Package: BPRMeth

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BPRMeth_1.4.0.tar.gz

StartedAt: 2018-04-12 01:06:17 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:09:57 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 220.2 seconds

RetCode: 0

Status:  OK

CheckDir: BPRMeth.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BPRMeth_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BPRMeth.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 ‘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 ... 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 sizes of PDF files under ‘inst/doc’ ... 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
boxplot_cluster_gex 39.516  0.185  40.588
plot_cluster_prof   35.344  0.072  35.872
bpr_cluster_wrap    34.374  0.078  34.914
bpr_optimize         5.689  0.014   5.770
* 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: OK

* installing *source* package ‘BPRMeth’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BPRMeth)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, 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

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: 57 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.506   0.130   3.647 

name	user	system	elapsed
boxplot_cluster_gex	39.516	0.185	40.588
bpr_cluster_wrap	34.374	0.078	34.914
bpr_optimize	5.689	0.014	5.770
bpr_predict_wrap	3.241	0.007	3.287
create_basis	0.001	0.000	0.002
create_methyl_region	1.125	0.010	1.139
create_prom_region	0.285	0.002	0.292
eval_functions	0.022	0.001	0.025
plot_cluster_prof	35.344	0.072	35.872
plot_fitted_profiles	3.479	0.007	3.507
plot_scatter_gex	3.267	0.007	3.319
pool_bs_seq_rep	0.915	0.022	0.943
predict_model_gex	0.006	0.000	0.007
preprocess_bs_seq	0.378	0.010	0.396
preprocess_final_HTS_data	0.670	0.010	0.687
process_haib_caltech_wrap	0.657	0.010	0.681
read_bs_bismark_cov	0.000	0.000	0.001
read_bs_encode_haib	0.257	0.006	0.269
read_chrom_size	0.005	0.000	0.011
read_encode_cgi	0.001	0.000	0.001
read_rna_encode_caltech	0.223	0.001	0.230
train_model_gex	0.016	0.000	0.017