FFE_macos_8.7.11.tgz.
2052-
[install4j] The size of the media file is 245.7 MB
2054+
[install4j] The size of the media file is 246.2 MB
20532055
[install4j] Writing md5sums.
20542056
[install4j] Writing updates.xml.
2055-
[install4j] Build completed in 52.4 seconds.
2057+
[install4j] Build completed in 46.9 seconds.
20562058
[gzip] Building: /Users/ponder/ffe/build/kits/build_8.7.11.log.gz
20572059
[gzip] Building: /Users/ponder/ffe/build/kits/error_8.7.11.log.gz
20582060
[delete] Deleting: /Users/ponder/ffe/build/kits/build_8.7.11.log
@@ -2061,4 +2063,4 @@ kits:
20612063
make:
20622064

20632065
BUILD SUCCESSFUL
2064-
Total time: 18 minutes 2 seconds
2066+
Total time: 17 minutes 52 seconds

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