CNORode 1.6.0
David Henriques
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CNORode | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNORode_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CNORode.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ version ‘1.6.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNORode’ can be installed ... [12s/13s] WARNING
Found the following significant warnings:
cvodes.c:8945:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/CNORode.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘CellNOptR’ ‘genalg’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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
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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.14-bioc/meat/CNORode.Rcheck/CNORode/libs/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 entry points 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 files in ‘vignettes’ ... OK
* checking examples ... [24s/25s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
parEstimationLBode 14.948 0.1 15.679
* 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
WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/CNORode.Rcheck/00check.log’
for details.
* installing *source* package ‘CNORode’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodea.c -o cvodea.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodea_io.c -o cvodea_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes.c -o cvodes.o
cvodes.c:8945:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
fprintf(stderr, msg);
^˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_band.c -o cvodes_band.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_dense.c -o cvodes_dense.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_diag.c -o cvodes_diag.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_direct.c -o cvodes_direct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_io.c -o cvodes_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_spils.c -o cvodes_spils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c decimal2binary.c -o decimal2binary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c findStates.c -o findStates.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c fnvector_serial.c -o fnvector_serial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c getNumBits.c -o getNumBits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c getNumInputs.c -o getNumInputs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c getStateIndex.c -o getStateIndex.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c getTruthTables.c -o getTruthTables.o
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
int i,j,k,m,n,counter1,input,miniterm;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c get_count_bits.c -o get_count_bits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c get_input_index.c -o get_input_index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c hill_function.c -o hill_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c linear_transfer_function.c -o linear_transfer_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c normHill.c -o normHill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c nvector_serial.c -o nvector_serial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c printAdjMat.c -o printAdjMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c printInterMat.c -o printInterMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c printNminiTerms.c -o printNminiTerms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c printTruthTables.c -o printTruthTables.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c rhsODE.c -o rhsODE.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sim_logic_ode.c -o sim_logic_ode.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c simulateODE.c -o simulateODE.o
simulateODE.c:150:11: warning: implicit declaration of function 'CVDense' is invalid in C99 [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_band.c -o sundials_band.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_dense.c -o sundials_dense.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_direct.c -o sundials_direct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_iterative.c -o sundials_iterative.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_math.c -o sundials_math.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_nvector.c -o sundials_nvector.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_spgmr.c -o sundials_spgmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./include -fPIC -Wall -mtune=core2 -g -O2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o
clang -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-2.14-bioc/meat/CNORode.Rcheck/CNORode/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORode)