Jacob Carey
| Snapshot Date: 2019-01-09 16:46:14 -0500 (Wed, 09 Jan 2019) |
| URL: https://git.bioconductor.org/packages/CNPBayes |
| Branch: master |
| Last Commit: 1e9cdbb |
| Last Changed Date: 2019-01-03 09:20:51 -0500 (Thu, 03 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-01-10 15:36:06 -0500 (Thu, 10 Jan 2019).
| Package 292/1651 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNPBayes 1.13.5 Jacob Carey
| malbec2 | Linux (Ubuntu 18.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: CNPBayes |
| Version: 1.13.5 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNPBayes.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNPBayes_1.13.5.tar.gz |
| StartedAt: 2019-01-10 02:39:03 -0500 (Thu, 10 Jan 2019) |
| EndedAt: 2019-01-10 03:08:11 -0500 (Thu, 10 Jan 2019) |
| EllapsedTime: 1748.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CNPBayes.Rcheck |
| Warnings: 4 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNPBayes.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNPBayes_1.13.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck'
* using R Under development (unstable) (2018-11-18 r75627)
* 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 '1.13.5'
* package encoding: UTF-8
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIFAfHZ/R.INSTALL1f145fdc4500/CNPBayes/man/tile-functions.Rd:28: file link 'ntile' in package 'dplyr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
R 1.9Mb
libs 2.7Mb
* 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
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'RcppArmadillo'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.simulate_data_multi2: no visible binding for global variable 'id'
augmentData: no visible binding for global variable 'medians'
augmentData: no visible binding for global variable 'nhom'
augmentData: no visible binding for global variable 'id'
augmentData: no visible binding for global variable 'batch_index'
bafLikelihood: no visible binding for global variable 'snpdat'
ci95.wrap: no visible global function definition for 't.test'
combineChains: no visible binding for global variable '.'
combineModels: no visible binding for global variable '.'
combineModels: no visible binding for global variable 'id'
component_stats: no visible binding for global variable 'batches'
component_stats: no visible binding for global variable 'copy_number'
component_stats: no visible binding for global variable 'log_ratio'
find_surrogates: no visible binding for global variable
'provisional_batch'
gibbs_trios2: no visible binding for global variable 'maplabel'
gibbs_trios2: no visible binding for global variable 'mprob'
gibbs_trios3: no visible binding for global variable 'maplabel'
gibbs_trios3: no visible binding for global variable 'mprob'
gibbs_trios_K2: no visible binding for global variable
'.gibbs_trios_mcmc2'
gibbs_trios_K3: no visible binding for global variable
'.gibbs_trios_mcmc3'
longFormatK: no visible binding for global variable '.'
longFormatK: no visible binding for global variable 's'
longFormatKB: no visible binding for global variable '.'
longFormatKB: no visible binding for global variable 's'
longFormatKB: no visible binding for global variable 'bk'
longFormatKB2: no visible binding for global variable '.'
longFormatKB2: no visible binding for global variable 's'
longFormatKB2: no visible binding for global variable 'bk'
modelSpecs: no visible binding for global variable 'model'
mprob.matrix: no visible global function definition for ':='
mprob.matrix: no visible binding for global variable 'parents'
mprob.matrix: no visible binding for global variable 'father'
mprob.matrix: no visible binding for global variable 'mother'
posteriorSimulationPooled: possible error in `mcmcParams<-`(object,
force = TRUE, value = `*tmpv*`): unused argument (force = TRUE)
predictiveTibble: no visible binding for global variable 'value'
simulate_data_multi2: no visible binding for global variable
'copy_number'
simulate_data_multi3: no visible binding for global variable
'copy_number'
startAtTrueValues2: no visible binding for global variable
'copy_number'
triodata: no visible binding for global variable 'id'
augmentData2,MultiBatchList: no visible binding for global variable
'model'
augmentData2,MultiBatchList: no visible binding for global variable '.'
augmentData2,MultiBatchList: no visible binding for global variable
'id'
batch<-,MultiBatch-numeric: no visible global function definition for
'spec'
batch<-,MultiBatch-numeric: no visible global function definition for
'spec<-'
coerce,McmcChains-list: no visible binding for global variable 's'
computePrec,MultiBatch: no visible binding for global variable 'prec'
findSurrogates,MultiBatch: no visible binding for global variable 'id'
findSurrogates,MultiBatch: no visible binding for global variable
'provisional_batch'
findSurrogates,MultiBatch: no visible binding for global variable
'batch_labels'
sigma,MultiBatchCopyNumberPooled: no visible binding for global
variable 's2'
Undefined global functions or variables:
. .gibbs_trios_mcmc2 .gibbs_trios_mcmc3 := batch_index batch_labels
batches bk copy_number father id log_ratio maplabel medians model
mother mprob nhom parents prec provisional_batch s s2 snpdat spec
spec<- t.test value
Consider adding
importFrom("stats", "t.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'TBM' 'findSurrogates' 'modelName' 'p'
Undocumented S4 methods:
generic '[' and siglist 'MixtureModel,logical,ANY,ANY'
generic '[' and siglist 'MixtureModel,numeric,ANY,ANY'
generic '[' and siglist 'MultiBatchList,ANY,ANY,ANY'
generic '[<-' and siglist 'MultiBatchList,ANY,ANY,ANY'
generic '[[' and siglist 'MultiBatchList,character,ANY'
generic '[[' and siglist 'MultiBatchList,numeric,ANY'
generic '[[<-' and siglist 'MultiBatchList,ANY,ANY'
generic 'batch' and siglist 'MultiBatch'
generic 'batch' and siglist 'MultiBatchList'
generic 'burnin' and siglist 'MultiBatch'
generic 'burnin' and siglist 'MultiBatchList'
generic 'burnin<-' and siglist 'MultiBatch,numeric'
generic 'burnin<-' and siglist 'MultiBatchList,numeric'
generic 'chains' and siglist 'MultiBatch'
generic 'chains' and siglist 'MultiBatchList'
generic 'dfr' and siglist 'MultiBatch'
generic 'dfr' and siglist 'MultiBatchList'
generic 'hyperParams' and siglist 'MultiBatch'
generic 'hyperParams' and siglist 'MultiBatchList'
generic 'hyperParams<-' and siglist 'MultiBatch,Hyperparameters'
generic 'hyperParams<-' and siglist 'MultiBatchList,Hyperparameters'
generic 'iter' and siglist 'McmcChains'
generic 'iter' and siglist 'MultiBatch'
generic 'iter' and siglist 'MultiBatchList'
generic 'iter<-' and siglist 'McmcChains,ANY'
generic 'iter<-' and siglist 'MultiBatch,numeric'
generic 'iter<-' and siglist 'MultiBatchList,numeric'
generic 'k' and siglist 'McmcChains'
generic 'k' and siglist 'MultiBatch'
generic 'k' and siglist 'MultiBatchList'
generic 'k<-' and siglist 'McmcChains'
generic 'label_switch' and siglist 'MultiBatch'
generic 'length' and siglist 'MultiBatchList'
generic 'logPrior' and siglist 'MultiBatch'
generic 'log_lik' and siglist 'MultiBatch'
generic 'marginal_lik' and siglist 'MultiBatch'
generic 'marginal_lik' and siglist 'MultiBatchList'
generic 'marginal_lik<-' and siglist 'MultiBatch,numeric'
generic 'mcmcParams' and siglist 'MultiBatch'
generic 'mcmcParams' and siglist 'MultiBatchList'
generic 'mcmcParams<-' and siglist 'MultiBatch,McmcParams'
generic 'mcmcParams<-' and siglist 'MultiBatchList,McmcParams'
generic 'modelName' and siglist 'MultiBatch'
generic 'modelName' and siglist 'MultiBatchList'
generic 'modes' and siglist 'MultiBatch'
generic 'modes' and siglist 'MultiBatchList'
generic 'modes<-' and siglist 'MultiBatch'
generic 'mu' and siglist 'MultiBatch'
generic 'nStarts' and siglist 'MultiBatch'
generic 'nStarts' and siglist 'MultiBatchList'
generic 'nStarts<-' and siglist 'MultiBatch,integer'
generic 'nStarts<-' and siglist 'MultiBatch,numeric'
generic 'nStarts<-' and siglist 'MultiBatchList,integer'
generic 'nStarts<-' and siglist 'MultiBatchList,numeric'
generic 'names' and siglist 'MultiBatchList'
generic 'nu.0' and siglist 'MultiBatch'
generic 'oned' and siglist 'MultiBatch'
generic 'oned' and siglist 'MultiBatchList'
generic 'p' and siglist 'McmcChains'
generic 'p' and siglist 'MultiBatch'
generic 'posteriorSimulation' and siglist 'MultiBatch'
generic 'posteriorSimulation' and siglist 'MultiBatchList'
generic 'posteriorSimulation' and siglist 'MultiBatchP'
generic 'posteriorSimulation' and siglist 'list'
generic 'probz' and siglist 'MultiBatch'
generic 'sigma2.0' and siglist 'MultiBatch'
generic 'sigma2' and siglist 'MultiBatch'
generic 'sigma' and siglist 'MultiBatchPooled'
generic 'sigma<-' and siglist 'MixtureModel'
generic 'sigma<-' and siglist 'MultiBatchPooled'
generic 'tau2' and siglist 'MultiBatch'
generic 'theta' and siglist 'MultiBatch'
generic 'theta<-' and siglist 'McmcChains,ANY'
generic 'theta<-' and siglist 'MixtureModel,ANY'
generic 'theta<-' and siglist 'MultiBatch,matrix'
generic 'theta<-' and siglist 'MultiBatchModel,ANY'
generic 'thin' and siglist 'MultiBatch'
generic 'thin' and siglist 'MultiBatchList'
generic 'thin<-' and siglist 'McmcParams,numeric'
generic 'thin<-' and siglist 'MultiBatch,numeric'
generic 'thin<-' and siglist 'MultiBatchList,numeric'
generic 'triodata_lrr' and siglist 'TrioBatchModel'
generic 'z' and siglist 'MultiBatch'
generic 'zFreq' and siglist 'MultiBatch'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'MixtureModel-class':
Slots for class 'MixtureModel'
Code: .internal.constraint .internal.counter batch batchElements data
data.mean data.prec hyperparams k label_switch loglik logprior
marginal_lik mcmc.chains mcmc.params modes mu nu.0 pi
predictive probz sigma2 sigma2.0 tau2 theta u z zfreq zstar
Docs: .internal.constraint .internal.counter batch batchElements data
data.mean data.prec hyperparams k label_switch loglik logprior
marginal_lik marginal_lik mcmc.chains mcmc.params modes mu nu.0
pi probz sigma2 sigma2.0 tau2 theta u z zfreq
S4 class codoc mismatches from documentation object 'MultiBatch-class':
Slots for class 'MultiBatch'
Code: chains current_values data down_sample flags parameters specs
summaries
Docs: chains current_values data down_sample flags parameters
summaries
S4 class codoc mismatches from documentation object 'MultiBatchModel-class':
Slots for class 'MultiBatchModel'
Code: .internal.constraint .internal.counter batch batchElements data
data.mean data.prec hyperparams k label_switch loglik logprior
marginal_lik mcmc.chains mcmc.params modes mu nu.0 pi
predictive probz sigma2 sigma2.0 tau2 theta u z zfreq zstar
Inherited: k hyperparams theta sigma2 nu.0 sigma2.0 pi mu tau2
predictive zstar data data.mean data.prec z zfreq probz u
logprior loglik mcmc.chains batch batchElements modes
mcmc.params label_switch marginal_lik .internal.constraint
.internal.counter
Docs: .internal.constraint batch batchElements data data.mean
data.prec hyperparams is_mendelian k label_switch loglik
logprior mcmc.chains mcmc.params modes mu nu.0 pi probz sigma2
sigma2.0 tau2 theta z zfreq
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'HyperparametersTrios'
'k' 'mu.0' 'tau2.0' 'eta.0' 'm2.0' 'alpha' 'beta' 'a' 'b' 'dfr'
Undocumented arguments in documentation object 'McmcParams'
'min_GR' 'min_effsize' 'max_burnin' 'min_chains'
Duplicated \argument entries in documentation object 'MultiBatchModel2':
'dat' 'batches' 'hp' 'mp'
Undocumented arguments in documentation object 'TrioBatchModel'
'mprob' 'maplabel'
Documented arguments not in \usage in documentation object 'TrioBatchModel':
'batches'
Undocumented arguments in documentation object 'gibbs'
'maplabel' 'mprob'
Documented arguments not in \usage in documentation object 'iter<-':
'force'
Documented arguments not in \usage in documentation object 'mcmcParams':
'force'
Undocumented arguments in documentation object 'sigma<-'
'value'
Undocumented arguments in documentation object 'singleBatchGuided,MultiBatchList,MultiBatch-method'
'x' 'guide'
Undocumented arguments in documentation object 'theta'
'value'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.9-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CNPBayes/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MultiBatchModel 120.64 0.28 120.96
ggplot-functions 48.01 0.78 48.81
MBP 14.71 0.29 15.05
gibbs 11.83 0.08 11.91
upSample2 7.32 0.04 7.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MultiBatchModel 65.25 0.08 65.36
ggplot-functions 43.42 0.06 43.50
MBP 14.80 0.07 14.90
gibbs 10.11 0.00 10.11
upSample2 5.42 0.07 5.50
* 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: 4 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck/00check.log'
for details.
CNPBayes.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNPBayes_1.13.5.tar.gz && rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNPBayes.buildbin-libdir CNPBayes_1.13.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNPBayes_1.13.5.zip && rm CNPBayes_1.13.5.tar.gz CNPBayes_1.13.5.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 893k 100 893k 0 0 14.0M 0 --:--:-- --:--:-- --:--:-- 15.8M
install for i386
* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c triomodel.cpp -o triomodel.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 multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'alpha' in package 'CNPBayes'
in method for 'convergence' with signature '"MultiBatchList"': no definition for class "MultiBatchList"
Creating a generic function from function 'sigma' in package 'CNPBayes'
Note: wrong number of arguments to '/'
** help
*** installing help indices
converting help for package 'CNPBayes'
finding HTML links ... done
BatchModelExample html
CNPBayes html
CopyNumber-classes html
CopyNumber-methods html
Defunct-classes html
Hyperparameters-class html
Hyperparameters html
HyperparametersBatch-class html
HyperparametersMarginal-class html
HyperparametersMultiBatch-class html
HyperparametersMultiBatch html
HyperparametersSingleBatch-class html
HyperparametersSingleBatch html
HyperparametersTrios-class html
HyperparametersTrios html
MBP html
MarginalModelExample html
McmcChains-class html
McmcParams-class html
McmcParams html
MixtureModel-class html
MultiBatch-class html
MultiBatchModel-class html
MultiBatchModel html
MultiBatchModelExample html
MultiBatchPooledExample html
SingleBatchModel-class html
SingleBatchModel html
SingleBatchModelExample html
TrioBatchModel html
bafLikelihood html
batch-method html
bayesFactor html
bic-method html
burnin-method html
chains-method html
chromosome html
collapseBatch-method html
consensusCNP html
copyNumber html
dfr-method html
downSample html
eta.0-method html
extract-methods html
findSurrogates-MultiBatch-method html
ggplot-functions html
gibbs html
hyperParams-method html
iter-method html
k-method html
label_switch html
logBayesFactor html
logPrior-method html
log_lik-method html
m2.0-method html
mapCnProbability html
mapParams html
map_z html
mapping html
marginalLik html
marginalLikelihood-method html
marginal_lik html
mcmcParams-method html
mlParams html
modelName-MixtureModel-method html
modes-method html
mu-method html
muMean html
muc html
nStarts-method html
names-methods html
nu.0-method html
numberObs-method html
oned-method html
orderModels html
p-MixtureModel-method html
pic html
posteriorPredictive html
posteriorSimulation-method html
posterior_cases html
pp html
probCopyNumber html
probz-method html
probzpar-method html
qInverseTau2 html
saveBatch html
sigma html
sigma2-method html
sigma2.0-method html
sigmac html
simulateBatchData html
simulateData html
singleBatchGuided-MultiBatchList-MultiBatch-method
html
tau html
tau2-method html
tauMean html
tauc html
theta-method html
thin-method html
tile-functions html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIFAfHZ/R.INSTALL1f145fdc4500/CNPBayes/man/tile-functions.Rd:28: file link 'ntile' in package 'dplyr' does not exist and so has been treated as a topic
triodata_lrr-method html
upSample2 html
y-method html
z-method html
zfreq-method html
zfreqpar-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c triomodel.cpp -o triomodel.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 multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNPBayes' as CNPBayes_1.13.5.zip
* DONE (CNPBayes)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CNPBayes' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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CNPBayes.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2018-11-18 r75627) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS"="")
> library(testthat)
> library(CNPBayes)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Attaching package: 'CNPBayes'
The following object is masked from 'package:stats':
sigma
> test_check("CNPBayes")
== testthat results ===========================================================
OK: 312 SKIPPED: 3 FAILED: 0
>
> proc.time()
user system elapsed
596.03 3.25 601.79
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CNPBayes.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2018-11-18 r75627) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS"="")
> library(testthat)
> library(CNPBayes)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Attaching package: 'CNPBayes'
The following object is masked from 'package:stats':
sigma
> test_check("CNPBayes")
== testthat results ===========================================================
OK: 312 SKIPPED: 3 FAILED: 0
>
> proc.time()
user system elapsed
517.34 0.79 518.21
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CNPBayes.Rcheck/examples_i386/CNPBayes-Ex.timings
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CNPBayes.Rcheck/examples_x64/CNPBayes-Ex.timings
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