CNORode 1.2.0
David Henriques
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CNORode | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CNORode.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CNORode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORode' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'MEIGOR'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'CNORode' can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
minlpLBodeSSm: no visible global function definition for 'essR'
parEstimationLBodeSSm: no visible global function definition for 'essR'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/CNORode.Rcheck/CNORode/libs/CNORode.so':
Found '___stderrp', possibly from 'stderr' (C)
Object: 'cvodes.o'
Found '_printf', possibly from 'printf' (C)
Objects: 'nvector_serial.o', 'printAdjMat.o', 'printInterMat.o',
'printNminiTerms.o', 'printTruthTables.o', 'sundials_direct.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [78s/80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
parEstimationLBode 52.024 0.369 53.812
parEstimationLBodeGA 19.161 0.142 19.619
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/CNORode.Rcheck/00check.log'
for details.
* installing *source* package 'CNORode' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodea.c -o cvodea.o
cvodea.c:169:46: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
ca_mem->dt_mem = (DtpntMem *) malloc((steps+1)*sizeof(struct DtpntMemRec *));
˜˜˜˜˜^˜ ˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodea_io.c -o cvodea_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes.c -o cvodes.o
cvodes.c:1585:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ncfS1 = (int*)malloc(Ns*sizeof(int));
^˜˜
cvodes.c:1587:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ncfnS1 = (long int*)malloc(Ns*sizeof(long int));
^˜˜
cvodes.c:1589:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nniS1 = (long int*)malloc(Ns*sizeof(long int));
^˜˜
cvodes.c:1720:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ncfS1 = (int*)malloc(Ns*sizeof(int));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:1722:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ncfnS1 = (long int*)malloc(Ns*sizeof(long int));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:1724:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
nniS1 = (long int*)malloc(Ns*sizeof(long int));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:1823:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cv_mem->cv_SabstolS = (realtype *)malloc(Ns*sizeof(realtype));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:2118:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cv_mem->cv_SabstolQS = (realtype *)malloc(Ns*sizeof(realtype));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:2349:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
glo = (realtype *) malloc(nrt*sizeof(realtype));
^˜˜˜
cvodes.c:2356:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ghi = (realtype *) malloc(nrt*sizeof(realtype));
^˜˜˜
cvodes.c:2364:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
grout = (realtype *) malloc(nrt*sizeof(realtype));
^˜˜˜
cvodes.c:2373:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
iroots = (int *) malloc(nrt*sizeof(int));
^˜˜˜
cvodes.c:2383:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rootdir = (int *) malloc(nrt*sizeof(int));
^˜˜˜
cvodes.c:2395:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
gactive = (booleantype *) malloc(nrt*sizeof(booleantype));
^˜˜˜
cvodes.c:4030:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
pbar = (realtype *)malloc(Ns*sizeof(realtype));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:4042:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
plist = (int *)malloc(Ns*sizeof(int));
^˜˜
cvodes.c:1653:22: note: expanded from macro 'Ns'
#define Ns (cv_mem->cv_Ns)
˜˜˜˜˜˜˜˜^˜˜˜˜
cvodes.c:8945:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
fprintf(stderr, msg);
^˜˜
17 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_band.c -o cvodes_band.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_dense.c -o cvodes_dense.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_diag.c -o cvodes_diag.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_direct.c -o cvodes_direct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_io.c -o cvodes_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_spils.c -o cvodes_spils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c decimal2binary.c -o decimal2binary.o
decimal2binary.c:15:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int* binary_value = (int*)malloc(nBits*sizeof(int));
^˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c findStates.c -o findStates.o
findStates.c:14:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *stateVec=malloc(n*sizeof(int));
^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c fnvector_serial.c -o fnvector_serial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
getAdjacencyMatrix.c:17:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int** adjMat= (int**) malloc(nRows * sizeof(int*));
^˜˜˜˜ ˜
getAdjacencyMatrix.c:20:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
adjMat[i] = (int*) malloc(nCols * sizeof(int));
^˜˜˜˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getNumBits.c -o getNumBits.o
getNumBits.c:14:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *numBits=(int*)malloc(n*sizeof(int));
^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getNumInputs.c -o getNumInputs.o
getNumInputs.c:14:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int* numInputs=(int*)malloc(n*sizeof(int));
^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getStateIndex.c -o getStateIndex.o
getStateIndex.c:6:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int* indexVec=malloc(n*sizeof(int));
^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getTruthTables.c -o getTruthTables.o
getTruthTables.c:24:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int** truthTables=malloc(nRows*sizeof(int*));
^˜˜˜˜˜
getTruthTables.c:25:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int** miniTermPositions=malloc(nRows*sizeof(int*));
^˜˜˜˜˜
getTruthTables.c:26:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int** miniTermInputs=malloc(nRows*sizeof(int*));
^˜˜˜˜˜
getTruthTables.c:28:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int* nMiniTerms=malloc(nRows*sizeof(int));
^˜˜˜˜˜
getTruthTables.c:43:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
miniTermPositions[i]=(int*)malloc(counter1*sizeof(int));
^˜˜˜˜˜˜˜˜
getTruthTables.c:57:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
miniTermInputs[j]=(int*)malloc(nInputs[j]*sizeof(int));
^˜˜˜˜˜˜˜˜˜˜
getTruthTables.c:66:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
miniTerms=(int***)malloc(nRows*sizeof(int**));
^˜˜˜˜˜
getTruthTables.c:69:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
miniTerms[i]=(int**)malloc(nInputs[i]*sizeof(int*));
^˜˜˜˜˜˜˜˜˜˜
getTruthTables.c:73:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
miniTerms[i][j]=(int*)malloc(nMiniTerms[i]*sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜
getTruthTables.c:113:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
truthTables[i]=(int*)malloc(nBits[i]*sizeof(int));
^˜˜˜˜˜˜˜˜
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
int i,j,k,m,n,counter1,input,miniterm;
^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c get_count_bits.c -o get_count_bits.o
get_count_bits.c:7:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *count_bits=(int*)malloc(n*sizeof(int));
^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c get_input_index.c -o get_input_index.o
get_input_index.c:8:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int **input_index=(int**)malloc(n*sizeof(int*));
^˜
get_input_index.c:12:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
input_index[j]=(int*)malloc(numInputs[j]*sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c:17:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int*** support_truth_tables=(int***)malloc(n*sizeof(int**));
^˜
get_support_truth_tables.c:21:58: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
support_truth_tables[i]=(int**)malloc(pow(2,nInputs[i])*sizeof(int*));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c get_truth_tables_index.c -o get_truth_tables_index.o
get_truth_tables_index.c:7:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int **truth_tables_index=(int**)malloc(n*sizeof(int*));
^˜
get_truth_tables_index.c:12:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
truth_tables_index[i]=(int*)malloc(count_bits[i]*sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c hill_function.c -o hill_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c linear_transfer_function.c -o linear_transfer_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c normHill.c -o normHill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c nvector_serial.c -o nvector_serial.o
nvector_serial.c:138:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
data = (realtype *) malloc(length * sizeof(realtype));
^˜˜˜˜˜ ˜
nvector_serial.c:183:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vs = (N_Vector *) malloc(count * sizeof(N_Vector));
^˜˜˜˜ ˜
nvector_serial.c:210:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vs = (N_Vector *) malloc(count * sizeof(N_Vector));
^˜˜˜˜ ˜
nvector_serial.c:351:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
data = (realtype *) malloc(length * sizeof(realtype));
^˜˜˜˜˜ ˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c printAdjMat.c -o printAdjMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c printInterMat.c -o printInterMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c printNminiTerms.c -o printNminiTerms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c printTruthTables.c -o printTruthTables.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rhsODE.c -o rhsODE.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sim_logic_ode.c -o sim_logic_ode.o
sim_logic_ode.c:96:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexSig=(int*)malloc(nSignals*sizeof(int));
^˜˜˜˜˜˜˜˜
sim_logic_ode.c:103:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexStim=(int*)malloc(nStimuli*sizeof(int));
^˜˜˜˜˜˜˜˜
sim_logic_ode.c:110:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexInh=(int*)malloc(nInhibitors*sizeof(int));
^˜˜˜˜˜˜˜˜˜˜˜
sim_logic_ode.c:116:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
odePARAMETERS=(double*)malloc(nPars*sizeof(double));
^˜˜˜˜˜
sim_logic_ode.c:123:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
interMAT = (int**) malloc(nRows * sizeof(int*));
^˜˜˜˜ ˜
sim_logic_ode.c:126:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
interMAT[i] = (int*) malloc(nCols * sizeof(int));
^˜˜˜˜ ˜
sim_logic_ode.c:134:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
notMAT = (int**)malloc(nRows * sizeof(int*));
^˜˜˜˜ ˜
sim_logic_ode.c:137:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
notMAT[i] = (int*)malloc(nCols*sizeof(int));
^˜˜˜˜˜
sim_logic_ode.c:145:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
adjMatrix = (int**)malloc(nRows * sizeof(int*));
^˜˜˜˜ ˜
sim_logic_ode.c:148:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
adjMatrix[i] = (int*)malloc(nRows*sizeof(int));
^˜˜˜˜˜
sim_logic_ode.c:156:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueSIGNALS = (double**)malloc(nExperiments * sizeof(double*));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
sim_logic_ode.c:159:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueSIGNALS[i] = (double*)malloc(nSignals*sizeof(double));
^˜˜˜˜˜˜˜˜
sim_logic_ode.c:166:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueINHIBITORS = (double**)malloc(nExperiments * sizeof(double*));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
sim_logic_ode.c:169:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueINHIBITORS[i] = (double*)malloc(nInhibitors*sizeof(double));
^˜˜˜˜˜˜˜˜˜˜˜
sim_logic_ode.c:177:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueSTIMULI = (double**)malloc(nExperiments * sizeof(double*));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
sim_logic_ode.c:180:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueSTIMULI[i] = (double*)malloc(nStimuli*sizeof(double));
^˜˜˜˜˜˜˜˜
sim_logic_ode.c:187:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
timeSig= (double*)malloc(nTimes*sizeof(double));
^˜˜˜˜˜˜
sim_logic_ode.c:232:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
state_array= (double*)malloc(tempData.nRows*sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
sim_logic_ode.c:233:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
inhibitor_array=(double*)malloc((tempData.nRows)*sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜ ˜
sim_logic_ode.c:252:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResults=(double***)malloc(nExperiments*sizeof(double**));
^˜˜˜˜˜˜˜˜˜˜˜˜
sim_logic_ode.c:254:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResults[i]=(double**)malloc(nTimes*sizeof(double*));
^˜˜˜˜˜˜
sim_logic_ode.c:258:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResults[i][j]=(double*)malloc(tempData.nStates*sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c simulateODE.c -o simulateODE.o
simulateODE.c:150:11: warning: implicit declaration of function 'CVDense' is invalid in C99 [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_band.c -o sundials_band.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_dense.c -o sundials_dense.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_direct.c -o sundials_direct.o
sundials_direct.c:38:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
A->data = (realtype *) malloc(M * N * sizeof(realtype));
˜˜^˜˜ ˜
sundials_direct.c:43:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
A->cols = (realtype **) malloc(N * sizeof(realtype *));
^ ˜
sundials_direct.c:70:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a = (realtype **) malloc(n * sizeof(realtype *));
^ ˜
sundials_direct.c:74:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a[0] = (realtype *) malloc(m * n * sizeof(realtype));
˜˜^˜˜ ˜
sundials_direct.c:99:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
A->data = (realtype *) malloc(N * colSize * sizeof(realtype));
˜˜^˜˜˜˜˜˜˜˜ ˜
sundials_direct.c:106:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
A->cols = (realtype **) malloc(N * sizeof(realtype *));
^ ˜
sundials_direct.c:136:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a = (realtype **) malloc(n * sizeof(realtype *));
^ ˜
sundials_direct.c:141:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a[0] = (realtype *) malloc(n * colSize * sizeof(realtype));
˜˜^˜˜˜˜˜˜˜˜ ˜
sundials_direct.c:172:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vec = (int *) malloc(N * sizeof(int));
^ ˜
sundials_direct.c:184:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
v = (int *) malloc(n * sizeof(int));
^ ˜
sundials_direct.c:196:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vec = (realtype *) malloc(N * sizeof(realtype));
^ ˜
sundials_direct.c:208:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
v = (realtype *) malloc(m * sizeof(realtype));
^ ˜
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_iterative.c -o sundials_iterative.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_math.c -o sundials_math.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_nvector.c -o sundials_nvector.o
sundials_nvector.c:187:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vs = (N_Vector *) malloc(count * sizeof(N_Vector));
^˜˜˜˜ ˜
sundials_nvector.c:208:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vs = (N_Vector *) malloc(count * sizeof(N_Vector));
^˜˜˜˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c:59:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Hes = (realtype **) malloc((l_max+1)*sizeof(realtype *));
˜˜˜˜˜^˜ ˜
sundials_spgmr.c:67:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Hes[k] = (realtype *) malloc(l_max*sizeof(realtype));
^˜˜˜˜˜
sundials_spgmr.c:79:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
givens = (realtype *) malloc(2*l_max*sizeof(realtype));
˜^˜˜˜˜˜˜
sundials_spgmr.c:101:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yg = (realtype *) malloc((l_max+1)*sizeof(realtype));
˜˜˜˜˜^˜ ˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sundials_sptfqmr.c -o sundials_sptfqmr.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o CNORode.so cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNORode.Rcheck/CNORode/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'CNORode'
* DONE (CNORode)