BioC 3.4: CHECK report for BPRMeth on morelia

Package: BPRMeth

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BPRMeth_1.0.0.tar.gz

StartedAt: 2017-04-14 23:20:41 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:24:20 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 219.2 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BPRMeth.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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 37.820  0.194  38.034
bpr_cluster_wrap    34.952  0.145  35.138
plot_cluster_prof   34.831  0.133  34.975
bpr_optimize         5.444  0.020   5.474
* 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-3.4-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	37.820	0.194	38.034
bpr_cluster_wrap	34.952	0.145	35.138
bpr_optimize	5.444	0.020	5.474
bpr_predict_wrap	2.769	0.007	2.777
create_basis	0.002	0.000	0.002
create_methyl_region	0.740	0.012	0.751
create_prom_region	0.259	0.004	0.263
eval_functions	0.004	0.000	0.005
plot_cluster_prof	34.831	0.133	34.975
plot_fitted_profiles	3.373	0.008	3.382
plot_scatter_gex	3.035	0.012	3.046
pool_bs_seq_rep	0.735	0.022	0.757
predict_model_gex	0.006	0.000	0.006
preprocess_bs_seq	0.618	0.010	0.629
preprocess_final_HTS_data	0.673	0.007	0.679
process_haib_caltech_wrap	0.870	0.015	0.884
read_bs_bismark_cov	0.001	0.000	0.001
read_bs_encode_haib	0.364	0.005	0.369
read_chrom_size	0.005	0.001	0.005
read_encode_cgi	0.000	0.000	0.001
read_rna_encode_caltech	0.227	0.003	0.229
train_model_gex	0.013	0.000	0.014