Enio Gjerga
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CNORode |
| git_branch: RELEASE_3_13 |
| git_last_commit: 06fde26 |
| git_last_commit_date: 2021-05-19 11:54:17 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 346/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNORode 1.34.0 (landing page) Enio Gjerga
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CNORode |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORode.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNORode_1.34.0.tar.gz |
| StartedAt: 2021-10-14 21:18:28 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:20:31 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 123.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CNORode.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORode.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNORode_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNORode.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNORode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORode' version '1.34.0'
* 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 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'library' or 'require' call not declared from: 'doParallel'
'library' or 'require' calls in package code:
'MEIGOR' 'doParallel'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: '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'
crossvalidateODE: no visible global function definition for 'error'
crossvalidateODE: no visible global function definition for '%dopar%'
crossvalidateODE: no visible global function definition for 'foreach'
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'
parEstimationLBodeGA: no visible global function definition for 'rbga'
parEstimationLBodeSSm: no visible global function definition for 'essR'
runCNORode: no visible global function definition for 'pdf'
runCNORode: no visible global function definition for 'dev.off'
Undefined global functions or variables:
%dopar% dev.off error essR foreach lines par pdf plot.new rbga 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 ... WARNING
Bad \usage lines found in documentation object 'crossvalidateODE':
crossvalidateODE = function(CNOlist = cnolist, model = model, nfolds=10, foldid=NULL, type="datapoint", parallel = FALSE,
ode_parameters = NULL, paramsSSm = NULL, method = "essm")
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Variables overriding user/site settings:
CPPFLAGS: -Wformat=0
CFLAGS: -Wno-format-security
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CNORode/libs/i386/CNORode.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CNORode/libs/x64/CNORode.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parEstimationLBode 8.96 0.22 9.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parEstimationLBode 9.45 0.17 9.63
* 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: 3 WARNINGs, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNORode.Rcheck/00check.log'
for details.
CNORode.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CNORode_1.34.0.tar.gz && rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNORode.buildbin-libdir CNORode_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNORode_1.34.0.zip && rm CNORode_1.34.0.tar.gz CNORode_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 365k 100 365k 0 0 587k 0 --:--:-- --:--:-- --:--:-- 588k
install for i386
* installing *source* package 'CNORode' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FG_transfer_function.c -o FG_transfer_function.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea_io.c -o cvodea_io.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_band.c -o cvodes_band.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bandpre.c -o cvodes_bandpre.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bbdpre.c -o cvodes_bbdpre.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_dense.c -o cvodes_dense.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_diag.c -o cvodes_diag.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_direct.c -o cvodes_direct.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_io.c -o cvodes_io.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spbcgs.c -o cvodes_spbcgs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spgmr.c -o cvodes_spgmr.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spils.c -o cvodes_spils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c decimal2binary.c -o decimal2binary.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findStates.c -o findStates.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fnvector_serial.c -o fnvector_serial.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumBits.c -o getNumBits.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumInputs.c -o getNumInputs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getStateIndex.c -o getStateIndex.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_count_bits.c -o get_count_bits.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_input_index.c -o get_input_index.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_truth_tables_index.c -o get_truth_tables_index.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hill_function.c -o hill_function.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c linear_transfer_function.c -o linear_transfer_function.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill.c -o normHill.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill_mod.c -o normHill_mod.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nvector_serial.c -o nvector_serial.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printAdjMat.c -o printAdjMat.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printInterMat.c -o printInterMat.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printNminiTerms.c -o printNminiTerms.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printTruthTables.c -o printTruthTables.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhsODE.c -o rhsODE.o
rhsODE.c:85: warning: "Ith" redefined
#define Ith(v,i) ( v[i] )
rhsODE.c:10: note: this is the location of the previous definition
#define Ith(v,i) ( NV_DATA_S(v)[i] )
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sim_logic_ode.c -o sim_logic_ode.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:169:11: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^~~~~~~
simulateODE.c:35:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^~~~~~~
simulateODE.c:255:4: warning: 'tout' may be used uninitialized in this function [-Wmaybe-uninitialized]
rhsODEF(tout,y0,ydot0, data);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_band.c -o sundials_band.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_dense.c -o sundials_dense.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_direct.c -o sundials_direct.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_iterative.c -o sundials_iterative.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_math.c -o sundials_math.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_nvector.c -o sundials_nvector.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spbcgs.c -o sundials_spbcgs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def 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 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CNORode.buildbin-libdir/00LOCK-CNORode/00new/CNORode/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNORode'
finding HTML links ... done
CNORode-package html
finding level-2 HTML links ... done
cnodata html
cnolist html
cnolistCNORodeExample html
createLBodeContPars html
crossvalidateODE html
defaultParametersGA html
defaultParametersSSm html
getLBodeContObjFunction html
getLBodeDataSim html
getLBodeMINLPObjFunction html
getLBodeModelSim html
getLBodeSimFunction html
getStates html
incidence2Adjacency html
indices html
minlpLBodeSSm html
model html
parEstimationLBode html
parEstimationLBodeGA html
parEstimationLBodeSSm html
pknmodel html
plotLBodeFitness html
plotLBodeModelSim html
runCNORode html
simdata2cnolist html
simulate html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CNORode' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FG_transfer_function.c -o FG_transfer_function.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea_io.c -o cvodea_io.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_band.c -o cvodes_band.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bandpre.c -o cvodes_bandpre.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bbdpre.c -o cvodes_bbdpre.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_dense.c -o cvodes_dense.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_diag.c -o cvodes_diag.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_direct.c -o cvodes_direct.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_io.c -o cvodes_io.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spbcgs.c -o cvodes_spbcgs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spgmr.c -o cvodes_spgmr.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spils.c -o cvodes_spils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c decimal2binary.c -o decimal2binary.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findStates.c -o findStates.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fnvector_serial.c -o fnvector_serial.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumBits.c -o getNumBits.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumInputs.c -o getNumInputs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getStateIndex.c -o getStateIndex.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_count_bits.c -o get_count_bits.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_input_index.c -o get_input_index.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_truth_tables_index.c -o get_truth_tables_index.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hill_function.c -o hill_function.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c linear_transfer_function.c -o linear_transfer_function.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill.c -o normHill.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill_mod.c -o normHill_mod.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nvector_serial.c -o nvector_serial.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printAdjMat.c -o printAdjMat.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printInterMat.c -o printInterMat.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printNminiTerms.c -o printNminiTerms.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printTruthTables.c -o printTruthTables.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhsODE.c -o rhsODE.o
rhsODE.c:85: warning: "Ith" redefined
#define Ith(v,i) ( v[i] )
rhsODE.c:10: note: this is the location of the previous definition
#define Ith(v,i) ( NV_DATA_S(v)[i] )
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sim_logic_ode.c -o sim_logic_ode.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:169:11: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^~~~~~~
simulateODE.c:35:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^~~~~~~
simulateODE.c:255:4: warning: 'tout' may be used uninitialized in this function [-Wmaybe-uninitialized]
rhsODEF(tout,y0,ydot0, data);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_band.c -o sundials_band.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_dense.c -o sundials_dense.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_direct.c -o sundials_direct.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_iterative.c -o sundials_iterative.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_math.c -o sundials_math.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_nvector.c -o sundials_nvector.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spbcgs.c -o sundials_spbcgs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORode' as CNORode_1.34.0.zip
* DONE (CNORode)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CNORode' successfully unpacked and MD5 sums checked
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CNORode.Rcheck/examples_i386/CNORode-Ex.timings
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CNORode.Rcheck/examples_x64/CNORode-Ex.timings
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