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BioC 3.6: INSTALL report for CNORode on malbec1

This page was generated on 2017-08-16 13:20:28 -0400 (Wed, 16 Aug 2017).

Package 251/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.19.0
David Henriques
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNORode
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNORode
Version: 1.19.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL CNORode
StartedAt: 2017-08-15 18:11:30 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:11:43 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 12.6 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL CNORode
###
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* installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’
* installing *source* package ‘CNORode’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -I./include  -fpic  -g -O2  -Wall -c cvodea.c -o cvodea.o
cvodea.c: In function ‘CVAhermiteStorePnt’:
cvodea.c:2445:11: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable]
   int is, retval;
           ^
cvodea.c: In function ‘CVArhsQ’:
cvodea.c:2941:7: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable]
   int flag, retval;
       ^
cvodea.c: In function ‘CVAhermiteGetY’:
cvodea.c:2572:7: warning: ‘ySd0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]);
       ^
cvodea.c:2591:5: warning: ‘yS0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
     ^
cvodea.c: In function ‘CVodeB’:
cvodea.c:1263:13: warning: ‘flag’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int sign, flag;
             ^
gcc -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -I./include  -fpic  -g -O2  -Wall -c cvodes.c -o cvodes.o
cvodes.c: In function ‘cvQuadSensRhs1InternalDQ’:
cvodes.c:8834:20: warning: variable ‘rDeltap’ set but not used [-Wunused-but-set-variable]
   realtype Deltap, rDeltap;
                    ^
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -I./include  -fpic  -g -O2  -Wall -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function ‘getTruthTables’:
getTruthTables.c:17:14: warning: unused variable ‘n’ [-Wunused-variable]
  int i,j,k,m,n,counter1,input,miniterm;
              ^
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -I./include  -fpic  -g -O2  -Wall -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function ‘get_support_truth_tables’:
get_support_truth_tables.c:16:10: warning: unused variable ‘k’ [-Wunused-variable]
  int i,j,k;
          ^
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -I./include  -fpic  -g -O2  -Wall -c simulateODE.c -o simulateODE.o
simulateODE.c: In function ‘simulateODE’:
simulateODE.c:150:11: warning: implicit declaration of function ‘CVDense’ [-Wimplicit-function-declaration]
    flag = CVDense(cvode_mem, neq);
           ^
simulateODE.c:32:14: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
  int i,j,neq,counter,flag;
              ^
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -I./include  -fpic  -g -O2  -Wall -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c: In function ‘SpgmrFree’:
sundials_spgmr.c:439:29: warning: variable ‘yg’ set but not used [-Wunused-but-set-variable]
   realtype **Hes, *givens, *yg;
                             ^
sundials_spgmr.c:439:20: warning: variable ‘givens’ set but not used [-Wunused-but-set-variable]
   realtype **Hes, *givens, *yg;
                    ^
gcc -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o CNORode.so cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/R/library/CNORode/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘CNORode-vignette.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (CNORode)