BioC 3.5: CHECK report for BPRMeth on tokay2

Package: BPRMeth

Version: 1.2.0

Command: rm -rf BPRMeth.buildbin-libdir BPRMeth.Rcheck && mkdir BPRMeth.buildbin-libdir BPRMeth.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BPRMeth.buildbin-libdir BPRMeth_1.2.0.tar.gz >BPRMeth.Rcheck\00install.out 2>&1 && cp BPRMeth.Rcheck\00install.out BPRMeth-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BPRMeth.buildbin-libdir --install="check:BPRMeth-install.out" --force-multiarch --no-vignettes --timings BPRMeth_1.2.0.tar.gz

StartedAt: 2017-10-17 22:24:46 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:30:37 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 351.2 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BPRMeth.buildbin-libdir BPRMeth_1.2.0.tar.gz >BPRMeth.Rcheck\00install.out 2>&1 && cp BPRMeth.Rcheck\00install.out BPRMeth-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BPRMeth.buildbin-libdir --install="check:BPRMeth-install.out" --force-multiarch --no-vignettes --timings BPRMeth_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BPRMeth.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.2.0'
* 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
boxplot_cluster_gex 29.17   0.05   29.22
plot_cluster_prof   27.19   0.00   27.21
bpr_cluster_wrap    26.19   0.00   26.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
boxplot_cluster_gex 34.67   0.02   34.70
plot_cluster_prof   32.00   0.00   32.00
bpr_cluster_wrap    31.28   0.00   31.29
* 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-3.5-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_1.2.0.zip
* DONE (BPRMeth)

name	user	system	elapsed
boxplot_cluster_gex	29.17	0.05	29.22
bpr_cluster_wrap	26.19	0.00	26.19
bpr_optimize	3.81	0.00	3.81
bpr_predict_wrap	2.22	0.01	2.23
create_basis	0	0	0
create_methyl_region	1.11	0.00	1.17
create_prom_region	0.23	0.00	0.24
eval_functions	0.02	0.00	0.01
plot_cluster_prof	27.19	0.00	27.21
plot_fitted_profiles	3.06	0.02	3.08
plot_scatter_gex	2.45	0.00	2.45
pool_bs_seq_rep	0.58	0.01	0.59
predict_model_gex	0	0	0
preprocess_bs_seq	0.39	0.00	0.39
preprocess_final_HTS_data	0.49	0.00	0.49
process_haib_caltech_wrap	0.61	0.00	0.61
read_bs_bismark_cov	0	0	0
read_bs_encode_haib	0.2	0.0	0.2
read_chrom_size	0	0	0
read_encode_cgi	0	0	0
read_rna_encode_caltech	0.16	0.00	0.16
train_model_gex	0.01	0.00	0.01

name	user	system	elapsed
boxplot_cluster_gex	34.67	0.02	34.70
bpr_cluster_wrap	31.28	0.00	31.29
bpr_optimize	4.82	0.00	4.81
bpr_predict_wrap	2.68	0.00	2.69
create_basis	0	0	0
create_methyl_region	0.80	0.03	0.83
create_prom_region	0.20	0.01	0.22
eval_functions	0.02	0.00	0.01
plot_cluster_prof	32	0	32
plot_fitted_profiles	3.31	0.02	3.33
plot_scatter_gex	3.01	0.00	3.02
pool_bs_seq_rep	0.55	0.01	0.56
predict_model_gex	0	0	0
preprocess_bs_seq	0.41	0.00	0.41
preprocess_final_HTS_data	0.50	0.02	0.51
process_haib_caltech_wrap	0.68	0.00	0.69
read_bs_bismark_cov	0	0	0
read_bs_encode_haib	0.18	0.00	0.17
read_chrom_size	0	0	0
read_encode_cgi	0	0	0
read_rna_encode_caltech	0.17	0.00	0.17
train_model_gex	0.02	0.00	0.01