CNORfuzzy 1.2.0
T. Cokelaer
| Snapshot Date: 2013-04-28 17:01:45 -0700 (Sun, 28 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CNORfuzzy | | Last Changed Rev: 75263 / Revision: 76110 | | 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/CNORfuzzy.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 'CNORfuzzy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORfuzzy' version '1.2.0'
* 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 'CNORfuzzy' can be installed ... [8s/9s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 ... [30s/31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CNORwrapFuzzy 22.744 0.183 23.338
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'runTests.R' [26s/26s]
[26s/26s] 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 'CNORfuzzy' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c simulatorT1.c -o simulatorT1.o
simulatorT1.c:67:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
maxIx = (int*) malloc(nReacs * sizeof(int));
^˜˜˜˜˜ ˜
simulatorT1.c:74:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexStimuli = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:81:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexInhibitors = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:88:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexSignals = (int*) malloc(nSignals * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:95:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorT1.c:97:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:105:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorT1.c:107:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:115:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorT1.c:117:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:125:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorT1.c:127:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors[i] = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorT1.c:135:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorT1.c:137:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli[i] = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorT1.c:148:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueGCube = (float**) malloc(nCube1 * sizeof(float*));
^˜˜˜˜˜ ˜
simulatorT1.c:151:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueGCube[counter] = (float*) malloc(nCube2 * sizeof(float));
^˜˜˜˜˜ ˜
simulatorT1.c:153:42: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
valueGCube[counter][k] = REAL(valueGCube_in)[i+k*nReacs];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
simulatorT1.c:162:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueKCube = (float**) malloc(nCube1 * sizeof(float*));
^˜˜˜˜˜ ˜
simulatorT1.c:165:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueKCube[counter] = (float*) malloc(nCube2 * sizeof(float));
^˜˜˜˜˜ ˜
simulatorT1.c:167:42: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
valueKCube[counter][k] = REAL(valueKCube_in)[i+k*nReacs];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
simulatorT1.c:177:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueNCube = (float**) malloc(nCube1 * sizeof(float*));
^˜˜˜˜˜ ˜
simulatorT1.c:180:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueNCube[counter] = (float*) malloc(nCube2 * sizeof(float));
^˜˜˜˜˜ ˜
simulatorT1.c:182:42: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
valueNCube[counter][k] = REAL(valueNCube_in)[i+k*nReacs];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
simulatorT1.c:190:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
powkn = (float**) malloc(nCube1 * sizeof(float*));
^˜˜˜˜˜ ˜
simulatorT1.c:192:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
powkn[i] = (float*) malloc(nCube2 * sizeof(float));
^˜˜˜˜˜ ˜
simulatorT1.c:194:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
powkn[i][j] = pow(valueKCube[i][j], valueNCube[i][j]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
simulatorT1.c:214:22: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float test_val = 1e-3;
˜˜˜˜˜˜˜˜ ^˜˜˜
simulatorT1.c:300:35: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float powxn = pow(x, valueNCube[i][j]);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
simulatorT1.c:305:87: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
transval_temp = valueGCube[i][j] * (1. + powkn[i][j]) * powxn / ( powxn + powkn[i][j] );
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
simulatorT1.c:320:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorT1.c:320:28: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
˜ ^ ˜
simulatorT1.c:320:28: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^˜
=
simulatorT1.c:435:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
diff = fabs((new_input[i][j] - output_prev[i][j]));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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 CNORfuzzy.so simulatorT1.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNORfuzzy.Rcheck/CNORfuzzy/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORfuzzy)