CNORode 1.14.0
David Henriques
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CNORode | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNORode_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CNORode.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ version ‘1.14.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘MEIGOR’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘CellNOptR’ ‘genalg’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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
createLBodeContPars: no visible global function definition for ‘runif’
getLBodeContObjFunction: no visible global function definition for
‘compatCNOlist’
getLBodeContObjFunction: no visible global function definition for
‘indexFinder’
getLBodeDataSim: no visible global function definition for
‘compatCNOlist’
getLBodeDataSim: no visible global function definition for
‘indexFinder’
getLBodeMINLPObjFunction: no visible global function definition for
‘compatCNOlist’
getLBodeMINLPObjFunction: no visible global function definition for
‘indexFinder’
getLBodeModelSim: no visible global function definition for
‘compatCNOlist’
getLBodeModelSim: no visible global function definition for
‘indexFinder’
minlpLBodeSSm: no visible global function definition for
‘compatCNOlist’
minlpLBodeSSm: no visible global function definition for ‘essR’
minlpLBodeSSm: no visible global function definition for ‘runif’
parEstimationLBode: no visible global function definition for
‘compatCNOlist’
parEstimationLBodeGA: no visible global function definition for
‘compatCNOlist’
parEstimationLBodeGA: no visible global function definition for
‘indexFinder’
parEstimationLBodeGA: no visible global function definition for
‘plot.new’
parEstimationLBodeGA : monitor_func: no visible global function
definition for ‘par’
parEstimationLBodeGA : monitor_func: no visible global function
definition for ‘plot’
parEstimationLBodeGA : monitor_func: no visible global function
definition for ‘lines’
parEstimationLBodeGA: no visible global function definition for ‘rbga’
parEstimationLBodeSSm: no visible global function definition for
‘compatCNOlist’
parEstimationLBodeSSm: no visible global function definition for
‘indexFinder’
parEstimationLBodeSSm: no visible global function definition for ‘essR’
plotLBodeFitness: no visible global function definition for
‘compatCNOlist’
plotLBodeFitness: no visible global function definition for
‘indexFinder’
plotLBodeFitness: no visible global function definition for
‘plotOptimResults’
plotLBodeFitness: no visible global function definition for
‘plotOptimResultsPan’
plotLBodeFitness: no visible global function definition for ‘CNOlist’
plotLBodeModelSim: no visible global function definition for
‘compatCNOlist’
plotLBodeModelSim: no visible global function definition for
‘indexFinder’
plotLBodeModelSim: no visible global function definition for
‘plotCNOlistLarge’
plotLBodeModelSim: no visible global function definition for ‘CNOlist’
plotLBodeModelSim: no visible global function definition for
‘plotCNOlist’
simdata2cnolist: no visible global function definition for
‘compatCNOlist’
simdata2cnolist: no visible global function definition for ‘CNOlist’
simulate: no visible global function definition for ‘compatCNOlist’
simulate: no visible global function definition for ‘indexFinder’
Undefined global functions or variables:
CNOlist compatCNOlist essR indexFinder lines par plot plot.new
plotCNOlist plotCNOlistLarge plotOptimResults plotOptimResultsPan
rbga runif
Consider adding
importFrom("graphics", "lines", "par", "plot", "plot.new")
importFrom("stats", "runif")
to your NAMESPACE file.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘CNORode/libs/CNORode.so’:
Found ‘putchar’, possibly from ‘putchar’ (C)
Objects: ‘nvector_serial.o’, ‘printInterMat.o’,
‘printNminiTerms.o’, ‘sundials_direct.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘printAdjMat.o’, ‘printTruthTables.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘cvodes.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
parEstimationLBode 21.022 0.035 21.458
parEstimationLBodeGA 10.421 0.016 10.515
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/CNORode.Rcheck/00check.log’
for details.
* installing *source* package ‘CNORode’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodea.c -o cvodea.o
cvodea.c: In function ‘CVAhermiteStorePnt’:
cvodea.c:2445:11: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable]
int is, retval;
^
cvodea.c: In function ‘CVArhsQ’:
cvodea.c:2941:7: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable]
int flag, retval;
^
cvodea.c: In function ‘CVAhermiteGetY’:
cvodea.c:2591:17: warning: ‘ySd0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
^
cvodea.c:2591:17: warning: ‘yS0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cvodea.c: In function ‘CVodeB’:
cvodea.c:1263:13: warning: ‘flag’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int sign, flag;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodea_io.c -o cvodea_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes.c -o cvodes.o
cvodes.c: In function ‘cvQuadSensRhs1InternalDQ’:
cvodes.c:8834:20: warning: variable ‘rDeltap’ set but not used [-Wunused-but-set-variable]
realtype Deltap, rDeltap;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_band.c -o cvodes_band.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_dense.c -o cvodes_dense.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_diag.c -o cvodes_diag.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_direct.c -o cvodes_direct.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_io.c -o cvodes_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spils.c -o cvodes_spils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c decimal2binary.c -o decimal2binary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c findStates.c -o findStates.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c fnvector_serial.c -o fnvector_serial.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getNumBits.c -o getNumBits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getNumInputs.c -o getNumInputs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getStateIndex.c -o getStateIndex.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function ‘getTruthTables’:
getTruthTables.c:17:14: warning: unused variable ‘n’ [-Wunused-variable]
int i,j,k,m,n,counter1,input,miniterm;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_count_bits.c -o get_count_bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_input_index.c -o get_input_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function ‘get_support_truth_tables’:
get_support_truth_tables.c:16:10: warning: unused variable ‘k’ [-Wunused-variable]
int i,j,k;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c hill_function.c -o hill_function.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c linear_transfer_function.c -o linear_transfer_function.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c normHill.c -o normHill.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c nvector_serial.c -o nvector_serial.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printAdjMat.c -o printAdjMat.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printInterMat.c -o printInterMat.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printNminiTerms.c -o printNminiTerms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printTruthTables.c -o printTruthTables.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c rhsODE.c -o rhsODE.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sim_logic_ode.c -o sim_logic_ode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c simulateODE.c -o simulateODE.o
simulateODE.c: In function ‘simulateODE’:
simulateODE.c:150:4: warning: implicit declaration of function ‘CVDense’ [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^
simulateODE.c:32:14: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_band.c -o sundials_band.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_dense.c -o sundials_dense.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_direct.c -o sundials_direct.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_iterative.c -o sundials_iterative.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_math.c -o sundials_math.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_nvector.c -o sundials_nvector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c: In function ‘SpgmrFree’:
sundials_spgmr.c:439:29: warning: variable ‘yg’ set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
sundials_spgmr.c:439:20: warning: variable ‘givens’ set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/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 -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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
* DONE (CNORode)