Back to Multiple platform build/check report for BioC 3.6
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CNPBayes on malbec1

This page was generated on 2018-04-12 13:14:15 -0400 (Thu, 12 Apr 2018).

Package 263/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.8.0
Jacob Carey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CNPBayes
Branch: RELEASE_3_6
Last Commit: 1534e14
Last Changed Date: 2017-10-30 12:41:08 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNPBayes
Version: 1.8.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.8.0.tar.gz
StartedAt: 2018-04-11 22:23:31 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:31:05 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 454.9 seconds
RetCode: 0
Status:  OK 
CheckDir: CNPBayes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CNPBayes_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CNPBayes.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ... NOTE
  installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  12.6Mb
* 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 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ggplot-functions 7.212  0.040   7.285
ggPredictive     5.928  0.004   5.945
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.



Installation output

CNPBayes.Rcheck/00install.out

* installing *source* package ‘CNPBayes’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c miscfunctions.cpp -o miscfunctions.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c multibatch.cpp -o multibatch.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c multibatch_pooledvar_reduced.cpp -o multibatch_pooledvar_reduced.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c multibatch_reduced.cpp -o multibatch_reduced.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c singlebatch.cpp -o singlebatch.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c singlebatch_pooledvar_reduced.cpp -o singlebatch_pooledvar_reduced.o
singlebatch_pooledvar_reduced.cpp: In function ‘Rcpp::NumericVector full_theta_pooled(Rcpp::S4)’:
singlebatch_pooledvar_reduced.cpp:46:10: warning: unused variable ‘prod’ [-Wunused-variable]
   double prod ;
          ^
singlebatch_pooledvar_reduced.cpp: In function ‘Rcpp::S4 reduced_sigma_pooled(Rcpp::S4)’:
singlebatch_pooledvar_reduced.cpp:86:7: warning: unused variable ‘K’ [-Wunused-variable]
   int K = thetastar.size() ;
       ^
singlebatch_pooledvar_reduced.cpp: In function ‘Rcpp::S4 reduced_mu_pooled(Rcpp::S4)’:
singlebatch_pooledvar_reduced.cpp:330:7: warning: unused variable ‘K’ [-Wunused-variable]
   int K = thetastar.size() ;
       ^
singlebatch_pooledvar_reduced.cpp: In function ‘Rcpp::NumericVector p_nu0_reduced_pooled(Rcpp::S4)’:
singlebatch_pooledvar_reduced.cpp:617:7: warning: unused variable ‘N’ [-Wunused-variable]
   int N = x.size() ;
       ^
singlebatch_pooledvar_reduced.cpp: In function ‘Rcpp::S4 reduced_s20_pooled(Rcpp::S4)’:
singlebatch_pooledvar_reduced.cpp:682:7: warning: unused variable ‘K’ [-Wunused-variable]
   int K = thetastar.size() ;
       ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c singlebatch_reduced.cpp -o singlebatch_reduced.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c update.cpp -o update.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o CNPBayes.so RcppExports.o miscfunctions.o multibatch.o multibatch_pooledvar.o multibatch_pooledvar_reduced.o multibatch_reduced.o singlebatch.o singlebatch_pooledvar.o singlebatch_pooledvar_reduced.o singlebatch_reduced.o update.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/CNPBayes.Rcheck/CNPBayes/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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: 169 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
163.072   0.472 164.444 

Example timings

CNPBayes.Rcheck/CNPBayes-Ex.timings

nameusersystemelapsed
CopyNumber-methods0.0040.0040.008
Hyperparameters0.0080.0000.005
HyperparametersMultiBatch0.0080.0000.009
HyperparametersSingleBatch0.0000.0000.002
McmcParams-class0.0240.0000.021
McmcParams0.0000.0000.001
MultiBatchModel20.7720.0040.774
SingleBatchModel20.1000.0000.101
batch-method0.0080.0000.011
bic-method1.0840.0081.091
burnin-method0.0040.0000.001
chains-method0.0040.0000.004
chromosome000
collapseBatch-method0.0120.0000.010
combinePlates-method0.0320.0000.032
consensusCNP0.4640.0040.468
copyNumber0.0400.0040.046
eta.0-method0.0000.0000.001
ggPredictive5.9280.0045.945
ggplot-functions7.2120.0407.285
gibbs0.0280.0000.025
gibbs_all0.0280.0000.030
gibbs_pooled0.0240.0040.030
hyperParams-method0.0000.0000.002
iter-method0.0000.0000.001
k-method0.0600.0040.062
label_switch0.0000.0000.001
logPrior-method000
log_lik-method0.0040.0000.000
m2.0-method0.0000.0000.001
mapComponents0.0000.0040.005
mapParams000
map_z0.0000.0040.005
mapping0.0040.0000.002
marginalLikelihood-method0.5400.0040.545
marginal_lik000
mcmcParams-method0.0000.0000.001
mlParams000
modes-method000
mu-method000
muMean0.0000.0000.001
muc0.0000.0000.001
nStarts-method0.0000.0000.002
nu.0-method0.0000.0000.001
numberObs-method000
p0.0040.0000.004
pic0.0000.0000.001
posteriorPredictive2.5120.0002.511
posteriorSimulation-method0.0400.0000.041
posterior_cases0.0080.0000.011
probz-method0.0120.0080.021
qInverseTau20.020.000.02
sigma0.0000.0000.001
sigma2-method0.0000.0000.001
sigma2.0-method000
sigmac000
simulateBatchData0.0160.0000.016
simulateData0.0280.0000.027
tau0.0000.0000.001
tau2-method0.0280.0000.028
tauMean0.0040.0000.001
tauc000
theta-method0.0080.0000.007
thin-method0.0000.0000.002
tile-functions3.0840.0003.088
y-method0.0000.0080.008
z-method0.0080.0000.004
zfreq-method0.0000.0000.001