David Henriques
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CNORode |
| Branch: RELEASE_3_7 |
| Last Commit: 0206d9f |
| Last Changed Date: 2018-04-30 10:35:27 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:50:55 -0400 (Wed, 17 Oct 2018).
| Package 275/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNORode 1.22.0 David Henriques
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CNORode |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORode.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORode_1.22.0.tar.gz |
| StartedAt: 2018-10-16 20:35:36 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:36:56 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 80.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNORode.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORode.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORode_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CNORode.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.0’
* 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 ‘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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/CNORode/libs/CNORode.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
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 14.095 0.188 14.518
parEstimationLBodeGA 5.670 0.045 5.813
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/CNORode.Rcheck/00check.log’
for details.
CNORode.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNORode
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CNORode’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodea.c -o cvodea.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodea_io.c -o cvodea_io.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes.c -o cvodes.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_band.c -o cvodes_band.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_dense.c -o cvodes_dense.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_diag.c -o cvodes_diag.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_direct.c -o cvodes_direct.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_io.c -o cvodes_io.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_spils.c -o cvodes_spils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c decimal2binary.c -o decimal2binary.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c findStates.c -o findStates.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c fnvector_serial.c -o fnvector_serial.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c getNumBits.c -o getNumBits.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c getNumInputs.c -o getNumInputs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c getStateIndex.c -o getStateIndex.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c getTruthTables.c -o getTruthTables.o
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
int i,j,k,m,n,counter1,input,miniterm;
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c get_count_bits.c -o get_count_bits.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c get_input_index.c -o get_input_index.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c hill_function.c -o hill_function.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c linear_transfer_function.c -o linear_transfer_function.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c normHill.c -o normHill.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c nvector_serial.c -o nvector_serial.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c printAdjMat.c -o printAdjMat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c printInterMat.c -o printInterMat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c printNminiTerms.c -o printNminiTerms.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c printTruthTables.c -o printTruthTables.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c rhsODE.c -o rhsODE.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sim_logic_ode.c -o sim_logic_ode.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c simulateODE.c -o simulateODE.o
simulateODE.c:150:11: warning: implicit declaration of function 'CVDense' is invalid in C99 [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_band.c -o sundials_band.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_dense.c -o sundials_dense.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_direct.c -o sundials_direct.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_iterative.c -o sundials_iterative.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_math.c -o sundials_math.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_nvector.c -o sundials_nvector.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_spgmr.c -o sundials_spgmr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -Wall -g -O2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/CNORode/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘CNORode-vignette.Rnw’ using ‘UTF-8’
** testing if installed package can be loaded
* DONE (CNORode)
CNORode.Rcheck/CNORode-Ex.timings
| name | user | system | elapsed | |
| createLBodeContPars | 0.022 | 0.002 | 0.024 | |
| getLBodeContObjFunction | 0.036 | 0.002 | 0.041 | |
| getLBodeDataSim | 0.014 | 0.002 | 0.015 | |
| getLBodeMINLPObjFunction | 0.033 | 0.002 | 0.036 | |
| getLBodeModelSim | 0.013 | 0.002 | 0.014 | |
| minlpLBodeSSm | 0.004 | 0.001 | 0.004 | |
| parEstimationLBode | 14.095 | 0.188 | 14.518 | |
| parEstimationLBodeGA | 5.670 | 0.045 | 5.813 | |
| parEstimationLBodeSSm | 0.003 | 0.000 | 0.003 | |
| plotLBodeFitness | 0.620 | 0.014 | 0.649 | |
| plotLBodeModelSim | 0.403 | 0.006 | 0.413 | |
| simdata2cnolist | 0.012 | 0.001 | 0.013 | |
| simulate | 0.016 | 0.002 | 0.019 | |