BioC 3.6: CHECK report for BPRMeth on tokay1

Package: BPRMeth

Version: 1.3.0

Command: rm -rf BPRMeth.buildbin-libdir BPRMeth.Rcheck && mkdir BPRMeth.buildbin-libdir BPRMeth.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BPRMeth.buildbin-libdir BPRMeth_1.3.0.tar.gz >BPRMeth.Rcheck\00install.out 2>&1 && cp BPRMeth.Rcheck\00install.out BPRMeth-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BPRMeth.buildbin-libdir --install="check:BPRMeth-install.out" --force-multiarch --no-vignettes --timings BPRMeth_1.3.0.tar.gz

StartedAt: 2017-08-15 22:05:43 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:11:45 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 361.8 seconds

RetCode: 0

Status:  OK

CheckDir: BPRMeth.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BPRMeth.buildbin-libdir BPRMeth.Rcheck && mkdir BPRMeth.buildbin-libdir BPRMeth.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BPRMeth.buildbin-libdir BPRMeth_1.3.0.tar.gz >BPRMeth.Rcheck\00install.out 2>&1 && cp BPRMeth.Rcheck\00install.out BPRMeth-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BPRMeth.buildbin-libdir --install="check:BPRMeth-install.out" --force-multiarch --no-vignettes --timings BPRMeth_1.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BPRMeth.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BPRMeth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BPRMeth' version '1.3.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plot_cluster_prof   33.83   0.02   33.85
boxplot_cluster_gex 30.26   0.03   30.30
bpr_cluster_wrap    29.05   0.02   29.06
bpr_optimize         5.01   0.00    5.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plot_cluster_prof   37.69   0.00   37.69
boxplot_cluster_gex 36.50   0.01   36.52
bpr_cluster_wrap    34.16   0.00   34.16
bpr_optimize         5.29   0.00    5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BPRMeth.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'BPRMeth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BPRMeth' as BPRMeth_1.3.0.zip
* DONE (BPRMeth)

name	user	system	elapsed
boxplot_cluster_gex	30.26	0.03	30.30
bpr_cluster_wrap	29.05	0.02	29.06
bpr_optimize	5.01	0.00	5.01
bpr_predict_wrap	3.03	0.00	3.03
create_basis	0	0	0
create_methyl_region	0.93	0.00	0.92
create_prom_region	0.26	0.00	0.27
eval_functions	0.03	0.00	0.03
plot_cluster_prof	33.83	0.02	33.85
plot_fitted_profiles	3.03	0.00	3.03
plot_scatter_gex	2.69	0.01	2.70
pool_bs_seq_rep	0.59	0.00	0.59
predict_model_gex	0.02	0.00	0.02
preprocess_bs_seq	0.39	0.00	0.39
preprocess_final_HTS_data	0.48	0.02	0.50
process_haib_caltech_wrap	0.52	0.00	0.52
read_bs_bismark_cov	0	0	0
read_bs_encode_haib	0.18	0.01	0.19
read_chrom_size	0	0	0
read_encode_cgi	0	0	0
read_rna_encode_caltech	0.31	0.00	0.32
train_model_gex	0.02	0.00	0.01

name	user	system	elapsed
boxplot_cluster_gex	36.50	0.01	36.52
bpr_cluster_wrap	34.16	0.00	34.16
bpr_optimize	5.29	0.00	5.29
bpr_predict_wrap	3.32	0.00	3.32
create_basis	0	0	0
create_methyl_region	0.92	0.04	0.95
create_prom_region	0.25	0.00	0.25
eval_functions	0.01	0.00	0.01
plot_cluster_prof	37.69	0.00	37.69
plot_fitted_profiles	3.49	0.01	3.50
plot_scatter_gex	3.32	0.00	3.33
pool_bs_seq_rep	0.83	0.00	0.83
predict_model_gex	0.02	0.00	0.01
preprocess_bs_seq	0.28	0.00	0.28
preprocess_final_HTS_data	0.53	0.00	0.54
process_haib_caltech_wrap	0.69	0.00	0.68
read_bs_bismark_cov	0	0	0
read_bs_encode_haib	0.22	0.00	0.22
read_chrom_size	0	0	0
read_encode_cgi	0.01	0.00	0.02
read_rna_encode_caltech	0.28	0.00	0.28
train_model_gex	0.02	0.00	0.01