Back to Multiple platform build/check report for BioC 3.13
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-07-23 15:05:59 -0400 (Fri, 23 Jul 2021).

INSTALL results for CNORode on tokay2

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.

raw results

Package 346/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.34.0  (landing page)
Enio Gjerga
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/CNORode
Branch: RELEASE_3_13
Last Commit: 06fde26
Last Changed Date: 2021-05-19 11:54:17 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CNORode
Version: 1.34.0
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
StartedAt: 2021-07-22 08:24:28 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 08:25:32 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 63.3 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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  1844k      0 --:--:-- --:--:-- --:--:-- 1857k

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