Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:40 -0000 (Sun, 29 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
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To the developers/maintainers of the CNORode package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORode.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 360/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNORode 1.41.0 (landing page) Attila Gabor
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: CNORode |
Version: 1.41.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CNORode_1.41.0.tar.gz |
StartedAt: 2023-01-28 20:12:56 -0000 (Sat, 28 Jan 2023) |
EndedAt: 2023-01-28 20:17:09 -0000 (Sat, 28 Jan 2023) |
EllapsedTime: 252.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CNORode.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CNORode_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘CNORode/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNORode’ version ‘1.41.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CNORode’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking package directory ... OK * checking ‘build’ 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 ... WARNING Invalid citation information in ‘inst/CITATION’: Error in .bibentry_check_bibentry1(rval): A bibentry of bibtype ‘Manual’ has to specify the field: title Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'CNORode' was found * 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 loading without being on the library search path ... WARNING Error in library(CNORode, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : there is no package called ‘CNORode’ Execution halted It looks like this package has a loading problem when not on .libPaths: see the messages for details. * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘knitr’ 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’ crossvalidateODE: no visible global function definition for ‘error’ minlpLBodeSSm: no visible global function definition for ‘essR’ minlpLBodeSSm: no visible global function definition for ‘runif’ 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 ‘lines’ runCNORode: no visible global function definition for ‘pdf’ runCNORode: no visible global function definition for ‘dev.off’ Undefined global functions or variables: dev.off error essR lines par pdf plot.new runif Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "lines", "par", "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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘CNORode-vignette.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck/00check.log’ for details.
CNORode.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CNORode ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘CNORode’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -Wall -c FG_transfer_function.c -o FG_transfer_function.o gcc -I"/home/biocbuild/bbs-3.17-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] 2445 | int is, retval; | ^~~~~~ cvodea.c: In function ‘CVArhsQ’: cvodea.c:2941:7: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable] 2941 | int flag, retval; | ^~~~ cvodea.c: In function ‘CVAhermiteGetY’: cvodea.c:2572:7: warning: ‘ySd0’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2572 | 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] 2591 | 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] 1263 | int sign, flag; | ^~~~ gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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] 4318 | if (count1 <= 2) | ^~ cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4320 | 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] 8834 | realtype Deltap, rDeltap; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -Wall -c getTruthTables.c -o getTruthTables.o gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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 gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -Wall -c normHill_mod.c -o normHill_mod.o gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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:37:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable] 37 | int i,j,neq,counter,flag; | ^~~~~~~ simulateODE.c:257:4: warning: ‘tout’ may be used uninitialized in this function [-Wmaybe-uninitialized] 257 | rhsODEF(tout,y0,ydot0, data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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] 439 | realtype **Hes, *givens, *yg; | ^~ sundials_spgmr.c:439:20: warning: variable ‘givens’ set but not used [-Wunused-but-set-variable] 439 | realtype **Hes, *givens, *yg; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o CNORode.so FG_transfer_function.o 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 normHill_mod.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-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-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 ** 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)