networkBMA 1.15.0
Ka Yee Yeung
| Snapshot Date: 2016-10-04 17:12:09 -0400 (Tue, 04 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/networkBMA | | Last Changed Rev: 117081 / Revision: 121758 | | Last Changed Date: 2016-05-03 17:30:44 -0400 (Tue, 03 May 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | TIMEOUT | skipped | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | 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 networkBMA_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘1.15.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘networkBMA’ can be installed ... OK
* 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:
‘BMA’ ‘Rcpp’ ‘RcppArmadillo’ ‘RcppEigen’
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
FastScanBMA.BIC: no visible global function definition for ‘ls.print’
FastScanBMA.BIC: no visible global function definition for ‘lsfit’
FastScanBMA.g: no visible global function definition for ‘ls.print’
FastScanBMA.g: no visible global function definition for ‘lsfit’
Optimizeg: no visible global function definition for ‘optim’
bicreg.pr: no visible global function definition for ‘leaps’
bicreg.pr: no visible global function definition for ‘lm’
bicreg.pr: no visible global function definition for ‘coef’
bicreg.pr: no visible global function definition for ‘logLik’
bicreg.pr.resid: no visible global function definition for ‘leaps’
bicreg.pr.resid: no visible global function definition for ‘lm’
bicreg.pr.resid: no visible global function definition for ‘coef’
bicreg.pr.resid: no visible global function definition for ‘logLik’
networkBMA: no visible global function definition for ‘lm.fit’
networkBMA : <anonymous>: no visible global function definition for
‘lm.fit’
prc: no visible global function definition for ‘plot’
prc: no visible global function definition for ‘abline’
prc : <anonymous>: no visible global function definition for ‘segments’
prc: no visible global function definition for ‘segments’
roc: no visible global function definition for ‘plot’
roc: no visible global function definition for ‘abline’
roc: no visible global function definition for ‘lines’
roc: no visible global function definition for ‘segments’
varord: no visible global function definition for ‘cor’
varord : bic1fun: no visible global function definition for ‘logLik’
varord : bic1fun: no visible global function definition for ‘lm’
writeEdges: no visible global function definition for ‘write.table’
Undefined global functions or variables:
abline coef cor leaps lines lm lm.fit logLik ls.print lsfit optim
plot segments write.table
Consider adding
importFrom("graphics", "abline", "lines", "plot", "segments")
importFrom("stats", "coef", "cor", "lm", "lm.fit", "logLik",
"ls.print", "lsfit", "optim")
importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... WARNING
File ‘networkBMA/libs/networkBMA.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Object: ‘ScanBMA_full.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ScanBMAcontrol 6.205 0.046 6.256
gControl 5.912 0.028 5.945
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck/00check.log’
for details.
* installing *source* package ‘networkBMA’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... no
checking tr1/unordered_set presence... no
checking for tr1/unordered_set... no
configure: creating ./config.status
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppEigen/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppEigen/include" -fPIC -Wall -mtune=core2 -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp:131:21: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:322:19: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:417:21: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:610:19: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
4 warnings generated.
clang++ -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 -o networkBMA.so RcppExports.o ScanBMA_full.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck/networkBMA/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 (networkBMA)