Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:01:41 -0400 (Wed, 16 Oct 2019).
Package 306/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CNORode 1.26.0 David Henriques
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: CNORode |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CNORode_1.26.0.tar.gz |
StartedAt: 2019-10-16 00:39:13 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 00:40:42 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 89.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNORode.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CNORode_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CNORode.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.26.0’ * 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 ‘/home/biocbuild/bbs-3.9-bioc/R/library/CNORode/libs/CNORode.so’: Found ‘putchar’, possibly from ‘putchar’ (C) Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘stderr’, possibly from ‘stderr’ (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 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 28.089 0.087 28.250 parEstimationLBodeGA 6.874 0.004 6.952 * 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/CNORode.Rcheck/00check.log’ for details.
CNORode.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CNORode ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘CNORode’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.9-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:2572:7: warning: ‘ySd0’ may be used uninitialized in this function [-Wmaybe-uninitialized] N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cvodea.c:2591:5: warning: ‘yS0’ may be used uninitialized in this function [-Wmaybe-uninitialized] N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cvodea.c: In function ‘CVodeB’: cvodea.c:1263:13: warning: ‘flag’ may be used uninitialized in this function [-Wmaybe-uninitialized] int sign, flag; ^~~~ gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodea_io.c -o cvodea_io.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes.c -o cvodes.o cvodes.c: In function ‘cvHin’: cvodes.c:4318:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (count1 <= 2) ^~ cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (retval == QRHSFUNC_RECVR) return(CV_REPTD_QRHSFUNC_ERR); ^~ cvodes.c: In function ‘cvQuadSensRhs1InternalDQ’: cvodes.c:8834:20: warning: variable ‘rDeltap’ set but not used [-Wunused-but-set-variable] realtype Deltap, rDeltap; ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_band.c -o cvodes_band.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_bandpre.c -o cvodes_bandpre.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_bbdpre.c -o cvodes_bbdpre.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_dense.c -o cvodes_dense.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_diag.c -o cvodes_diag.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_direct.c -o cvodes_direct.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_io.c -o cvodes_io.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spbcgs.c -o cvodes_spbcgs.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spgmr.c -o cvodes_spgmr.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_spils.c -o cvodes_spils.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c decimal2binary.c -o decimal2binary.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c findStates.c -o findStates.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c fnvector_serial.c -o fnvector_serial.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getNumBits.c -o getNumBits.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getNumInputs.c -o getNumInputs.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getStateIndex.c -o getStateIndex.o gcc -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c hill_function.c -o hill_function.o gcc -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c normHill.c -o normHill.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c nvector_serial.c -o nvector_serial.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printAdjMat.c -o printAdjMat.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printInterMat.c -o printInterMat.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printNminiTerms.c -o printNminiTerms.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c printTruthTables.c -o printTruthTables.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c rhsODE.c -o rhsODE.o gcc -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-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:150:11: 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 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_band.c -o sundials_band.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_dense.c -o sundials_dense.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_direct.c -o sundials_direct.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_iterative.c -o sundials_iterative.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_math.c -o sundials_math.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_nvector.c -o sundials_nvector.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_spbcgs.c -o sundials_spbcgs.o gcc -I"/home/biocbuild/bbs-3.9-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 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c sundials_sptfqmr.c -o sundials_sptfqmr.o gcc -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CNORode/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CNORode)
CNORode.Rcheck/CNORode-Ex.timings
name | user | system | elapsed | |
createLBodeContPars | 0.022 | 0.000 | 0.023 | |
getLBodeContObjFunction | 0.058 | 0.000 | 0.058 | |
getLBodeDataSim | 0.016 | 0.000 | 0.015 | |
getLBodeMINLPObjFunction | 0.067 | 0.000 | 0.068 | |
getLBodeModelSim | 0.011 | 0.004 | 0.015 | |
minlpLBodeSSm | 0.001 | 0.000 | 0.000 | |
parEstimationLBode | 28.089 | 0.087 | 28.250 | |
parEstimationLBodeGA | 6.874 | 0.004 | 6.952 | |
parEstimationLBodeSSm | 0 | 0 | 0 | |
plotLBodeFitness | 0.716 | 0.012 | 0.942 | |
plotLBodeModelSim | 0.394 | 0.004 | 0.500 | |
simdata2cnolist | 0.019 | 0.000 | 0.019 | |
simulate | 0.015 | 0.000 | 0.015 | |