CNPBayes 1.6.1
Jacob Carey
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CNPBayes | | Last Changed Rev: 129423 / Revision: 131943 | | Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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###
### Running command:
###
### rm -rf CNPBayes.buildbin-libdir CNPBayes.Rcheck && mkdir CNPBayes.buildbin-libdir CNPBayes.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNPBayes.buildbin-libdir CNPBayes_1.6.1.tar.gz >CNPBayes.Rcheck\00install.out 2>&1 && cp CNPBayes.Rcheck\00install.out CNPBayes-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CNPBayes.buildbin-libdir --install="check:CNPBayes-install.out" --force-multiarch --no-vignettes --timings CNPBayes_1.6.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNPBayes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNPBayes' version '1.6.1'
* 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 whether package 'CNPBayes' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 1.0Mb
libs 3.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'GenomicRanges'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
consensusRegion: no visible global function definition for
'elementLengths'
Undefined global functions or variables:
elementLengths
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'labelSwitching':
labelSwitching
Code: function(object, ...)
Docs: function(object, merge = TRUE)
Argument names in code not in docs:
...
Argument names in docs not in code:
merge
Mismatches in argument names:
Position: 2 Code: ... Docs: merge
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/i386/CNPBayes.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot 5.02 0.01 5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot 5.29 0.06 5.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o
reduced_pooledvariance.cpp: In function 'Rcpp::NumericVector full_theta_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:46:10: warning: unused variable 'prod' [-Wunused-variable]
double prod ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::S4 reduced_sigma_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:86:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::S4 reduced_mu_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:330:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::NumericVector p_nu0_reduced_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:617:7: warning: unused variable 'N' [-Wunused-variable]
int N = x.size() ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::S4 reduced_s20_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:682:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c update.cpp -o update.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_batch.cpp -o updates_batch.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_marginal.cpp -o updates_marginal.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_reduced_batch.cpp -o updates_reduced_batch.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CNPBayes.dll tmp.def RcppExports.o miscfunctions.o reduced_pooledvariance.o singlebatch_pooledvar.o update.o updates_batch.o updates_marginal.o updates_reduced_batch.o updates_reduced_marginal.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o
reduced_pooledvariance.cpp: In function 'Rcpp::NumericVector full_theta_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:46:10: warning: unused variable 'prod' [-Wunused-variable]
double prod ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::S4 reduced_sigma_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:86:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::S4 reduced_mu_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:330:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::NumericVector p_nu0_reduced_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:617:7: warning: unused variable 'N' [-Wunused-variable]
int N = x.size() ;
^
reduced_pooledvariance.cpp: In function 'Rcpp::S4 reduced_s20_pooled(Rcpp::S4)':
reduced_pooledvariance.cpp:682:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c update.cpp -o update.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_batch.cpp -o updates_batch.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_marginal.cpp -o updates_marginal.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_reduced_batch.cpp -o updates_reduced_batch.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CNPBayes.dll tmp.def RcppExports.o miscfunctions.o reduced_pooledvariance.o singlebatch_pooledvar.o update.o updates_batch.o updates_marginal.o updates_reduced_batch.o updates_reduced_marginal.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNPBayes' as CNPBayes_1.6.1.zip
* DONE (CNPBayes)