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CHECK report for BPRMeth on merida2

This page was generated on 2019-04-09 13:34:18 -0400 (Tue, 09 Apr 2019).

Package 178/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.9.4
Chantriolnt-Andreas Kapourani
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BPRMeth
Branch: master
Last Commit: abc23bd
Last Changed Date: 2019-02-16 06:30:29 -0400 (Sat, 16 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: BPRMeth
Version: 1.9.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BPRMeth_1.9.4.tar.gz
StartedAt: 2019-04-08 23:34:53 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:37:47 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 174.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BPRMeth_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BPRMeth.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BPRMeth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BPRMeth’ version ‘1.9.4’
* 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 ‘BPRMeth’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
bpr_cluster_wrap        5.985  0.873   5.739
old_plot_cluster_prof   6.011  0.099   6.144
old_boxplot_cluster_gex 6.005  0.085   6.139
cluster_profiles_mle    5.500  0.131   5.673
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.



Installation output

BPRMeth.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BPRMeth
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BPRMeth’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2  -c model_likelihood.cpp -o model_likelihood.o
clang++ -std=gnu++11 -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 BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -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/3.6/Resources/library/BPRMeth/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BPRMeth)

Tests output

BPRMeth.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(BPRMeth)
Loading required package: GenomicRanges
Loading required package: stats4
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, 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

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("BPRMeth")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 70 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.106   0.285   4.392 

Example timings

BPRMeth.Rcheck/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr4.3440.4724.467
bpr_cluster_wrap5.9850.8735.739
bpr_optimize1.8080.0121.829
bpr_predict_wrap1.3730.0051.383
cluster_profiles_mle5.5000.1315.673
cluster_profiles_vb4.6800.2414.972
create_anno_region0.3530.3510.095
create_basis0.0110.0120.002
create_region_object0.0020.0020.000
design_matrix0.0150.0150.003
eval_functions0.0250.0220.006
infer_profiles_gibbs4.1240.4163.942
infer_profiles_mle1.8650.0071.901
infer_profiles_vb3.1000.0553.186
inner_predict_model_expr0.0110.0010.012
inner_train_model_expr0.0330.0020.036
old_boxplot_cluster_gex6.0050.0856.139
old_plot_cluster_prof6.0110.0996.144
old_plot_fitted_profiles1.0160.0031.025
plot_cluster_profiles3.6570.1873.859
plot_infer_profiles1.7550.0581.820
plot_predicted_expr1.9200.2711.897
pool_bs_seq_rep1.5441.6410.423
predict_expr1.8910.1681.934
preprocess_bs_seq0.7620.8860.192
preprocess_final_HTS_data1.8462.0420.476
process_haib_caltech_wrap1.7591.7600.515
read_anno0.1380.1420.038
read_bs_encode_haib0.3130.3400.078
read_chrom_size0.0320.0290.007
read_expr0.0150.0160.004
read_met0.1230.1280.030
read_rna_encode_caltech0.7770.8160.191