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CHECK report for BPRMeth on tokay1

This page was generated on 2018-04-12 13:29:03 -0400 (Thu, 12 Apr 2018).

Package 154/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.4.0
Chantriolnt-Andreas Kapourani
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BPRMeth
Branch: RELEASE_3_6
Last Commit: 9c75633
Last Changed Date: 2017-10-30 12:41:23 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BPRMeth
Version: 1.4.0
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_1.4.0.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_1.4.0.tar.gz
StartedAt: 2018-04-11 22:35:18 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:41:18 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 359.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BPRMeth.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running 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_1.4.0.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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BPRMeth.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.4.0'
* 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 whether package 'BPRMeth' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_methyl_region.Rd:11: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_methyl_region.Rd:18: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_prom_region.Rd:11: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_prom_region.Rd:23: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/pool_bs_seq_rep.Rd:20: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/preprocess_bs_seq.Rd:27: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/preprocess_final_HTS_data.Rd:14: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/preprocess_final_HTS_data.Rd:18: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/process_haib_caltech_wrap.Rd:72: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/process_haib_caltech_wrap.Rd:76: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_bs_bismark_cov.Rd:18: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_bs_encode_haib.Rd:18: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_encode_cgi.Rd:16: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_rna_encode_caltech.Rd:18: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BPRMeth.Rcheck/00install.out' for details.
* 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
boxplot_cluster_gex 31.50   0.03   31.53
plot_cluster_prof   31.34   0.00   31.38
bpr_cluster_wrap    26.58   0.00   26.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plot_cluster_prof   38.84   0.01   38.87
boxplot_cluster_gex 35.78   0.00   35.78
bpr_cluster_wrap    33.52   0.00   33.51
bpr_optimize         5.21   0.00    5.22
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BPRMeth.Rcheck/00check.log'
for details.

Installation output

BPRMeth.Rcheck/00install.out


install for i386

* installing *source* package 'BPRMeth' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BPRMeth'
    finding HTML links ... done
    BPRMeth                                 html  
    boxplot_cluster_gex                     html  
    bpr_cluster_wrap                        html  
    bpr_optimize                            html  
    bpr_predict_wrap                        html  
    create_basis                            html  
    create_methyl_region                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_methyl_region.Rd:11: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_methyl_region.Rd:18: missing file link 'GRanges'
    create_prom_region                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_prom_region.Rd:11: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/create_prom_region.Rd:23: missing file link 'GRanges'
    eval_functions                          html  
    gex_data                                html  
    meth_data                               html  
    plot_cluster_prof                       html  
    plot_fitted_profiles                    html  
    plot_scatter_gex                        html  
    pool_bs_seq_rep                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/pool_bs_seq_rep.Rd:20: missing file link 'GRanges'
    predict_model_gex                       html  
    preprocess_bs_seq                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/preprocess_bs_seq.Rd:27: missing file link 'GRanges'
    preprocess_final_HTS_data               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/preprocess_final_HTS_data.Rd:14: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/preprocess_final_HTS_data.Rd:18: missing file link 'GRanges'
    process_haib_caltech_wrap               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/process_haib_caltech_wrap.Rd:72: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/process_haib_caltech_wrap.Rd:76: missing file link 'GRanges'
    read_bs_bismark_cov                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_bs_bismark_cov.Rd:18: missing file link 'GRanges'
    read_bs_encode_haib                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_bs_encode_haib.Rd:18: missing file link 'GRanges'
    read_chrom_size                         html  
    read_encode_cgi                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_encode_cgi.Rd:16: missing file link 'GRanges'
    read_rna_encode_caltech                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8GY7Hd/R.INSTALL61c14921af6/BPRMeth/man/read_rna_encode_caltech.Rd:18: missing file link 'GRanges'
    train_model_gex                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BPRMeth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BPRMeth' as BPRMeth_1.4.0.zip
* DONE (BPRMeth)
In R CMD INSTALL
In R CMD INSTALL

Tests output

BPRMeth.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   3.75    0.15    3.89

BPRMeth.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   5.56    0.14    5.68

Example timings

BPRMeth.Rcheck/examples_i386/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_gex31.50 0.0331.53
bpr_cluster_wrap26.58 0.0026.61
bpr_optimize4.310.004.31
bpr_predict_wrap2.590.002.59
create_basis000
create_methyl_region1.110.011.13
create_prom_region0.220.000.22
eval_functions0.020.000.01
plot_cluster_prof31.34 0.0031.38
plot_fitted_profiles3.370.003.38
plot_scatter_gex2.750.002.83
pool_bs_seq_rep0.640.000.64
predict_model_gex000
preprocess_bs_seq0.430.000.42
preprocess_final_HTS_data0.510.000.52
process_haib_caltech_wrap0.660.000.65
read_bs_bismark_cov000
read_bs_encode_haib0.180.020.20
read_chrom_size000
read_encode_cgi000
read_rna_encode_caltech0.160.000.16
train_model_gex0.030.000.03

BPRMeth.Rcheck/examples_x64/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_gex35.78 0.0035.78
bpr_cluster_wrap33.52 0.0033.51
bpr_optimize5.210.005.22
bpr_predict_wrap3.290.003.28
create_basis000
create_methyl_region0.930.020.95
create_prom_region0.250.000.25
eval_functions0.020.000.02
plot_cluster_prof38.84 0.0138.87
plot_fitted_profiles3.490.003.49
plot_scatter_gex3.230.003.23
pool_bs_seq_rep0.560.000.56
predict_model_gex000
preprocess_bs_seq0.410.000.41
preprocess_final_HTS_data0.510.000.51
process_haib_caltech_wrap0.500.020.52
read_bs_bismark_cov0.020.000.01
read_bs_encode_haib0.180.000.19
read_chrom_size000
read_encode_cgi000
read_rna_encode_caltech0.180.000.17
train_model_gex000