CNORdt 1.2.0
A. MacNamara
| 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/CNORdt | | 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/CNORdt.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 'CNORdt/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORdt' 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 'CNORdt' can be installed ... [8s/8s] 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [68s/70s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
cutAndPlotResultsDT 32.350 0.216 33.022
gaBinaryDT 30.775 0.190 32.143
* 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 'CNORdt' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c simulatorDT.c -o simulatorDT.o
simulatorDT.c:63:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
maxIx = (int*) malloc(nReacs * sizeof(int));
^˜˜˜˜˜ ˜
simulatorDT.c:70:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexStimuli = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorDT.c:77:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
indexInhibitors = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:84:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorDT.c:86:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
finalCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:94:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorDT.c:96:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ixNeg[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:104:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube = (int**) malloc(nReacs * sizeof(int*));
^˜˜˜˜˜ ˜
simulatorDT.c:106:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ignoreCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
^˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:114:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorDT.c:116:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueInhibitors[i] = (int*) malloc(nInhibitors * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:124:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorDT.c:126:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
valueStimuli[i] = (int*) malloc(nStimuli * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorDT.c:134:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
prevSim = (int**) malloc(nCond * sizeof(int*));
^˜˜˜˜ ˜
simulatorDT.c:136:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
prevSim[i] = (int*) malloc(nSpecies * sizeof(int));
^˜˜˜˜˜˜˜ ˜
simulatorDT.c:243:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorDT.c:243:19: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
˜ ^ ˜
simulatorDT.c:243:19: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^˜
=
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
int nTimes = INTEGER(nTimes_in)[0];
^
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
int nSignals = INTEGER(nSignals_in)[0];
^
18 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 CNORdt.so simulatorDT.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNORdt.Rcheck/CNORdt/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 (CNORdt)