Jacob Carey
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CNPBayes |
| Branch: RELEASE_3_8 |
| Last Commit: 01190fc |
| Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:05 -0400 (Tue, 16 Apr 2019).
| Package 292/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNPBayes 1.12.0 Jacob Carey
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CNPBayes |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNPBayes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNPBayes_1.12.0.tar.gz |
| StartedAt: 2019-04-15 23:07:05 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:16:23 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 558.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNPBayes.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNPBayes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNPBayes_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNPBayes.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNPBayes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNPBayes’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNPBayes’ 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 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 ... OK
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ggplot-functions 43.818 5.288 50.823
MultiBatchModel2 27.486 0.897 28.588
MB 18.118 0.514 18.850
MBP 13.715 0.475 14.390
gibbs 9.648 0.229 10.283
upSample2 6.047 0.158 7.203
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 NOTE
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.
CNPBayes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNPBayes ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘CNPBayes’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c miscfunctions.cpp -o miscfunctions.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c multibatch.cpp -o multibatch.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c multibatch_reduced.cpp -o multibatch_reduced.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c pooledvar_reduced.cpp -o pooledvar_reduced.o 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 CNPBayes.so RcppExports.o miscfunctions.o multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/CNPBayes/libs ** 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’ Creating a generic function from function ‘sigma’ in package ‘CNPBayes’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (CNPBayes)
CNPBayes.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, lengths, 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
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: 140 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
191.201 15.980 210.640
CNPBayes.Rcheck/CNPBayes-Ex.timings
| name | user | system | elapsed | |
| CopyNumber-methods | 0.012 | 0.002 | 0.014 | |
| Hyperparameters | 0.007 | 0.001 | 0.008 | |
| HyperparametersMultiBatch | 0.001 | 0.000 | 0.002 | |
| HyperparametersSingleBatch | 0.003 | 0.001 | 0.004 | |
| MB | 18.118 | 0.514 | 18.850 | |
| MBP | 13.715 | 0.475 | 14.390 | |
| McmcParams-class | 0.006 | 0.000 | 0.006 | |
| McmcParams | 0.000 | 0.000 | 0.001 | |
| MultiBatchModel2 | 27.486 | 0.897 | 28.588 | |
| SingleBatchModel | 0.342 | 0.020 | 0.362 | |
| batch-method | 0.005 | 0.005 | 0.011 | |
| bic-method | 1.249 | 0.022 | 1.280 | |
| burnin-method | 0.001 | 0.000 | 0.001 | |
| chains-method | 0.006 | 0.001 | 0.007 | |
| chromosome | 0.051 | 0.000 | 0.052 | |
| collapseBatch-method | 0.421 | 0.005 | 0.429 | |
| consensusCNP | 0.206 | 0.002 | 0.209 | |
| copyNumber | 0.006 | 0.000 | 0.006 | |
| dfr-method | 0.002 | 0.000 | 0.002 | |
| downSample | 0.063 | 0.001 | 0.065 | |
| eta.0-method | 0.001 | 0.000 | 0.001 | |
| ggplot-functions | 43.818 | 5.288 | 50.823 | |
| gibbs | 9.648 | 0.229 | 10.283 | |
| hyperParams-method | 0.003 | 0.000 | 0.005 | |
| iter-method | 0.000 | 0.000 | 0.001 | |
| k-method | 0.088 | 0.001 | 0.089 | |
| label_switch | 0.001 | 0.000 | 0.000 | |
| logPrior-method | 0.001 | 0.000 | 0.001 | |
| log_lik-method | 0.001 | 0.000 | 0.001 | |
| m2.0-method | 0.001 | 0.000 | 0.001 | |
| mapParams | 0.000 | 0.000 | 0.001 | |
| map_z | 0.001 | 0.001 | 0.001 | |
| mapping | 0.002 | 0.000 | 0.003 | |
| marginalLikelihood-method | 1.134 | 0.049 | 1.291 | |
| marginal_lik | 0.001 | 0.000 | 0.000 | |
| mcmcParams-method | 0.002 | 0.000 | 0.002 | |
| mlParams | 0.000 | 0.000 | 0.001 | |
| modelName | 0.001 | 0.000 | 0.001 | |
| modes-method | 0.001 | 0.000 | 0.000 | |
| mu-method | 0 | 0 | 0 | |
| muMean | 0.001 | 0.000 | 0.001 | |
| muc | 0.001 | 0.001 | 0.002 | |
| nStarts-method | 0.002 | 0.000 | 0.002 | |
| nu.0-method | 0 | 0 | 0 | |
| numberObs-method | 0.001 | 0.000 | 0.001 | |
| p | 0 | 0 | 0 | |
| pic | 0.001 | 0.001 | 0.001 | |
| posteriorPredictive | 2.490 | 0.083 | 2.824 | |
| posteriorSimulation-method | 0.059 | 0.001 | 0.061 | |
| posterior_cases | 0.000 | 0.000 | 0.001 | |
| probz-method | 0.001 | 0.000 | 0.001 | |
| qInverseTau2 | 0.007 | 0.000 | 0.008 | |
| sigma | 0.000 | 0.001 | 0.001 | |
| sigma2-method | 0.001 | 0.000 | 0.001 | |
| sigma2.0-method | 0 | 0 | 0 | |
| sigmac | 0.012 | 0.016 | 0.038 | |
| simulateBatchData | 4.306 | 0.070 | 4.714 | |
| simulateData | 3.169 | 0.249 | 3.568 | |
| tau | 0.001 | 0.000 | 0.001 | |
| tau2-method | 0.030 | 0.001 | 0.032 | |
| tauMean | 0.002 | 0.001 | 0.001 | |
| tauc | 0.010 | 0.015 | 0.027 | |
| theta-method | 0.001 | 0.001 | 0.000 | |
| thin-method | 0.002 | 0.000 | 0.002 | |
| upSample2 | 6.047 | 0.158 | 7.203 | |
| y-method | 0.000 | 0.000 | 0.001 | |
| z-method | 0.001 | 0.000 | 0.000 | |
| zfreq-method | 0 | 0 | 0 | |