| Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:25:44 -0400 (Wed, 15 Apr 2020).
| Package 323/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Jacob Carey
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: CNPBayes |
| Version: 1.16.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CNPBayes_1.16.0.tar.gz && rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNPBayes.buildbin-libdir CNPBayes_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CNPBayes_1.16.0.zip && rm CNPBayes_1.16.0.tar.gz CNPBayes_1.16.0.zip |
| StartedAt: 2020-04-14 19:37:37 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 19:40:53 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 196.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CNPBayes_1.16.0.tar.gz && rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNPBayes.buildbin-libdir CNPBayes_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CNPBayes_1.16.0.zip && rm CNPBayes_1.16.0.tar.gz CNPBayes_1.16.0.zip
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install for i386
* installing *source* package 'CNPBayes' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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++ -std=gnu++11 -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-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CNPBayes.buildbin-libdir/00LOCK-CNPBayes/00new/CNPBayes/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'SummarizedExperiment' for request: 'SummarizedExperiment' when loading 'CNPBayes'
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-3.10-bioc/tmpdir/RtmpcNX1Nk/R.INSTALL19404b7737e5/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 from temporary location
No methods found in package 'SummarizedExperiment' for request: 'SummarizedExperiment' when loading 'CNPBayes'
Warning: Package 'CNPBayes' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package can be loaded from final location
No methods found in package 'SummarizedExperiment' for request: 'SummarizedExperiment' when loading 'CNPBayes'
Warning: Package 'CNPBayes' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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++ -std=gnu++11 -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-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/x64
** testing if installed package can be loaded
No methods found in package 'SummarizedExperiment' for request: 'SummarizedExperiment' when loading 'CNPBayes'
Warning: Package 'CNPBayes' is deprecated and will be removed from Bioconductor
version 3.11
* MD5 sums
packaged installation of 'CNPBayes' as CNPBayes_1.16.0.zip
* DONE (CNPBayes)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CNPBayes' successfully unpacked and MD5 sums checked