Jacob Carey
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CNPBayes |
| Branch: RELEASE_3_7 |
| Last Commit: 103b6b1 |
| Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:55:36 -0400 (Wed, 17 Oct 2018).
| Package 276/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNPBayes 1.10.0 Jacob Carey
| malbec2 | Linux (Ubuntu 16.04.1 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 | |
| Package: CNPBayes |
| Version: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2018-10-16 20:35:39 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:43:00 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 441.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CNPBayes.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CNPBayes.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ... 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 ... NOTE
copyNumber,SingleBatchCopyNumber: no visible binding for global
variable ‘theta.star’
Undefined global functions or variables:
theta.star
* 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 ... WARNING
Undocumented arguments in documentation object 'marginal_lik'
‘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 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 6.852 0.215 7.134
ggPredictive 6.259 0.115 6.422
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.
CNPBayes.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNPBayes
###
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* 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_pooledvar_reduced.cpp -o multibatch_pooledvar_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 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 singlebatch.cpp -o singlebatch.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 singlebatch_pooledvar.cpp -o singlebatch_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 singlebatch_pooledvar_reduced.cpp -o singlebatch_pooledvar_reduced.o
singlebatch_pooledvar_reduced.cpp:46:10: warning: unused variable 'prod' [-Wunused-variable]
double prod ;
^
singlebatch_pooledvar_reduced.cpp:86:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
singlebatch_pooledvar_reduced.cpp:330:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
singlebatch_pooledvar_reduced.cpp:617:7: warning: unused variable 'N' [-Wunused-variable]
int N = x.size() ;
^
singlebatch_pooledvar_reduced.cpp:682:7: warning: unused variable 'K' [-Wunused-variable]
int K = thetastar.size() ;
^
5 warnings generated.
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 singlebatch_reduced.cpp -o singlebatch_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 update.cpp -o update.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_pooledvar_reduced.o multibatch_reduced.o singlebatch.o singlebatch_pooledvar.o singlebatch_pooledvar_reduced.o singlebatch_reduced.o update.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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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")
── 1. Failure: extdata is current (@test_currentExtData.R#9) ──────────────────
`grl` not identical to `grl2`.
Attributes: < Component "class": 1 string mismatch >
Attributes: < Component "partitioning": Attributes: < Component "elementType": 1 string mismatch > >
Attributes: < Component "unlistData": Attributes: < Names: 5 string mismatches > >
Attributes: < Component "unlistData": Attributes: < Length mismatch: comparison on first 7 components > >
Attributes: < Component "unlistData": Attributes: < Component 3: Modes: list, character > >
Attributes: < Component "unlistData": Attributes: < Component 3: Length mismatch: comparison on first 0 components > >
Attributes: < Component "unlistData": Attributes: < Component 4: Modes: S4, list > >
Attributes: < Component "unlistData": Attributes: < Component 4: Lengths: 25, 0 > >
Attributes: < Component "unlistData": Attributes: < Component 4: Attributes: < Modes: list, NULL > > >
...
══ testthat results ═══════════════════════════════════════════════════════════
OK: 168 SKIPPED: 1 FAILED: 1
1. Failure: extdata is current (@test_currentExtData.R#9)
Error: testthat unit tests failed
recover called non-interactively; frames dumped, use debugger() to view
>
> proc.time()
user system elapsed
189.786 8.978 204.453
CNPBayes.Rcheck/CNPBayes-Ex.timings
| name | user | system | elapsed | |
| CopyNumber-methods | 0.072 | 0.008 | 0.081 | |
| Hyperparameters | 0.009 | 0.001 | 0.010 | |
| HyperparametersMultiBatch | 0.002 | 0.000 | 0.002 | |
| HyperparametersSingleBatch | 0.004 | 0.000 | 0.005 | |
| McmcParams-class | 0.011 | 0.001 | 0.012 | |
| McmcParams | 0.003 | 0.000 | 0.003 | |
| MultiBatchModel2 | 0.556 | 0.019 | 0.584 | |
| SingleBatchModel2 | 0.065 | 0.002 | 0.068 | |
| batch-method | 0.016 | 0.010 | 0.025 | |
| bic-method | 1.100 | 0.031 | 1.138 | |
| burnin-method | 0.002 | 0.000 | 0.003 | |
| chains-method | 0.007 | 0.000 | 0.007 | |
| chromosome | 0.001 | 0.000 | 0.001 | |
| collapseBatch-method | 0.015 | 0.000 | 0.015 | |
| combinePlates-method | 0.015 | 0.001 | 0.015 | |
| consensusCNP | 0.300 | 0.010 | 0.312 | |
| copyNumber | 0.411 | 0.087 | 0.502 | |
| eta.0-method | 0.002 | 0.000 | 0.003 | |
| ggPredictive | 6.259 | 0.115 | 6.422 | |
| ggplot-functions | 6.852 | 0.215 | 7.134 | |
| gibbs | 0.038 | 0.006 | 0.045 | |
| gibbs_all | 0.025 | 0.003 | 0.028 | |
| gibbs_pooled | 0.029 | 0.002 | 0.032 | |
| hyperParams-method | 0.004 | 0.000 | 0.005 | |
| iter-method | 0.001 | 0.000 | 0.002 | |
| k-method | 0.063 | 0.001 | 0.064 | |
| label_switch | 0.001 | 0.000 | 0.002 | |
| logPrior-method | 0.001 | 0.000 | 0.001 | |
| log_lik-method | 0.001 | 0.000 | 0.001 | |
| m2.0-method | 0.002 | 0.000 | 0.001 | |
| mapComponents | 0.155 | 0.003 | 0.159 | |
| mapParams | 0.002 | 0.000 | 0.002 | |
| map_z | 0.008 | 0.008 | 0.016 | |
| mapping | 0.035 | 0.001 | 0.037 | |
| marginalLikelihood-method | 0.508 | 0.035 | 0.556 | |
| marginal_lik | 0.001 | 0.000 | 0.001 | |
| mcmcParams-method | 0.001 | 0.000 | 0.002 | |
| mlParams | 0.001 | 0.001 | 0.001 | |
| modes-method | 0.001 | 0.000 | 0.001 | |
| mu-method | 0.001 | 0.000 | 0.001 | |
| muMean | 0.001 | 0.000 | 0.001 | |
| muc | 0.000 | 0.000 | 0.001 | |
| nStarts-method | 0.002 | 0.000 | 0.002 | |
| nu.0-method | 0.001 | 0.000 | 0.001 | |
| numberObs-method | 0.001 | 0.001 | 0.001 | |
| p | 0.002 | 0.000 | 0.001 | |
| pic | 0.001 | 0.000 | 0.001 | |
| posteriorPredictive | 2.523 | 0.125 | 2.672 | |
| posteriorSimulation-method | 0.047 | 0.007 | 0.054 | |
| posterior_cases | 0.011 | 0.001 | 0.011 | |
| probz-method | 0.030 | 0.031 | 0.062 | |
| qInverseTau2 | 0.009 | 0.001 | 0.010 | |
| sigma | 0.001 | 0.000 | 0.002 | |
| sigma2-method | 0.002 | 0.001 | 0.002 | |
| sigma2.0-method | 0.002 | 0.000 | 0.002 | |
| sigmac | 0.001 | 0.000 | 0.001 | |
| simulateBatchData | 0.024 | 0.002 | 0.027 | |
| simulateData | 0.033 | 0.006 | 0.039 | |
| tau | 0.001 | 0.000 | 0.001 | |
| tau2-method | 0.043 | 0.001 | 0.046 | |
| tauMean | 0.002 | 0.000 | 0.002 | |
| tauc | 0.002 | 0.000 | 0.002 | |
| theta-method | 0.012 | 0.001 | 0.014 | |
| thin-method | 0.003 | 0.001 | 0.003 | |
| tile-functions | 4.705 | 0.060 | 4.811 | |
| y-method | 0.012 | 0.012 | 0.025 | |
| z-method | 0.008 | 0.010 | 0.018 | |
| zfreq-method | 0.002 | 0.000 | 0.001 | |