ternarynet 1.4.0
Matthew N. McCall
| 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/ternarynet | | 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/ternarynet.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 'ternarynet/DESCRIPTION' ... OK
* this is package 'ternarynet' version '1.4.0'
* 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 'ternarynet' can be installed ... [6s/6s] 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 ... [98s/99s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
graphPosterior 9.940 0.020 10.033
plotFit 9.851 0.028 10.239
ternaryPost-class 9.793 0.022 9.901
plotPost 9.754 0.028 10.020
predictAttractor 9.733 0.018 9.803
tnetfit 9.701 0.022 9.795
ternaryFit-class 9.549 0.014 9.600
plotTraces 9.500 0.027 9.677
tnetpost 9.442 0.020 9.569
attractorSummary 9.291 0.019 9.387
* 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 'ternarynet' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tnetfit.cc -o tnetfit.o
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:522:70: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (pathwayList[nGene*(iTemp-1)+jTemp-1] != pathwayOut[jTemp]) ListPos=0;
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
tnetfuncs.cc:533:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (pathwayList[nGene*(i-1)+j-1] < 0) {
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
tnetfuncs.cc:535:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (pathwayList[nGene*(i-1)+j-1] > 0) {
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
tnetfuncs.cc:469:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
^
tnetfuncs.cc:477:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
tnetfuncs.cc:615:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
u = unif_rand();
˜ ^˜˜˜˜˜˜˜˜˜˜
tnetfuncs.cc:571:16: warning: unused variable 'i' [-Wunused-variable]
int m1, m2, i;
^
tnetfuncs.cc:567:6: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tnetpost.cc -o tnetpost.o
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
double newScore, oldScore, minScore, finalScore;
^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
int m0fit;
^
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
8 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 ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ternarynet.Rcheck/ternarynet/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 (ternarynet)