1. CoGAPS
  2. Commit 16472f1067d047938f6ceab89eb84f2f890c8a27
Browse code

framework with dispatcher compiling and running

Tom Sherman authored on 18/06/2018 13:49:06
Showing 41 changed files
DESCRIPTION
History View file @ 16472f106
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: CoGAPS
2 
-Version: 3.1.2
2 
+Version: 3.1.3
3 3 
 Date: 2018-04-24
4 4 
 Title: Coordinated Gene Activity in Pattern Sets
5 5 
 Author: Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,
NAMESPACE
History View file @ 16472f106
... ... 
@@ -2,6 +2,7 @@
2 2
3 3 
 export(CoGAPS)
4 4 
 export(CoGAPSFromFile)
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+export(CoGapsFromCheckpoint)
5 6 
 export(GWCoGAPS)
6 7 
 export(GWCoGapsFromCheckpoint)
7 8 
 export(binaryA)
R/CoGAPS.R
History View file @ 16472f106
... ... 
@@ -44,7 +44,7 @@
44 44 
 #' @export
45 45 
 CoGAPS <- function(D, S, nFactor=7, nEquil=250, nSample=250, nOutputs=1000,
46 46 
 nSnapshots=0, alphaA=0.01, alphaP=0.01, maxGibbmassA=100, maxGibbmassP=100,
47 
-seed=-1, messages=TRUE, singleCellRNASeq=FALSE, whichMatrixFixed='N',
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+seed=NA, messages=TRUE, singleCellRNASeq=FALSE, whichMatrixFixed='N',
48 48 
 fixedPatterns=matrix(0), checkpointInterval=0,
49 49 
 checkpointFile="gaps_checkpoint.out", nCores=1, ...)
50 50 
 {
... ... 
@@ -91,18 +91,14 @@ checkpointFile="gaps_checkpoint.out", nCores=1, ...)
91 91 
     thresholdEnum <- c("unique", "cut")
92 92
93 93 
     # get seed
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-    if (seed < 0)
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+    if (is.na(seed))
95 95 
     {
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-        # TODO get time in milliseconds
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-        seed <- 0
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+        seed <- 0 # TODO get time in milliseconds
98 97 
     }
99 98
100 99 
     # run algorithm with call to C++ code
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-    result <- cogaps_cpp(D, S, nFactor, nEquil, nEquil/10, nSample, nOutputs,
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-        nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages,
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-        singleCellRNASeq, whichMatrixFixed, fixedPatterns, checkpointInterval,
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-        checkpointFile, which(thresholdEnum==pumpThreshold), nPumpSamples,
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-        nCores)
100 
+    result <- cogaps_cpp(D, nFactor, nEquil, nOutputs, seed, alphaA, alphaP,
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+        maxGibbmassA, maxGibbmassP, messages, singleCellRNASeq)
106 102
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     # label matrices and return list
108 104 
     patternNames <- paste('Patt', 1:nFactor, sep='')
R/RcppExports.R
History View file @ 16472f106
... ... 
@@ -1,16 +1,12 @@
1 1 
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
2 2 
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
3 3
4 
-cogaps_cpp <- function(D, S, nFactor, nEquil, nEquilCool, nSample, nOutputs, nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages, singleCellRNASeq, whichMatrixFixed, FP, checkpointInterval, cptFile, pumpThreshold, nPumpSamples, nCores) {
5 
-    .Call('_CoGAPS_cogaps_cpp', PACKAGE = 'CoGAPS', D, S, nFactor, nEquil, nEquilCool, nSample, nOutputs, nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages, singleCellRNASeq, whichMatrixFixed, FP, checkpointInterval, cptFile, pumpThreshold, nPumpSamples, nCores)
4 
+cogapsFromFile_cpp <- function(D, nPatterns, maxIter, outputFrequency, seed, alphaA, alphaP, maxGibbsMassA, maxGibbsMassP, messages, singleCellRNASeq) {
5 
+    .Call('_CoGAPS_cogapsFromFile_cpp', PACKAGE = 'CoGAPS', D, nPatterns, maxIter, outputFrequency, seed, alphaA, alphaP, maxGibbsMassA, maxGibbsMassP, messages, singleCellRNASeq)
6 6 
 }
7 7
8 
-cogapsFromCheckpoint_cpp <- function(D, S, nFactor, nEquil, nSample, fileName, cptFile) {
9 
-    .Call('_CoGAPS_cogapsFromCheckpoint_cpp', PACKAGE = 'CoGAPS', D, S, nFactor, nEquil, nSample, fileName, cptFile)
10 
-}
11 
-
12 
-cogapsFromFile_cpp <- function(D) {
13 
-    invisible(.Call('_CoGAPS_cogapsFromFile_cpp', PACKAGE = 'CoGAPS', D))
8 
+cogaps_cpp <- function(D, nPatterns, maxIter, outputFrequency, seed, alphaA, alphaP, maxGibbsMassA, maxGibbsMassP, messages, singleCellRNASeq) {
9 
+    .Call('_CoGAPS_cogaps_cpp', PACKAGE = 'CoGAPS', D, nPatterns, maxIter, outputFrequency, seed, alphaA, alphaP, maxGibbsMassA, maxGibbsMassP, messages, singleCellRNASeq)
14 10 
 }
15 11
16 12 
 getBuildReport_cpp <- function() {
config.log
History View file @ 16472f106
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new file mode 100644
... ... 
@@ -0,0 +1,534 @@
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+This file contains any messages produced by compilers while
2 
+running configure, to aid debugging if configure makes a mistake.
3 
+
4 
+It was created by CoGAPS configure 3.1.2, which was
5 
+generated by GNU Autoconf 2.69.  Invocation command line was
6 
+
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+  $ ./configure
8 
+
9 
+## --------- ##
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+## Platform. ##
11 
+## --------- ##
12 
+
13 
+hostname = MBL-D518NN2
14 
+uname -m = x86_64
15 
+uname -r = 4.4.0-43-Microsoft
16 
+uname -s = Linux
17 
+uname -v = #1-Microsoft Wed Dec 31 14:42:53 PST 2014
18 
+
19 
+/usr/bin/uname -p = unknown
20 
+/bin/uname -X     = unknown
21 
+
22 
+/bin/arch              = unknown
23 
+/usr/bin/arch -k       = unknown
24 
+/usr/convex/getsysinfo = unknown
25 
+/usr/bin/hostinfo      = unknown
26 
+/bin/machine           = unknown
27 
+/usr/bin/oslevel       = unknown
28 
+/bin/universe          = unknown
29 
+
30 
+PATH: /usr/local/sbin
31 
+PATH: /usr/local/bin
32 
+PATH: /usr/sbin
33 
+PATH: /usr/bin
34 
+PATH: /sbin
35 
+PATH: /bin
36 
+PATH: /snap/bin
37 
+
38 
+
39 
+## ----------- ##
40 
+## Core tests. ##
41 
+## ----------- ##
42 
+
43 
+configure:2189: checking for C++ compiler version
44 
+configure:2198: ccache g++ --version >&5
45 
+g++ (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609
46 
+Copyright (C) 2015 Free Software Foundation, Inc.
47 
+This is free software; see the source for copying conditions.  There is NO
48 
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
49 
+
50 
+configure:2209: $? = 0
51 
+configure:2198: ccache g++ -v >&5
52 
+Using built-in specs.
53 
+COLLECT_GCC=/usr/bin/g++
54 
+COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
55 
+Target: x86_64-linux-gnu
56 
+Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.9' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
57 
+Thread model: posix
58 
+gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.9)
59 
+configure:2209: $? = 0
60 
+configure:2198: ccache g++ -V >&5
61 
+g++: error: unrecognized command line option '-V'
62 
+g++: fatal error: no input files
63 
+compilation terminated.
64 
+configure:2209: $? = 1
65 
+configure:2198: ccache g++ -qversion >&5
66 
+g++: error: unrecognized command line option '-qversion'
67 
+g++: fatal error: no input files
68 
+compilation terminated.
69 
+configure:2209: $? = 1
70 
+configure:2229: checking whether the C++ compiler works
71 
+configure:2251: ccache g++ -UNDEBUG -Wall -pedantic -g -O0   conftest.cpp  >&5
72 
+configure:2255: $? = 0
73 
+configure:2303: result: yes
74 
+configure:2306: checking for C++ compiler default output file name
75 
+configure:2308: result: a.out
76 
+configure:2314: checking for suffix of executables
77 
+configure:2321: ccache g++ -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.cpp  >&5
78 
+configure:2325: $? = 0
79 
+configure:2347: result:
80 
+configure:2369: checking whether we are cross compiling
81 
+configure:2377: ccache g++ -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.cpp  >&5
82 
+configure:2381: $? = 0
83 
+configure:2388: ./conftest
84 
+configure:2392: $? = 0
85 
+configure:2407: result: no
86 
+configure:2412: checking for suffix of object files
87 
+configure:2434: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
88 
+configure:2438: $? = 0
89 
+configure:2459: result: o
90 
+configure:2463: checking whether we are using the GNU C++ compiler
91 
+configure:2482: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
92 
+configure:2482: $? = 0
93 
+configure:2491: result: yes
94 
+configure:2500: checking whether ccache g++ accepts -g
95 
+configure:2520: ccache g++ -c -g  conftest.cpp >&5
96 
+configure:2520: $? = 0
97 
+configure:2561: result: yes
98 
+configure:2590: checking how to run the C++ preprocessor
99 
+configure:2617: ccache g++ -E  conftest.cpp
100 
+configure:2617: $? = 0
101 
+configure:2631: ccache g++ -E  conftest.cpp
102 
+conftest.cpp:9:28: fatal error: ac_nonexistent.h: No such file or directory
103 
+compilation terminated.
104 
+configure:2631: $? = 1
105 
+configure: failed program was:
106 
+| /* confdefs.h */
107 
+| #define PACKAGE_NAME "CoGAPS"
108 
+| #define PACKAGE_TARNAME "cogaps"
109 
+| #define PACKAGE_VERSION "3.1.2"
110 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
111 
+| #define PACKAGE_BUGREPORT ""
112 
+| #define PACKAGE_URL ""
113 
+| /* end confdefs.h.  */
114 
+| #include <ac_nonexistent.h>
115 
+configure:2656: result: ccache g++ -E
116 
+configure:2676: ccache g++ -E  conftest.cpp
117 
+configure:2676: $? = 0
118 
+configure:2690: ccache g++ -E  conftest.cpp
119 
+conftest.cpp:9:28: fatal error: ac_nonexistent.h: No such file or directory
120 
+compilation terminated.
121 
+configure:2690: $? = 1
122 
+configure: failed program was:
123 
+| /* confdefs.h */
124 
+| #define PACKAGE_NAME "CoGAPS"
125 
+| #define PACKAGE_TARNAME "cogaps"
126 
+| #define PACKAGE_VERSION "3.1.2"
127 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
128 
+| #define PACKAGE_BUGREPORT ""
129 
+| #define PACKAGE_URL ""
130 
+| /* end confdefs.h.  */
131 
+| #include <ac_nonexistent.h>
132 
+configure:2832: checking for C++ compiler version
133 
+configure:2841: ccache g++ --version >&5
134 
+g++ (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609
135 
+Copyright (C) 2015 Free Software Foundation, Inc.
136 
+This is free software; see the source for copying conditions.  There is NO
137 
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
138 
+
139 
+configure:2852: $? = 0
140 
+configure:2841: ccache g++ -v >&5
141 
+Using built-in specs.
142 
+COLLECT_GCC=/usr/bin/g++
143 
+COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
144 
+Target: x86_64-linux-gnu
145 
+Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.9' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
146 
+Thread model: posix
147 
+gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.9)
148 
+configure:2852: $? = 0
149 
+configure:2841: ccache g++ -V >&5
150 
+g++: error: unrecognized command line option '-V'
151 
+g++: fatal error: no input files
152 
+compilation terminated.
153 
+configure:2852: $? = 1
154 
+configure:2841: ccache g++ -qversion >&5
155 
+g++: error: unrecognized command line option '-qversion'
156 
+g++: fatal error: no input files
157 
+compilation terminated.
158 
+configure:2852: $? = 1
159 
+configure:2856: checking whether we are using the GNU C++ compiler
160 
+configure:2884: result: yes
161 
+configure:2893: checking whether ccache g++ accepts -g
162 
+configure:2954: result: yes
163 
+configure:3011: checking for C++ compiler vendor
164 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
165 
+conftest.cpp: In function 'int main()':
166 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
167 
+         thisisanerror;
168 
+         ^
169 
+configure:3059: $? = 1
170 
+configure: failed program was:
171 
+| /* confdefs.h */
172 
+| #define PACKAGE_NAME "CoGAPS"
173 
+| #define PACKAGE_TARNAME "cogaps"
174 
+| #define PACKAGE_VERSION "3.1.2"
175 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
176 
+| #define PACKAGE_BUGREPORT ""
177 
+| #define PACKAGE_URL ""
178 
+| /* end confdefs.h.  */
179 
+|
180 
+| int
181 
+| main ()
182 
+| {
183 
+|
184 
+|       #if !(defined(__ICC) || defined(__ECC) || defined(__INTEL_COMPILER))
185 
+|         thisisanerror;
186 
+|       #endif
187 
+|
188 
+|   ;
189 
+|   return 0;
190 
+| }
191 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
192 
+conftest.cpp: In function 'int main()':
193 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
194 
+         thisisanerror;
195 
+         ^
196 
+configure:3059: $? = 1
197 
+configure: failed program was:
198 
+| /* confdefs.h */
199 
+| #define PACKAGE_NAME "CoGAPS"
200 
+| #define PACKAGE_TARNAME "cogaps"
201 
+| #define PACKAGE_VERSION "3.1.2"
202 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
203 
+| #define PACKAGE_BUGREPORT ""
204 
+| #define PACKAGE_URL ""
205 
+| /* end confdefs.h.  */
206 
+|
207 
+| int
208 
+| main ()
209 
+| {
210 
+|
211 
+|       #if !(defined(__xlc__) || defined(__xlC__) || defined(__IBMC__) || defined(__IBMCPP__))
212 
+|         thisisanerror;
213 
+|       #endif
214 
+|
215 
+|   ;
216 
+|   return 0;
217 
+| }
218 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
219 
+conftest.cpp: In function 'int main()':
220 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
221 
+         thisisanerror;
222 
+         ^
223 
+configure:3059: $? = 1
224 
+configure: failed program was:
225 
+| /* confdefs.h */
226 
+| #define PACKAGE_NAME "CoGAPS"
227 
+| #define PACKAGE_TARNAME "cogaps"
228 
+| #define PACKAGE_VERSION "3.1.2"
229 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
230 
+| #define PACKAGE_BUGREPORT ""
231 
+| #define PACKAGE_URL ""
232 
+| /* end confdefs.h.  */
233 
+|
234 
+| int
235 
+| main ()
236 
+| {
237 
+|
238 
+|       #if !(defined(__PATHCC__) || defined(__PATHSCALE__))
239 
+|         thisisanerror;
240 
+|       #endif
241 
+|
242 
+|   ;
243 
+|   return 0;
244 
+| }
245 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
246 
+conftest.cpp: In function 'int main()':
247 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
248 
+         thisisanerror;
249 
+         ^
250 
+configure:3059: $? = 1
251 
+configure: failed program was:
252 
+| /* confdefs.h */
253 
+| #define PACKAGE_NAME "CoGAPS"
254 
+| #define PACKAGE_TARNAME "cogaps"
255 
+| #define PACKAGE_VERSION "3.1.2"
256 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
257 
+| #define PACKAGE_BUGREPORT ""
258 
+| #define PACKAGE_URL ""
259 
+| /* end confdefs.h.  */
260 
+|
261 
+| int
262 
+| main ()
263 
+| {
264 
+|
265 
+|       #if !(defined(__clang__))
266 
+|         thisisanerror;
267 
+|       #endif
268 
+|
269 
+|   ;
270 
+|   return 0;
271 
+| }
272 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
273 
+conftest.cpp: In function 'int main()':
274 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
275 
+         thisisanerror;
276 
+         ^
277 
+configure:3059: $? = 1
278 
+configure: failed program was:
279 
+| /* confdefs.h */
280 
+| #define PACKAGE_NAME "CoGAPS"
281 
+| #define PACKAGE_TARNAME "cogaps"
282 
+| #define PACKAGE_VERSION "3.1.2"
283 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
284 
+| #define PACKAGE_BUGREPORT ""
285 
+| #define PACKAGE_URL ""
286 
+| /* end confdefs.h.  */
287 
+|
288 
+| int
289 
+| main ()
290 
+| {
291 
+|
292 
+|       #if !(defined(_CRAYC))
293 
+|         thisisanerror;
294 
+|       #endif
295 
+|
296 
+|   ;
297 
+|   return 0;
298 
+| }
299 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
300 
+conftest.cpp: In function 'int main()':
301 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
302 
+         thisisanerror;
303 
+         ^
304 
+configure:3059: $? = 1
305 
+configure: failed program was:
306 
+| /* confdefs.h */
307 
+| #define PACKAGE_NAME "CoGAPS"
308 
+| #define PACKAGE_TARNAME "cogaps"
309 
+| #define PACKAGE_VERSION "3.1.2"
310 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
311 
+| #define PACKAGE_BUGREPORT ""
312 
+| #define PACKAGE_URL ""
313 
+| /* end confdefs.h.  */
314 
+|
315 
+| int
316 
+| main ()
317 
+| {
318 
+|
319 
+|       #if !(defined(__FUJITSU))
320 
+|         thisisanerror;
321 
+|       #endif
322 
+|
323 
+|   ;
324 
+|   return 0;
325 
+| }
326 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
327 
+conftest.cpp:14:38: error: operator "defined" requires an identifier
328 
+       #if !(defined(SDCC) || defined())
329 
+                                      ^
330 
+conftest.cpp: In function 'int main()':
331 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
332 
+         thisisanerror;
333 
+         ^
334 
+configure:3059: $? = 1
335 
+configure: failed program was:
336 
+| /* confdefs.h */
337 
+| #define PACKAGE_NAME "CoGAPS"
338 
+| #define PACKAGE_TARNAME "cogaps"
339 
+| #define PACKAGE_VERSION "3.1.2"
340 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
341 
+| #define PACKAGE_BUGREPORT ""
342 
+| #define PACKAGE_URL ""
343 
+| /* end confdefs.h.  */
344 
+|
345 
+| int
346 
+| main ()
347 
+| {
348 
+|
349 
+|       #if !(defined(SDCC) || defined())
350 
+|         thisisanerror;
351 
+|       #endif
352 
+|
353 
+|   ;
354 
+|   return 0;
355 
+| }
356 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
357 
+conftest.cpp: In function 'int main()':
358 
+conftest.cpp:15:9: error: 'thisisanerror' was not declared in this scope
359 
+         thisisanerror;
360 
+         ^
361 
+configure:3059: $? = 1
362 
+configure: failed program was:
363 
+| /* confdefs.h */
364 
+| #define PACKAGE_NAME "CoGAPS"
365 
+| #define PACKAGE_TARNAME "cogaps"
366 
+| #define PACKAGE_VERSION "3.1.2"
367 
+| #define PACKAGE_STRING "CoGAPS 3.1.2"
368 
+| #define PACKAGE_BUGREPORT ""
369 
+| #define PACKAGE_URL ""
370 
+| /* end confdefs.h.  */
371 
+|
372 
+| int
373 
+| main ()
374 
+| {
375 
+|
376 
+|       #if !(defined(__SDCC))
377 
+|         thisisanerror;
378 
+|       #endif
379 
+|
380 
+|   ;
381 
+|   return 0;
382 
+| }
383 
+configure:3059: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  conftest.cpp >&5
384 
+configure:3059: $? = 0
385 
+configure:3067: result: gnu
386 
+configure:3070: checking for a sed that does not truncate output
387 
+configure:3134: result: /bin/sed
388 
+configure:3141: checking for C++ compiler version
389 
+configure:3363: ccache g++ -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.cpp  >&5
390 
+configure:3363: $? = 0
391 
+configure:3363: ./conftest
392 
+configure:3363: $? = 0
393 
+configure:3372: ccache g++ -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.cpp  >&5
394 
+configure:3372: $? = 0
395 
+configure:3372: ./conftest
396 
+configure:3372: $? = 0
397 
+configure:3381: ccache g++ -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.cpp  >&5
398 
+configure:3381: $? = 0
399 
+configure:3381: ./conftest
400 
+configure:3381: $? = 0
401 
+configure:4098: result: 5.4.0
402 
+configure:4103: checking for OpenMP flag of C++ compiler
403 
+configure:4148: ccache g++ -o conftest -UNDEBUG -Wall -pedantic -g -O0 -fopenmp   conftest.cpp  >&5
404 
+configure:4148: $? = 0
405 
+configure:4157: result: -fopenmp
406 
+configure:4365: checking whether C++ compiler accepts -msse4.2
407 
+configure:4384: ccache g++ -c -UNDEBUG -Wall -pedantic -g -O0  -msse4.2  conftest.cpp >&5
408 
+configure:4384: $? = 0
409 
+configure:4392: result: yes
410 
+configure:4639: creating ./config.status
411 
+
412 
+## ---------------------- ##
413 
+## Running config.status. ##
414 
+## ---------------------- ##
415 
+
416 
+This file was extended by CoGAPS config.status 3.1.2, which was
417 
+generated by GNU Autoconf 2.69.  Invocation command line was
418 
+
419 
+  CONFIG_FILES    =
420 
+  CONFIG_HEADERS  =
421 
+  CONFIG_LINKS    =
422 
+  CONFIG_COMMANDS =
423 
+  $ ./config.status
424 
+
425 
+on MBL-D518NN2
426 
+
427 
+config.status:725: creating src/Makevars
428 
+
429 
+## ---------------- ##
430 
+## Cache variables. ##
431 
+## ---------------- ##
432 
+
433 
+ac_cv_cxx_compiler_gnu=yes
434 
+ac_cv_env_CCC_set=
435 
+ac_cv_env_CCC_value=
436 
+ac_cv_env_CPPFLAGS_set=
437 
+ac_cv_env_CPPFLAGS_value=
438 
+ac_cv_env_CXXCPP_set=
439 
+ac_cv_env_CXXCPP_value=
440 
+ac_cv_env_CXXFLAGS_set=set
441 
+ac_cv_env_CXXFLAGS_value='-UNDEBUG -Wall -pedantic -g -O0'
442 
+ac_cv_env_CXX_set=
443 
+ac_cv_env_CXX_value=
444 
+ac_cv_env_LDFLAGS_set=
445 
+ac_cv_env_LDFLAGS_value=
446 
+ac_cv_env_LIBS_set=
447 
+ac_cv_env_LIBS_value=
448 
+ac_cv_env_build_alias_set=
449 
+ac_cv_env_build_alias_value=
450 
+ac_cv_env_host_alias_set=
451 
+ac_cv_env_host_alias_value=
452 
+ac_cv_env_target_alias_set=
453 
+ac_cv_env_target_alias_value=
454 
+ac_cv_objext=o
455 
+ac_cv_path_SED=/bin/sed
456 
+ac_cv_prog_CXXCPP='ccache g++ -E'
457 
+ac_cv_prog_cxx_g=yes
458 
+ax_cv_check_cxxflags___msse4_2=yes
459 
+ax_cv_cxx_compiler_vendor=gnu
460 
+ax_cv_cxx_compiler_version=5.4.0
461 
+ax_cv_cxx_openmp=-fopenmp
462 
+
463 
+## ----------------- ##
464 
+## Output variables. ##
465 
+## ----------------- ##
466 
+
467 
+CPPFLAGS=''
468 
+CXX='ccache g++'
469 
+CXXCPP='ccache g++ -E'
470 
+CXXFLAGS='-UNDEBUG -Wall -pedantic -g -O0'
471 
+DEFS='-DPACKAGE_NAME=\"CoGAPS\" -DPACKAGE_TARNAME=\"cogaps\" -DPACKAGE_VERSION=\"3.1.2\" -DPACKAGE_STRING=\"CoGAPS\ 3.1.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_OPENMP=1'
472 
+ECHO_C=''
473 
+ECHO_N='-n'
474 
+ECHO_T=''
475 
+EXEEXT=''
476 
+GAPS_CPP_FLAGS=' -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ '
477 
+GAPS_CXX_FLAGS=' -fopenmp  -msse4.2 '
478 
+GAPS_LIBS=' -fopenmp '
479 
+LDFLAGS=''
480 
+LIBOBJS=''
481 
+LIBS=''
482 
+LTLIBOBJS=''
483 
+OBJEXT='o'
484 
+PACKAGE_BUGREPORT=''
485 
+PACKAGE_NAME='CoGAPS'
486 
+PACKAGE_STRING='CoGAPS 3.1.2'
487 
+PACKAGE_TARNAME='cogaps'
488 
+PACKAGE_URL=''
489 
+PACKAGE_VERSION='3.1.2'
490 
+PATH_SEPARATOR=':'
491 
+SED='/bin/sed'
492 
+SHELL='/bin/bash'
493 
+ac_ct_CXX=''
494 
+bindir='${exec_prefix}/bin'
495 
+build_alias=''
496 
+datadir='${datarootdir}'
497 
+datarootdir='${prefix}/share'
498 
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
499 
+dvidir='${docdir}'
500 
+exec_prefix='${prefix}'
501 
+host_alias=''
502 
+htmldir='${docdir}'
503 
+includedir='${prefix}/include'
504 
+infodir='${datarootdir}/info'
505 
+libdir='${exec_prefix}/lib'
506 
+libexecdir='${exec_prefix}/libexec'
507 
+localedir='${datarootdir}/locale'
508 
+localstatedir='${prefix}/var'
509 
+mandir='${datarootdir}/man'
510 
+oldincludedir='/usr/include'
511 
+pdfdir='${docdir}'
512 
+prefix='/usr/local'
513 
+program_transform_name='s,x,x,'
514 
+psdir='${docdir}'
515 
+runstatedir='${localstatedir}/run'
516 
+sbindir='${exec_prefix}/sbin'
517 
+sharedstatedir='${prefix}/com'
518 
+sysconfdir='${prefix}/etc'
519 
+target_alias=''
520 
+
521 
+## ----------- ##
522 
+## confdefs.h. ##
523 
+## ----------- ##
524 
+
525 
+/* confdefs.h */
526 
+#define PACKAGE_NAME "CoGAPS"
527 
+#define PACKAGE_TARNAME "cogaps"
528 
+#define PACKAGE_VERSION "3.1.2"
529 
+#define PACKAGE_STRING "CoGAPS 3.1.2"
530 
+#define PACKAGE_BUGREPORT ""
531 
+#define PACKAGE_URL ""
532 
+#define HAVE_OPENMP 1
533 
+
534 
+configure: exit 0
config.status
History View file @ 16472f106
0 535 
new file mode 100644
... ... 
@@ -0,0 +1,892 @@
1 
+#! /bin/bash
2 
+# Generated by configure.
3 
+# Run this file to recreate the current configuration.
4 
+# Compiler output produced by configure, useful for debugging
5 
+# configure, is in config.log if it exists.
6 
+
7 
+debug=false
8 
+ac_cs_recheck=false
9 
+ac_cs_silent=false
10 
+
11 
+SHELL=${CONFIG_SHELL-/bin/bash}
12 
+export SHELL
13 
+## -------------------- ##
14 
+## M4sh Initialization. ##
15 
+## -------------------- ##
16 
+
17 
+# Be more Bourne compatible
18 
+DUALCASE=1; export DUALCASE # for MKS sh
19 
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
20 
+  emulate sh
21 
+  NULLCMD=:
22 
+  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
23 
+  # is contrary to our usage.  Disable this feature.
24 
+  alias -g '${1+"$@"}'='"$@"'
25 
+  setopt NO_GLOB_SUBST
26 
+else
27 
+  case `(set -o) 2>/dev/null` in #(
28 
+  *posix*) :
29 
+    set -o posix ;; #(
30 
+  *) :
31 
+     ;;
32 
+esac
33 
+fi
34 
+
35 
+
36 
+as_nl='
37 
+'
38 
+export as_nl
39 
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
40 
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
41 
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
42 
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
43 
+# Prefer a ksh shell builtin over an external printf program on Solaris,
44 
+# but without wasting forks for bash or zsh.
45 
+if test -z "$BASH_VERSION$ZSH_VERSION" \
46 
+    && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
47 
+  as_echo='print -r --'
48 
+  as_echo_n='print -rn --'
49 
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
50 
+  as_echo='printf %s\n'
51 
+  as_echo_n='printf %s'
52 
+else
53 
+  if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
54 
+    as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
55 
+    as_echo_n='/usr/ucb/echo -n'
56 
+  else
57 
+    as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
58 
+    as_echo_n_body='eval
59 
+      arg=$1;
60 
+      case $arg in #(
61 
+      *"$as_nl"*)
62 
+	expr "X$arg" : "X\\(.*\\)$as_nl";
63 
+	arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
64 
+      esac;
65 
+      expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
66 
+    '
67 
+    export as_echo_n_body
68 
+    as_echo_n='sh -c $as_echo_n_body as_echo'
69 
+  fi
70 
+  export as_echo_body
71 
+  as_echo='sh -c $as_echo_body as_echo'
72 
+fi
73 
+
74 
+# The user is always right.
75 
+if test "${PATH_SEPARATOR+set}" != set; then
76 
+  PATH_SEPARATOR=:
77 
+  (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
78 
+    (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
79 
+      PATH_SEPARATOR=';'
80 
+  }
81 
+fi
82 
+
83 
+
84 
+# IFS
85 
+# We need space, tab and new line, in precisely that order.  Quoting is
86 
+# there to prevent editors from complaining about space-tab.
87 
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
88 
+# splitting by setting IFS to empty value.)
89 
+IFS=" ""	$as_nl"
90 
+
91 
+# Find who we are.  Look in the path if we contain no directory separator.
92 
+as_myself=
93 
+case $0 in #((
94 
+  *[\\/]* ) as_myself=$0 ;;
95 
+  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
96 
+for as_dir in $PATH
97 
+do
98 
+  IFS=$as_save_IFS
99 
+  test -z "$as_dir" && as_dir=.
100 
+    test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
101 
+  done
102 
+IFS=$as_save_IFS
103 
+
104 
+     ;;
105 
+esac
106 
+# We did not find ourselves, most probably we were run as `sh COMMAND'
107 
+# in which case we are not to be found in the path.
108 
+if test "x$as_myself" = x; then
109 
+  as_myself=$0
110 
+fi
111 
+if test ! -f "$as_myself"; then
112 
+  $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
113 
+  exit 1
114 
+fi
115 
+
116 
+# Unset variables that we do not need and which cause bugs (e.g. in
117 
+# pre-3.0 UWIN ksh).  But do not cause bugs in bash 2.01; the "|| exit 1"
118 
+# suppresses any "Segmentation fault" message there.  '((' could
119 
+# trigger a bug in pdksh 5.2.14.
120 
+for as_var in BASH_ENV ENV MAIL MAILPATH
121 
+do eval test x\${$as_var+set} = xset \
122 
+  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
123 
+done
124 
+PS1='$ '
125 
+PS2='> '
126 
+PS4='+ '
127 
+
128 
+# NLS nuisances.
129 
+LC_ALL=C
130 
+export LC_ALL
131 
+LANGUAGE=C
132 
+export LANGUAGE
133 
+
134 
+# CDPATH.
135 
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
136 
+
137 
+
138 
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
139 
+# ----------------------------------------
140 
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
141 
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
142 
+# script with STATUS, using 1 if that was 0.
143 
+as_fn_error ()
144 
+{
145 
+  as_status=$1; test $as_status -eq 0 && as_status=1
146 
+  if test "$4"; then
147 
+    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
148 
+    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
149 
+  fi
150 
+  $as_echo "$as_me: error: $2" >&2
151 
+  as_fn_exit $as_status
152 
+} # as_fn_error
153 
+
154 
+
155 
+# as_fn_set_status STATUS
156 
+# -----------------------
157 
+# Set $? to STATUS, without forking.
158 
+as_fn_set_status ()
159 
+{
160 
+  return $1
161 
+} # as_fn_set_status
162 
+
163 
+# as_fn_exit STATUS
164 
+# -----------------
165 
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
166 
+as_fn_exit ()
167 
+{
168 
+  set +e
169 
+  as_fn_set_status $1
170 
+  exit $1
171 
+} # as_fn_exit
172 
+
173 
+# as_fn_unset VAR
174 
+# ---------------
175 
+# Portably unset VAR.
176 
+as_fn_unset ()
177 
+{
178 
+  { eval $1=; unset $1;}
179 
+}
180 
+as_unset=as_fn_unset
181 
+# as_fn_append VAR VALUE
182 
+# ----------------------
183 
+# Append the text in VALUE to the end of the definition contained in VAR. Take
184 
+# advantage of any shell optimizations that allow amortized linear growth over
185 
+# repeated appends, instead of the typical quadratic growth present in naive
186 
+# implementations.
187 
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
188 
+  eval 'as_fn_append ()
189 
+  {
190 
+    eval $1+=\$2
191 
+  }'
192 
+else
193 
+  as_fn_append ()
194 
+  {
195 
+    eval $1=\$$1\$2
196 
+  }
197 
+fi # as_fn_append
198 
+
199 
+# as_fn_arith ARG...
200 
+# ------------------
201 
+# Perform arithmetic evaluation on the ARGs, and store the result in the
202 
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
203 
+# must be portable across $(()) and expr.
204 
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
205 
+  eval 'as_fn_arith ()
206 
+  {
207 
+    as_val=$(( $* ))
208 
+  }'
209 
+else
210 
+  as_fn_arith ()
211 
+  {
212 
+    as_val=`expr "$@" || test $? -eq 1`
213 
+  }
214 
+fi # as_fn_arith
215 
+
216 
+
217 
+if expr a : '\(a\)' >/dev/null 2>&1 &&
218 
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
219 
+  as_expr=expr
220 
+else
221 
+  as_expr=false
222 
+fi
223 
+
224 
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
225 
+  as_basename=basename
226 
+else
227 
+  as_basename=false
228 
+fi
229 
+
230 
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
231 
+  as_dirname=dirname
232 
+else
233 
+  as_dirname=false
234 
+fi
235 
+
236 
+as_me=`$as_basename -- "$0" ||
237 
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
238 
+	 X"$0" : 'X\(//\)$' \| \
239 
+	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
240 
+$as_echo X/"$0" |
241 
+    sed '/^.*\/\([^/][^/]*\)\/*$/{
242 
+	    s//\1/
243 
+	    q
244 
+	  }
245 
+	  /^X\/\(\/\/\)$/{
246 
+	    s//\1/
247 
+	    q
248 
+	  }
249 
+	  /^X\/\(\/\).*/{
250 
+	    s//\1/
251 
+	    q
252 
+	  }
253 
+	  s/.*/./; q'`
254 
+
255 
+# Avoid depending upon Character Ranges.
256 
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
257 
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
258 
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
259 
+as_cr_digits='0123456789'
260 
+as_cr_alnum=$as_cr_Letters$as_cr_digits
261 
+
262 
+ECHO_C= ECHO_N= ECHO_T=
263 
+case `echo -n x` in #(((((
264 
+-n*)
265 
+  case `echo 'xy\c'` in
266 
+  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
267 
+  xy)  ECHO_C='\c';;
268 
+  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null
269 
+       ECHO_T='	';;
270 
+  esac;;
271 
+*)
272 
+  ECHO_N='-n';;
273 
+esac
274 
+
275 
+rm -f conf$$ conf$$.exe conf$$.file
276 
+if test -d conf$$.dir; then
277 
+  rm -f conf$$.dir/conf$$.file
278 
+else
279 
+  rm -f conf$$.dir
280 
+  mkdir conf$$.dir 2>/dev/null
281 
+fi
282 
+if (echo >conf$$.file) 2>/dev/null; then
283 
+  if ln -s conf$$.file conf$$ 2>/dev/null; then
284 
+    as_ln_s='ln -s'
285 
+    # ... but there are two gotchas:
286 
+    # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
287 
+    # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
288 
+    # In both cases, we have to default to `cp -pR'.
289 
+    ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
290 
+      as_ln_s='cp -pR'
291 
+  elif ln conf$$.file conf$$ 2>/dev/null; then
292 
+    as_ln_s=ln
293 
+  else
294 
+    as_ln_s='cp -pR'
295 
+  fi
296 
+else
297 
+  as_ln_s='cp -pR'
298 
+fi
299 
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
300 
+rmdir conf$$.dir 2>/dev/null
301 
+
302 
+
303 
+# as_fn_mkdir_p
304 
+# -------------
305 
+# Create "$as_dir" as a directory, including parents if necessary.
306 
+as_fn_mkdir_p ()
307 
+{
308 
+
309 
+  case $as_dir in #(
310 
+  -*) as_dir=./$as_dir;;
311 
+  esac
312 
+  test -d "$as_dir" || eval $as_mkdir_p || {
313 
+    as_dirs=
314 
+    while :; do
315 
+      case $as_dir in #(
316 
+      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
317 
+      *) as_qdir=$as_dir;;
318 
+      esac
319 
+      as_dirs="'$as_qdir' $as_dirs"
320 
+      as_dir=`$as_dirname -- "$as_dir" ||
321 
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
322 
+	 X"$as_dir" : 'X\(//\)[^/]' \| \
323 
+	 X"$as_dir" : 'X\(//\)$' \| \
324 
+	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
325 
+$as_echo X"$as_dir" |
326 
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
327 
+	    s//\1/
328 
+	    q
329 
+	  }
330 
+	  /^X\(\/\/\)[^/].*/{
331 
+	    s//\1/
332 
+	    q
333 
+	  }
334 
+	  /^X\(\/\/\)$/{
335 
+	    s//\1/
336 
+	    q
337 
+	  }
338 
+	  /^X\(\/\).*/{
339 
+	    s//\1/
340 
+	    q
341 
+	  }
342 
+	  s/.*/./; q'`
343 
+      test -d "$as_dir" && break
344 
+    done
345 
+    test -z "$as_dirs" || eval "mkdir $as_dirs"
346 
+  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
347 
+
348 
+
349 
+} # as_fn_mkdir_p
350 
+if mkdir -p . 2>/dev/null; then
351 
+  as_mkdir_p='mkdir -p "$as_dir"'
352 
+else
353 
+  test -d ./-p && rmdir ./-p
354 
+  as_mkdir_p=false
355 
+fi
356 
+
357 
+
358 
+# as_fn_executable_p FILE
359 
+# -----------------------
360 
+# Test if FILE is an executable regular file.
361 
+as_fn_executable_p ()
362 
+{
363 
+  test -f "$1" && test -x "$1"
364 
+} # as_fn_executable_p
365 
+as_test_x='test -x'
366 
+as_executable_p=as_fn_executable_p
367 
+
368 
+# Sed expression to map a string onto a valid CPP name.
369 
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
370 
+
371 
+# Sed expression to map a string onto a valid variable name.
372 
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
373 
+
374 
+
375 
+exec 6>&1
376 
+## ----------------------------------- ##
377 
+## Main body of $CONFIG_STATUS script. ##
378 
+## ----------------------------------- ##
379 
+# Save the log message, to keep $0 and so on meaningful, and to
380 
+# report actual input values of CONFIG_FILES etc. instead of their
381 
+# values after options handling.
382 
+ac_log="
383 
+This file was extended by CoGAPS $as_me 3.1.2, which was
384 
+generated by GNU Autoconf 2.69.  Invocation command line was
385 
+
386 
+  CONFIG_FILES    = $CONFIG_FILES
387 
+  CONFIG_HEADERS  = $CONFIG_HEADERS
388 
+  CONFIG_LINKS    = $CONFIG_LINKS
389 
+  CONFIG_COMMANDS = $CONFIG_COMMANDS
390 
+  $ $0 $@
391 
+
392 
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
393 
+"
394 
+
395 
+# Files that config.status was made for.
396 
+config_files=" src/Makevars"
397 
+
398 
+ac_cs_usage="\
399 
+\`$as_me' instantiates files and other configuration actions
400 
+from templates according to the current configuration.  Unless the files
401 
+and actions are specified as TAGs, all are instantiated by default.
402 
+
403 
+Usage: $0 [OPTION]... [TAG]...
404 
+
405 
+  -h, --help       print this help, then exit
406 
+  -V, --version    print version number and configuration settings, then exit
407 
+      --config     print configuration, then exit
408 
+  -q, --quiet, --silent
409 
+                   do not print progress messages
410 
+  -d, --debug      don't remove temporary files
411 
+      --recheck    update $as_me by reconfiguring in the same conditions
412 
+      --file=FILE[:TEMPLATE]
413 
+                   instantiate the configuration file FILE
414 
+
415 
+Configuration files:
416 
+$config_files
417 
+
418 
+Report bugs to the package provider."
419 
+
420 
+ac_cs_config="'CXXFLAGS=-UNDEBUG -Wall -pedantic -g -O0'"
421 
+ac_cs_version="\
422 
+CoGAPS config.status 3.1.2
423 
+configured by ./configure, generated by GNU Autoconf 2.69,
424 
+  with options \"$ac_cs_config\"
425 
+
426 
+Copyright (C) 2012 Free Software Foundation, Inc.
427 
+This config.status script is free software; the Free Software Foundation
428 
+gives unlimited permission to copy, distribute and modify it."
429 
+
430 
+ac_pwd='/mnt/c/Users/tsherma4/Documents/CoGAPS/Repo'
431 
+srcdir='.'
432 
+test -n "$AWK" || AWK=awk
433 
+# The default lists apply if the user does not specify any file.
434 
+ac_need_defaults=:
435 
+while test $# != 0
436 
+do
437 
+  case $1 in
438 
+  --*=?*)
439 
+    ac_option=`expr "X$1" : 'X\([^=]*\)='`
440 
+    ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
441 
+    ac_shift=:
442 
+    ;;
443 
+  --*=)
444 
+    ac_option=`expr "X$1" : 'X\([^=]*\)='`
445 
+    ac_optarg=
446 
+    ac_shift=:
447 
+    ;;
448 
+  *)
449 
+    ac_option=$1
450 
+    ac_optarg=$2
451 
+    ac_shift=shift
452 
+    ;;
453 
+  esac
454 
+
455 
+  case $ac_option in
456 
+  # Handling of the options.
457 
+  -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
458 
+    ac_cs_recheck=: ;;
459 
+  --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
460 
+    $as_echo "$ac_cs_version"; exit ;;
461 
+  --config | --confi | --conf | --con | --co | --c )
462 
+    $as_echo "$ac_cs_config"; exit ;;
463 
+  --debug | --debu | --deb | --de | --d | -d )
464 
+    debug=: ;;
465 
+  --file | --fil | --fi | --f )
466 
+    $ac_shift
467 
+    case $ac_optarg in
468 
+    *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
469 
+    '') as_fn_error $? "missing file argument" ;;
470 
+    esac
471 
+    as_fn_append CONFIG_FILES " '$ac_optarg'"
472 
+    ac_need_defaults=false;;
473 
+  --he | --h |  --help | --hel | -h )
474 
+    $as_echo "$ac_cs_usage"; exit ;;
475 
+  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
476 
+  | -silent | --silent | --silen | --sile | --sil | --si | --s)
477 
+    ac_cs_silent=: ;;
478 
+
479 
+  # This is an error.
480 
+  -*) as_fn_error $? "unrecognized option: \`$1'
481 
+Try \`$0 --help' for more information." ;;
482 
+
483 
+  *) as_fn_append ac_config_targets " $1"
484 
+     ac_need_defaults=false ;;
485 
+
486 
+  esac
487 
+  shift
488 
+done
489 
+
490 
+ac_configure_extra_args=
491 
+
492 
+if $ac_cs_silent; then
493 
+  exec 6>/dev/null
494 
+  ac_configure_extra_args="$ac_configure_extra_args --silent"
495 
+fi
496 
+
497 
+if $ac_cs_recheck; then
498 
+  set X /bin/bash './configure'  'CXXFLAGS=-UNDEBUG -Wall -pedantic -g -O0' $ac_configure_extra_args --no-create --no-recursion
499 
+  shift
500 
+  $as_echo "running CONFIG_SHELL=/bin/bash $*" >&6
501 
+  CONFIG_SHELL='/bin/bash'
502 
+  export CONFIG_SHELL
503 
+  exec "$@"
504 
+fi
505 
+
506 
+exec 5>>config.log
507 
+{
508 
+  echo
509 
+  sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
510 
+## Running $as_me. ##
511 
+_ASBOX
512 
+  $as_echo "$ac_log"
513 
+} >&5
514 
+
515 
+
516 
+# Handling of arguments.
517 
+for ac_config_target in $ac_config_targets
518 
+do
519 
+  case $ac_config_target in
520 
+    "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
521 
+
522 
+  *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
523 
+  esac
524 
+done
525 
+
526 
+
527 
+# If the user did not use the arguments to specify the items to instantiate,
528 
+# then the envvar interface is used.  Set only those that are not.
529 
+# We use the long form for the default assignment because of an extremely
530 
+# bizarre bug on SunOS 4.1.3.
531 
+if $ac_need_defaults; then
532 
+  test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
533 
+fi
534 
+
535 
+# Have a temporary directory for convenience.  Make it in the build tree
536 
+# simply because there is no reason against having it here, and in addition,
537 
+# creating and moving files from /tmp can sometimes cause problems.
538 
+# Hook for its removal unless debugging.
539 
+# Note that there is a small window in which the directory will not be cleaned:
540 
+# after its creation but before its name has been assigned to `$tmp'.
541 
+$debug ||
542 
+{
543 
+  tmp= ac_tmp=
544 
+  trap 'exit_status=$?
545 
+  : "${ac_tmp:=$tmp}"
546 
+  { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
547 
+' 0
548 
+  trap 'as_fn_exit 1' 1 2 13 15
549 
+}
550 
+# Create a (secure) tmp directory for tmp files.
551 
+
552 
+{
553 
+  tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
554 
+  test -d "$tmp"
555 
+}  ||
556 
+{
557 
+  tmp=./conf$$-$RANDOM
558 
+  (umask 077 && mkdir "$tmp")
559 
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
560 
+ac_tmp=$tmp
561 
+
562 
+# Set up the scripts for CONFIG_FILES section.
563 
+# No need to generate them if there are no CONFIG_FILES.
564 
+# This happens for instance with `./config.status config.h'.
565 
+if test -n "$CONFIG_FILES"; then
566 
+
567 
+
568 
+ac_cr=`echo X | tr X '\015'`
569 
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
570 
+# But we know of no other shell where ac_cr would be empty at this
571 
+# point, so we can use a bashism as a fallback.
572 
+if test "x$ac_cr" = x; then
573 
+  eval ac_cr=\$\'\\r\'
574 
+fi
575 
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
576 
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
577 
+  ac_cs_awk_cr='\\r'
578 
+else
579 
+  ac_cs_awk_cr=$ac_cr
580 
+fi
581 
+
582 
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
583 
+cat >>"$ac_tmp/subs1.awk" <<\_ACAWK &&
584 
+S["LTLIBOBJS"]=""
585 
+S["LIBOBJS"]=""
586 
+S["GAPS_LIBS"]=" -fopenmp "
587 
+S["GAPS_CXX_FLAGS"]=" -fopenmp  -msse4.2 "
588 
+S["GAPS_CPP_FLAGS"]=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ "
589 
+S["SED"]="/bin/sed"
590 
+S["CXXCPP"]="ccache g++ -E"
591 
+S["OBJEXT"]="o"
592 
+S["EXEEXT"]=""
593 
+S["ac_ct_CXX"]=""
594 
+S["CPPFLAGS"]=""
595 
+S["LDFLAGS"]=""
596 
+S["CXXFLAGS"]="-UNDEBUG -Wall -pedantic -g -O0"
597 
+S["CXX"]="ccache g++"
598 
+S["target_alias"]=""
599 
+S["host_alias"]=""
600 
+S["build_alias"]=""
601 
+S["LIBS"]=""
602 
+S["ECHO_T"]=""
603 
+S["ECHO_N"]="-n"
604 
+S["ECHO_C"]=""
605 
+S["DEFS"]="-DPACKAGE_NAME=\\\"CoGAPS\\\" -DPACKAGE_TARNAME=\\\"cogaps\\\" -DPACKAGE_VERSION=\\\"3.1.2\\\" -DPACKAGE_STRING=\\\"CoGAPS\\ 3.1.2\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPAC"\
606 
+"KAGE_URL=\\\"\\\" -DHAVE_OPENMP=1"
607 
+S["mandir"]="${datarootdir}/man"
608 
+S["localedir"]="${datarootdir}/locale"
609 
+S["libdir"]="${exec_prefix}/lib"
610 
+S["psdir"]="${docdir}"
611 
+S["pdfdir"]="${docdir}"
612 
+S["dvidir"]="${docdir}"
613 
+S["htmldir"]="${docdir}"
614 
+S["infodir"]="${datarootdir}/info"
615 
+S["docdir"]="${datarootdir}/doc/${PACKAGE_TARNAME}"
616 
+S["oldincludedir"]="/usr/include"
617 
+S["includedir"]="${prefix}/include"
618 
+S["runstatedir"]="${localstatedir}/run"
619 
+S["localstatedir"]="${prefix}/var"
620 
+S["sharedstatedir"]="${prefix}/com"
621 
+S["sysconfdir"]="${prefix}/etc"
622 
+S["datadir"]="${datarootdir}"
623 
+S["datarootdir"]="${prefix}/share"
624 
+S["libexecdir"]="${exec_prefix}/libexec"
625 
+S["sbindir"]="${exec_prefix}/sbin"
626 
+S["bindir"]="${exec_prefix}/bin"
627 
+S["program_transform_name"]="s,x,x,"
628 
+S["prefix"]="/usr/local"
629 
+S["exec_prefix"]="${prefix}"
630 
+S["PACKAGE_URL"]=""
631 
+S["PACKAGE_BUGREPORT"]=""
632 
+S["PACKAGE_STRING"]="CoGAPS 3.1.2"
633 
+S["PACKAGE_VERSION"]="3.1.2"
634 
+S["PACKAGE_TARNAME"]="cogaps"
635 
+S["PACKAGE_NAME"]="CoGAPS"
636 
+S["PATH_SEPARATOR"]=":"
637 
+S["SHELL"]="/bin/bash"
638 
+_ACAWK
639 
+cat >>"$ac_tmp/subs1.awk" <<_ACAWK &&
640 
+  for (key in S) S_is_set[key] = 1
641 
+  FS = ""
642 
+
643 
+}
644 
+{
645 
+  line = $ 0
646 
+  nfields = split(line, field, "@")
647 
+  substed = 0
648 
+  len = length(field[1])
649 
+  for (i = 2; i < nfields; i++) {
650 
+    key = field[i]
651 
+    keylen = length(key)
652 
+    if (S_is_set[key]) {
653 
+      value = S[key]
654 
+      line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
655 
+      len += length(value) + length(field[++i])
656 
+      substed = 1
657 
+    } else
658 
+      len += 1 + keylen
659 
+  }
660 
+
661 
+  print line
662 
+}
663 
+
664 
+_ACAWK
665 
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
666 
+  sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
667 
+else
668 
+  cat
669 
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
670 
+  || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
671 
+fi # test -n "$CONFIG_FILES"
672 
+
673 
+
674 
+eval set X "  :F $CONFIG_FILES      "
675 
+shift
676 
+for ac_tag
677 
+do
678 
+  case $ac_tag in
679 
+  :[FHLC]) ac_mode=$ac_tag; continue;;
680 
+  esac
681 
+  case $ac_mode$ac_tag in
682 
+  :[FHL]*:*);;
683 
+  :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
684 
+  :[FH]-) ac_tag=-:-;;
685 
+  :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
686 
+  esac
687 
+  ac_save_IFS=$IFS
688 
+  IFS=:
689 
+  set x $ac_tag
690 
+  IFS=$ac_save_IFS
691 
+  shift
692 
+  ac_file=$1
693 
+  shift
694 
+
695 
+  case $ac_mode in
696 
+  :L) ac_source=$1;;
697 
+  :[FH])
698 
+    ac_file_inputs=
699 
+    for ac_f
700 
+    do
701 
+      case $ac_f in
702 
+      -) ac_f="$ac_tmp/stdin";;
703 
+      *) # Look for the file first in the build tree, then in the source tree
704 
+	 # (if the path is not absolute).  The absolute path cannot be DOS-style,
705 
+	 # because $ac_f cannot contain `:'.
706 
+	 test -f "$ac_f" ||
707 
+	   case $ac_f in
708 
+	   [\\/$]*) false;;
709 
+	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
710 
+	   esac ||
711 
+	   as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
712 
+      esac
713 
+      case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
714 
+      as_fn_append ac_file_inputs " '$ac_f'"
715 
+    done
716 
+
717 
+    # Let's still pretend it is `configure' which instantiates (i.e., don't
718 
+    # use $as_me), people would be surprised to read:
719 
+    #    /* config.h.  Generated by config.status.  */
720 
+    configure_input='Generated from '`
721 
+	  $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
722 
+	`' by configure.'
723 
+    if test x"$ac_file" != x-; then
724 
+      configure_input="$ac_file.  $configure_input"
725 
+      { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
726 
+$as_echo "$as_me: creating $ac_file" >&6;}
727 
+    fi
728 
+    # Neutralize special characters interpreted by sed in replacement strings.
729 
+    case $configure_input in #(
730 
+    *\&* | *\|* | *\\* )
731 
+       ac_sed_conf_input=`$as_echo "$configure_input" |
732 
+       sed 's/[\\\\&|]/\\\\&/g'`;; #(
733 
+    *) ac_sed_conf_input=$configure_input;;
734 
+    esac
735 
+
736 
+    case $ac_tag in
737 
+    *:-:* | *:-) cat >"$ac_tmp/stdin" \
738 
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
739 
+    esac
740 
+    ;;
741 
+  esac
742 
+
743 
+  ac_dir=`$as_dirname -- "$ac_file" ||
744 
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
745 
+	 X"$ac_file" : 'X\(//\)[^/]' \| \
746 
+	 X"$ac_file" : 'X\(//\)$' \| \
747 
+	 X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
748 
+$as_echo X"$ac_file" |
749 
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
750 
+	    s//\1/
751 
+	    q
752 
+	  }
753 
+	  /^X\(\/\/\)[^/].*/{
754 
+	    s//\1/
755 
+	    q
756 
+	  }
757 
+	  /^X\(\/\/\)$/{
758 
+	    s//\1/
759 
+	    q
760 
+	  }
761 
+	  /^X\(\/\).*/{
762 
+	    s//\1/
763 
+	    q
764 
+	  }
765 
+	  s/.*/./; q'`
766 
+  as_dir="$ac_dir"; as_fn_mkdir_p
767 
+  ac_builddir=.
768 
+
769 
+case "$ac_dir" in
770 
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
771 
+*)
772 
+  ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
773 
+  # A ".." for each directory in $ac_dir_suffix.
774 
+  ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
775 
+  case $ac_top_builddir_sub in
776 
+  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
777 
+  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
778 
+  esac ;;
779 
+esac
780 
+ac_abs_top_builddir=$ac_pwd
781 
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
782 
+# for backward compatibility:
783 
+ac_top_builddir=$ac_top_build_prefix
784 
+
785 
+case $srcdir in
786