CellNOptR 1.14.0
T.Cokelaer
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CellNOptR | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | 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 CellNOptR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CellNOptR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellNOptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellNOptR’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘RBGL’ ‘graph’ ‘hash’ ‘ggplot2’ ‘RCurl’ ‘Rgraphviz’ ‘XML’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘CellNOptR’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘hash’ ‘RBGL’ ‘RCurl’ ‘Rgraphviz’ ‘XML’
Please remove these calls from your code.
'library' or 'require' call to ‘igraph’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘ggplot2’ ‘hash’ ‘methods’ ‘RCurl’ ‘Rgraphviz’ ‘XML’
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
CNOdata: no visible global function definition for ‘getURL’
gaBinaryT1: no visible global function definition for ‘hash’
gaBinaryT1 : getObj: no visible global function definition for
‘has.key’
gaBinaryT2: no visible global function definition for ‘hash’
gaBinaryT2 : getObj: no visible global function definition for
‘has.key’
gaBinaryTN: no visible global function definition for ‘hash’
gaBinaryTN : getObj: no visible global function definition for
‘has.key’
model2igraph: no visible global function definition for
‘igraph.from.graphNEL’
plotCNOlist2: no visible global function definition for ‘ggplot’
plotCNOlist2: no visible global function definition for ‘aes’
plotCNOlist2: no visible binding for global variable ‘values’
plotCNOlist2: no visible global function definition for ‘geom_point’
plotCNOlist2: no visible global function definition for ‘geom_line’
plotCNOlist2: no visible global function definition for ‘xlab’
plotCNOlist2: no visible global function definition for ‘ylab’
plotCNOlist2: no visible global function definition for ‘facet_grid’
plotCNOlist2: no visible global function definition for ‘theme_bw’
plotCNOlist2: no visible global function definition for ‘theme’
plotCNOlist2: no visible global function definition for ‘element_text’
plotCNOlist2: no visible global function definition for ‘element_rect’
plotCNOlist2: no visible global function definition for ‘ylim’
plotModel: no visible global function definition for ‘layoutGraph’
plotModel: no visible global function definition for ‘renderGraph’
plotModel: no visible global function definition for ‘toDot’
readSBMLQual: no visible global function definition for ‘xmlTreeParse’
readSBMLQual: no visible global function definition for ‘xmlRoot’
readSBMLQual: no visible global function definition for ‘xmlChildren’
readSBMLQual: no visible global function definition for ‘xmlApply’
readSBMLQual : <anonymous>: no visible global function definition for
‘xmlGetAttr’
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/29s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_gaBinaryT1.R’ [6s/6s]
Running ‘test_gaBinaryT2.R’ [8s/8s]
Running ‘test_gaBinaryT3.R’ [11s/11s]
Running ‘test_manySteadyStates.R’ [18s/18s]
Running ‘test_priorBitString.R’ [4s/4s]
Running ‘test_simulateTN.R’ [5s/5s]
[52s/52s] OK
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/CellNOptR.Rcheck/00check.log’
for details.
* installing *source* package ‘CellNOptR’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=core2 -g -O2 -Wall -c getFit.c -o getFit.o
getFit.c: In function ‘getFit’:
getFit.c:47: warning: unused variable ‘nReacs’
getFit.c:42: warning: unused variable ‘selCounter’
getFit.c:41: warning: unused variable ‘selection’
getFit.c:40: warning: unused variable ‘or_max’
getFit.c:39: warning: unused variable ‘curr_max’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=core2 -g -O2 -Wall -c simulatorT1.c -o simulatorT1.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./include -fPIC -mtune=core2 -g -O2 -Wall -c simulatorTN.c -o simulatorTN.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/CellNOptR.Rcheck/CellNOptR/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 (CellNOptR)