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CHECK report for CNPBayes on merida1

This page was generated on 2019-04-16 11:59:05 -0400 (Tue, 16 Apr 2019).

Package 292/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.12.0
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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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.



Installation output

CNPBayes.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

CNPBayes.Rcheck/CNPBayes-Ex.timings

nameusersystemelapsed
CopyNumber-methods0.0120.0020.014
Hyperparameters0.0070.0010.008
HyperparametersMultiBatch0.0010.0000.002
HyperparametersSingleBatch0.0030.0010.004
MB18.118 0.51418.850
MBP13.715 0.47514.390
McmcParams-class0.0060.0000.006
McmcParams0.0000.0000.001
MultiBatchModel227.486 0.89728.588
SingleBatchModel0.3420.0200.362
batch-method0.0050.0050.011
bic-method1.2490.0221.280
burnin-method0.0010.0000.001
chains-method0.0060.0010.007
chromosome0.0510.0000.052
collapseBatch-method0.4210.0050.429
consensusCNP0.2060.0020.209
copyNumber0.0060.0000.006
dfr-method0.0020.0000.002
downSample0.0630.0010.065
eta.0-method0.0010.0000.001
ggplot-functions43.818 5.28850.823
gibbs 9.648 0.22910.283
hyperParams-method0.0030.0000.005
iter-method0.0000.0000.001
k-method0.0880.0010.089
label_switch0.0010.0000.000
logPrior-method0.0010.0000.001
log_lik-method0.0010.0000.001
m2.0-method0.0010.0000.001
mapParams0.0000.0000.001
map_z0.0010.0010.001
mapping0.0020.0000.003
marginalLikelihood-method1.1340.0491.291
marginal_lik0.0010.0000.000
mcmcParams-method0.0020.0000.002
mlParams0.0000.0000.001
modelName0.0010.0000.001
modes-method0.0010.0000.000
mu-method000
muMean0.0010.0000.001
muc0.0010.0010.002
nStarts-method0.0020.0000.002
nu.0-method000
numberObs-method0.0010.0000.001
p000
pic0.0010.0010.001
posteriorPredictive2.4900.0832.824
posteriorSimulation-method0.0590.0010.061
posterior_cases0.0000.0000.001
probz-method0.0010.0000.001
qInverseTau20.0070.0000.008
sigma0.0000.0010.001
sigma2-method0.0010.0000.001
sigma2.0-method000
sigmac0.0120.0160.038
simulateBatchData4.3060.0704.714
simulateData3.1690.2493.568
tau0.0010.0000.001
tau2-method0.0300.0010.032
tauMean0.0020.0010.001
tauc0.0100.0150.027
theta-method0.0010.0010.000
thin-method0.0020.0000.002
upSample26.0470.1587.203
y-method0.0000.0000.001
z-method0.0010.0000.000
zfreq-method000