lgc - Log Gaussian Cox Processes for fish abundance modelling - check results
RForge.net

lgc

About lgc
SVN access
Download/Files
Check results
Package R docs

Version: 1.4
Result: ERROR
Check time: 2014-03-29 15:14

Distribution log

--- running R CMD build for lgc (project lgc)
* checking for file ‘lgc/DESCRIPTION’ ... OK
* preparing ‘lgc’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘lgc/inst’
* looking to see if a ‘data/datalist’ file should be added
* building ‘lgc_1.4.tar.gz’

Distribution log

SVN checkout/GIT clone log


Build log for Windows 7 (R 3.0.x)

(lgc 1.4)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'lgc' ...
** libs

*** arch - i386
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chol.c -o chol.o
chol.c: In function 'kronecker_parallel':
chol.c:93:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c: In function 'inner_prod':
chol.c:111:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c:112:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c: In function 'chol':
chol.c:202:7: warning: variable 'n' set but not used [-Wunused-but-set-variable]
chol.c: In function 'inv':
chol.c:357:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:331:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:328:11: warning: unused variable 'k' [-Wunused-variable]
chol.c: In function 'recursion':
chol.c:414:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:416:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:438:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:458:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:400:46: warning: unused variable 'Li' [-Wunused-variable]
chol.c: In function 'inv_up':
chol.c:531:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:537:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
chol.c:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:516:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:516:16: warning: unused variable 'Lii' [-Wunused-variable]
chol.c:516:10: warning: unused variable 'sigij' [-Wunused-variable]
chol.c:515:21: warning: unused variable 'Sigmax' [-Wunused-variable]
chol.c:515:11: warning: unused variable 'Lx' [-Wunused-variable]
chol.c:514:46: warning: unused variable 'Sigmap' [-Wunused-variable]
chol.c:514:28: warning: unused variable 'Sigmai' [-Wunused-variable]
chol.c:514:18: warning: unused variable 'Lp' [-Wunused-variable]
chol.c:514:8: warning: unused variable 'Li' [-Wunused-variable]
chol.c:513:18: warning: unused variable 'nL0' [-Wunused-variable]
chol.c:513:15: warning: unused variable 'pt' [-Wunused-variable]
chol.c:513:11: warning: unused variable 'k' [-Wunused-variable]
chol.c:513:9: warning: unused variable 'j' [-Wunused-variable]
chol.c: At top level:
chol.c:183:12: warning: 'cs_diag' defined but not used [-Wunused-function]
chol.c: In function 'recursion':
chol.c:430:11: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
chol.c:398:6: warning: 'p' may be used uninitialized in this function [-Wuninitialized]
chol.c: In function 'inv_up':
chol.c:442:3: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
chol.c:400:59: note: 'pdiag' was declared here
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dist.c -o dist.o
dist.c: In function 'distkm':
dist.c:37:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
dist.c: In function 'nearestkm':
dist.c:56:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c lgc_sparse.c -o lgc_sparse.o
lgc_sparse.c: In function 'lgc_newton':
lgc_sparse.c:402:3: warning: suggest parentheses around operand of '!' or change '|' to '||' or '!' to '~' [-Wparentheses]
lgc_sparse.c:390:28: warning: variable 'Hp' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:13: warning: variable 'Hi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:8: warning: variable 'Qi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:388:10: warning: variable 'mgc_previous' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:387:27: warning: unused variable 'zero' [-Wunused-variable]
lgc_sparse.c:381:22: warning: unused variable 'mgc2' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_gradient':
lgc_sparse.c:562:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:572:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:575:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:588:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:550:7: warning: unused variable 'ndata' [-Wunused-variable]
lgc_sparse.c:549:8: warning: unused variable 'dataindex' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inner_prod':
lgc_sparse.c:703:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c:704:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:839:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:841:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:863:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:883:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:825:46: warning: unused variable 'Li' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inv_up':
lgc_sparse.c:929:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c: In function 'lgc_recursion_super':
lgc_sparse.c:1035:8: warning: unused variable 'p' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_recursion.constprop.0':
lgc_sparse.c:867:3: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:855:11: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
lgc_sparse.c:823:6: warning: 'p' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c local_stubs.c -o local_stubs.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ops.c -o ops.o
ops.c: In function 'mul_sparse':
ops.c:67:72: warning: unused variable 'Bnzmax' [-Wunused-variable]
ops.c:67:43: warning: unused variable 'Bn' [-Wunused-variable]
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c winfix.c -o winfix.o
gcc -m32 -shared -s -static-libgcc -o lgc.dll tmp.def chol.o dist.o lgc_sparse.o local_stubs.o ops.o winfix.o C:/PROGRA~1/r/r-3.0/library/Matrix/libs//i386/Matrix.dll -LC:/PROGRA~1/r/r-3.0/bin/i386 -lRlapack -LC:/PROGRA~1/r/r-3.0/bin/i386 -lRblas -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/i386 -lR
installing to z:/rforge/Rlib/win7-3.0/lgc/libs/i386

*** arch - x64
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chol.c -o chol.o
chol.c: In function 'kronecker_parallel':
chol.c:93:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c: In function 'inner_prod':
chol.c:111:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c:112:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
chol.c: In function 'chol':
chol.c:202:7: warning: variable 'n' set but not used [-Wunused-but-set-variable]
chol.c: In function 'inv':
chol.c:357:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:331:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:328:11: warning: unused variable 'k' [-Wunused-variable]
chol.c: In function 'recursion':
chol.c:414:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:416:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:438:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:458:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
chol.c:400:46: warning: unused variable 'Li' [-Wunused-variable]
chol.c: In function 'inv_up':
chol.c:531:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:537:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
chol.c:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
chol.c:516:20: warning: unused variable 'sum' [-Wunused-variable]
chol.c:516:16: warning: unused variable 'Lii' [-Wunused-variable]
chol.c:516:10: warning: unused variable 'sigij' [-Wunused-variable]
chol.c:515:21: warning: unused variable 'Sigmax' [-Wunused-variable]
chol.c:515:11: warning: unused variable 'Lx' [-Wunused-variable]
chol.c:514:46: warning: unused variable 'Sigmap' [-Wunused-variable]
chol.c:514:28: warning: unused variable 'Sigmai' [-Wunused-variable]
chol.c:514:18: warning: unused variable 'Lp' [-Wunused-variable]
chol.c:514:8: warning: unused variable 'Li' [-Wunused-variable]
chol.c:513:18: warning: unused variable 'nL0' [-Wunused-variable]
chol.c:513:15: warning: unused variable 'pt' [-Wunused-variable]
chol.c:513:11: warning: unused variable 'k' [-Wunused-variable]
chol.c:513:9: warning: unused variable 'j' [-Wunused-variable]
chol.c: At top level:
chol.c:183:12: warning: 'cs_diag' defined but not used [-Wunused-function]
chol.c: In function 'recursion':
chol.c:398:6: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dist.c -o dist.o
dist.c: In function 'distkm':
dist.c:37:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
dist.c: In function 'nearestkm':
dist.c:56:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c lgc_sparse.c -o lgc_sparse.o
lgc_sparse.c: In function 'lgc_newton':
lgc_sparse.c:402:3: warning: suggest parentheses around operand of '!' or change '|' to '||' or '!' to '~' [-Wparentheses]
lgc_sparse.c:390:28: warning: variable 'Hp' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:13: warning: variable 'Hi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:390:8: warning: variable 'Qi' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:388:10: warning: variable 'mgc_previous' set but not used [-Wunused-but-set-variable]
lgc_sparse.c:387:27: warning: unused variable 'zero' [-Wunused-variable]
lgc_sparse.c:381:22: warning: unused variable 'mgc2' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_gradient':
lgc_sparse.c:562:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:572:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:575:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:588:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c:550:7: warning: unused variable 'ndata' [-Wunused-variable]
lgc_sparse.c:549:8: warning: unused variable 'dataindex' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inner_prod':
lgc_sparse.c:703:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c:704:5: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:839:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:841:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:863:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:883:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
lgc_sparse.c:825:46: warning: unused variable 'Li' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_inv_up':
lgc_sparse.c:929:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
lgc_sparse.c: In function 'lgc_recursion_super':
lgc_sparse.c:1035:8: warning: unused variable 'p' [-Wunused-variable]
lgc_sparse.c: In function 'lgc_recursion':
lgc_sparse.c:823:6: warning: 'pdiag' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c local_stubs.c -o local_stubs.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ops.c -o ops.o
ops.c: In function 'mul_sparse':
ops.c:67:72: warning: unused variable 'Bnzmax' [-Wunused-variable]
ops.c:67:43: warning: unused variable 'Bn' [-Wunused-variable]
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I./MatrixHeaders -D_WINFIX_ -I"C:/Program Files/R/R-3.0/library/Matrix/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c winfix.c -o winfix.o
gcc -m64 -shared -s -static-libgcc -o lgc.dll tmp.def chol.o dist.o lgc_sparse.o local_stubs.o ops.o winfix.o C:/PROGRA~1/r/r-3.0/library/Matrix/libs//x64/Matrix.dll -LC:/PROGRA~1/r/r-3.0/bin/x64 -lRlapack -LC:/PROGRA~1/r/r-3.0/bin/x64 -lRblas -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/x64 -lR
installing to z:/rforge/Rlib/win7-3.0/lgc/libs/x64
** R
** data
** demo
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'lgc'
Creating a generic function for 'simulate' from package 'stats' in package 'lgc'
Warning: in method for 'coerce' with signature '"gridFactor","distFactor"': no definition for classes "gridFactor", "distFactor"
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: ignoring .First.lib() for package 'lgc'
*** arch - x64
Warning: ignoring .First.lib() for package 'lgc'
* MD5 sums
packaged installation of 'lgc' as lgc_1.4.zip
* DONE (lgc)