BioC 3.5: CHECK report for BPRMeth on oaxaca

Package: BPRMeth

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BPRMeth_1.1.0.tar.gz

StartedAt: 2017-03-03 23:49:37 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:53:14 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 216.8 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BPRMeth.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
boxplot_cluster_gex 37.554  0.174  37.742
plot_cluster_prof   35.623  0.127  35.760
bpr_cluster_wrap    32.830  0.131  32.972
* 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-3.5-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
boxplot_cluster_gex	37.554	0.174	37.742
bpr_cluster_wrap	32.830	0.131	32.972
bpr_optimize	4.469	0.009	4.478
bpr_predict_wrap	2.631	0.009	2.640
create_basis	0.001	0.000	0.001
create_methyl_region	0.976	0.006	0.982
create_prom_region	0.249	0.002	0.251
eval_functions	0.021	0.000	0.021
plot_cluster_prof	35.623	0.127	35.760
plot_fitted_profiles	3.996	0.013	4.029
plot_scatter_gex	3.766	0.010	3.807
pool_bs_seq_rep	1.146	0.027	1.172
predict_model_gex	0.009	0.001	0.009
preprocess_bs_seq	0.506	0.012	0.518
preprocess_final_HTS_data	0.929	0.008	0.937
process_haib_caltech_wrap	1.113	0.018	1.132
read_bs_bismark_cov	0.000	0.000	0.001
read_bs_encode_haib	0.386	0.008	0.394
read_chrom_size	0.005	0.001	0.006
read_encode_cgi	0	0	0
read_rna_encode_caltech	0.274	0.002	0.276
train_model_gex	0.022	0.001	0.022