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Package 126/609HostnameOS / ArchBUILDCHECKBUILD BIN
CNORode 1.0.0
David Henriques
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/CNORode
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: CNORode
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNORode_1.0.0.tar.gz
StartedAt: 2013-03-24 23:06:34 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:08:01 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 86.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNORode.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CNORode.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CNORode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORode' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'MEIGOR'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'CNORode' can be installed ... WARNING
Found the following significant warnings:
  sim_logic_ode.c:274: warning: 'tempData.nExperiments' is used uninitialized in this function
  sim_logic_ode.c:274: warning: 'tempData.isInput' is used uninitialized in this function
See '/Users/biocbuild/bbs-2.11-bioc/meat/CNORode.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
minlpLBodeSSm: no visible global function definition for 'essR'
parEstimationLBodeSSm: no visible global function definition for 'essR'
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.11-bioc/meat/CNORode.Rcheck/CNORode/libs/i386/CNORode.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Object: 'cvodes.o'
  Found '_printf', possibly from 'printf' (C)
    Objects: 'nvector_serial.o', 'printAdjMat.o', 'printInterMat.o',
      'printNminiTerms.o', 'printTruthTables.o', 'sundials_direct.o'
  Found '_putchar', possibly from 'putchar' (C)
    Objects: 'nvector_serial.o', 'printInterMat.o',
      'printNminiTerms.o', 'sundials_direct.o'
  Found '_puts', possibly from 'printf' (C), 'puts' (C)
    Objects: 'printAdjMat.o', 'printTruthTables.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
parEstimationLBode   26.806  0.434  27.391
parEstimationLBodeGA  9.955  0.187  10.300
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/CNORode.Rcheck/00check.log'
for details.

CNORode.Rcheck/00install.out:

* installing *source* package 'CNORode' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVodeB':
cvodea.c:1263: warning: 'flag' may be used uninitialized in this function
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2507: warning: 'ySd0' may be used uninitialized in this function
cvodea.c:2507: warning: 'yS0' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodea_io.c -o cvodea_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes.c -o cvodes.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_band.c -o cvodes_band.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_dense.c -o cvodes_dense.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_diag.c -o cvodes_diag.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_direct.c -o cvodes_direct.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_io.c -o cvodes_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spils.c -o cvodes_spils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c decimal2binary.c -o decimal2binary.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c findStates.c -o findStates.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c fnvector_serial.c -o fnvector_serial.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getNumBits.c -o getNumBits.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getNumInputs.c -o getNumInputs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getStateIndex.c -o getStateIndex.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17: warning: unused variable 'n'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_count_bits.c -o get_count_bits.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_input_index.c -o get_input_index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -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: warning: unused variable 'k'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c hill_function.c -o hill_function.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c linear_transfer_function.c -o linear_transfer_function.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c normHill.c -o normHill.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c nvector_serial.c -o nvector_serial.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printAdjMat.c -o printAdjMat.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printInterMat.c -o printInterMat.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printNminiTerms.c -o printNminiTerms.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printTruthTables.c -o printTruthTables.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c rhsODE.c -o rhsODE.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sim_logic_ode.c -o sim_logic_ode.o
sim_logic_ode.c: In function 'sim_logic_ode':
sim_logic_ode.c:274: warning: 'tempData.nExperiments' is used uninitialized in this function
sim_logic_ode.c:274: warning: 'tempData.isInput' is used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150: warning: implicit declaration of function 'CVDense'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_band.c -o sundials_band.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_dense.c -o sundials_dense.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_direct.c -o sundials_direct.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_iterative.c -o sundials_iterative.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_math.c -o sundials_math.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_nvector.c -o sundials_nvector.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_spgmr.c -o sundials_spgmr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/CNORode.Rcheck/CNORode/libs/i386
** 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)

CNORode.Rcheck/CNORode-Ex.timings:

nameusersystemelapsed
createLBodeContPars0.0130.0050.018
getLBodeContObjFunction0.0530.0060.058
getLBodeDataSim0.0170.0050.022
getLBodeMINLPObjFunction0.0580.0050.064
getLBodeModelSim0.0620.0060.069
minlpLBodeSSm0.0000.0010.001
parEstimationLBode26.806 0.43427.391
parEstimationLBodeGA 9.955 0.18710.300
parEstimationLBodeSSm000
plotLBodeFitness0.9930.0261.024
plotLBodeModelSim0.3130.0160.333