CellNOptR 1.6.0
T.Cokelaer
| 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/CellNOptR | | 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/CellNOptR.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 'CellNOptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellNOptR' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'CellNOptR' can be installed ... [10s/11s] 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 ... OK
* 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [36s/42s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'test_gaBinaryT1.R' [7s/8s]
Running 'test_gaBinaryT2.R' [10s/10s]
Running 'test_gaBinaryT3.R' [12s/12s]
Running 'test_manySteadyStates.R' [22s/23s]
Running 'test_priorBitString.R' [3s/4s]
Running 'test_simulateTN.R' [5s/6s]
[60s/64s] OK
* 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
* installing *source* package 'CellNOptR' ...
** 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 getFit.c -o getFit.o
getFit.c:52:16: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float NAFac = REAL(NAFac_in)[0];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getFit.c:53:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float sizeFac = REAL(sizeFac_in)[0];
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getFit.c:82:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cnolist0 = (float**) malloc(nCond * sizeof(float*));
^˜˜˜˜ ˜
getFit.c:84:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cnolist0[i] = (float*) malloc(nSignals * sizeof(float));
^˜˜˜˜˜˜˜ ˜
getFit.c:86:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
cnolist0[i][j] = REAL(cnolist0_in)[j+nSignals*i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getFit.c:91:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cnolist1 = (float**) malloc(nCond * sizeof(float*));
^˜˜˜˜ ˜
getFit.c:93:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cnolist1[i] = (float*) malloc(nSignals * sizeof(float));
^˜˜˜˜˜˜˜ ˜
getFit.c:95:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
cnolist1[i][j] = REAL(cnolist1_in)[j+nSignals*i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getFit.c:100:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResT0 = (float**) malloc(nCond * sizeof(float*));
^˜˜˜˜ ˜
getFit.c:102:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResT0[i] = (float*) malloc(nSignals * sizeof(float));
^˜˜˜˜˜˜˜ ˜
getFit.c:104:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
simResT0[i][j] = REAL(simResT0_in)[j+nSignals*i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getFit.c:109:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResT1 = (float**) malloc(nCond * sizeof(float*));
^˜˜˜˜ ˜
getFit.c:111:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
simResT1[i] = (float*) malloc(nSignals * sizeof(float));
^˜˜˜˜˜˜˜ ˜
getFit.c:113:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
simResT1[i][j] = REAL(simResT1_in)[j+nSignals*i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getFit.c:119:19: warning: implicit conversion turns floating-point number into integer: 'float' to 'int' [-Wconversion]
NAPen = NAFac * NAs;
˜ ˜˜˜˜˜˜^˜˜˜˜
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
int nReacs = INTEGER(nReacs_in)[0];
^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
int selCounter = 0;
^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
int or_max = 0;
^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
int curr_max = 0;
^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
int selection[40];
^
20 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 simulatorT1.c -o simulatorT1.o
simulatorT1.c:66:22: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float test_val = 1e-3;
˜˜˜˜˜˜˜˜ ^˜˜˜
simulatorT1.c:82:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
maxIx = (int*) malloc(nReacs * sizeof(int));
^˜˜˜˜˜ ˜
simulatorT1.c:89:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexStimuli = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:96:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexInhibitors = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:103:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexSignals = (int*) malloc(nSignals * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:110:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorT1.c:112:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:120:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorT1.c:122:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:130:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorT1.c:132:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:141:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorT1.c:143:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors[i] = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:150:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorT1.c:152:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors[i] = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:162:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorT1.c:164:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli[i] = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:171:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorT1.c:173:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli[i] = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:195:16: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
test_val = 1e-3;
˜ ^˜˜˜
simulatorT1.c:285:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorT1.c:285:28: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
˜ ^ ˜
simulatorT1.c:285:28: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^˜
=
21 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 simulatorTN.c -o simulatorTN.o
simulatorTN.c:97:22: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float test_val = 1e-3;
˜˜˜˜˜˜˜˜ ^˜˜˜
simulatorTN.c:122:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
times = (int*) malloc(nTimes * sizeof(int));
^˜˜˜˜˜ ˜
simulatorTN.c:128:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
maxIx = (int*) malloc(nReacs * sizeof(int));
^˜˜˜˜˜ ˜
simulatorTN.c:134:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexStimuli = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:140:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexInhibitors = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorTN.c:146:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexSignals = (int*) malloc(nSignals * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:152:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
interMat = (int**) malloc(nSpecies * sizeof(int*));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:154:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
interMat[i] = (int*) malloc(nReacs * sizeof(int));
^˜˜˜˜˜ ˜
simulatorTN.c:162:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
prevSimResults = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorTN.c:164:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
prevSimResults[i] = (int*) malloc(nSpecies * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:171:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorTN.c:173:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorTN.c:180:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorTN.c:182:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorTN.c:189:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorTN.c:191:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorTN.c:198:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorTN.c:200:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors[i] = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorTN.c:207:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorTN.c:209:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli[i] = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:223:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
output_prev = (int**) malloc(nCond*sizeof(int*));
^˜˜˜˜˜
simulatorTN.c:224:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
new_input = (int**) malloc(nCond*sizeof(int*));
^˜˜˜˜˜
simulatorTN.c:225:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
first_iter = (int**) malloc(nCond*sizeof(int*));
^˜˜˜˜˜
simulatorTN.c:228:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
output_prev[i] = (int*) malloc(nSpecies * sizeof(int*));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:229:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
new_input[i] = (int*) malloc(nSpecies * sizeof(int*));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:230:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
first_iter[i] = (int*) malloc(nSpecies * sizeof(int*));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:239:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
end_ix = (int*) malloc(nSpecies * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:252:16: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
test_val = 1e-3;
˜ ^˜˜˜
simulatorTN.c:303:24: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorTN.c:303:24: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
˜ ^ ˜
simulatorTN.c:303:24: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^˜
=
simulatorTN.c:346:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
reacsTN = (int*) malloc(nreacsTN * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorTN.c:501:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorTN.c:501:28: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
˜ ^ ˜
simulatorTN.c:501:28: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^˜
=
31 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CellNOptR.Rcheck/CellNOptR/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
* DONE (CellNOptR)