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CHECK report for BPRMeth on tokay1

This page was generated on 2020-08-07 12:10:48 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BPRMeth PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 190/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.15.3
Chantriolnt-Andreas Kapourani
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BPRMeth
Branch: master
Last Commit: 39fa242
Last Changed Date: 2020-06-10 12:32:32 -0400 (Wed, 10 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BPRMeth
Version: 1.15.3
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BPRMeth.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BPRMeth_1.15.3.tar.gz
StartedAt: 2020-08-07 03:30:35 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 03:35:59 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 323.7 seconds
RetCode: 0
Status:  OK  
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BPRMeth.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BPRMeth_1.15.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BPRMeth.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.15.3'
* package encoding: UTF-8
* 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 ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    libs      2.1Mb
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'BiocStyle'
  All declared Imports should be used.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BPRMeth/libs/i386/BPRMeth.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BPRMeth/libs/x64/BPRMeth.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
cluster_profiles_mle    9.11   0.06    9.17
old_plot_cluster_prof   7.75   0.00    7.78
bpr_cluster_wrap        6.55   0.05    6.59
old_boxplot_cluster_gex 6.34   0.00    6.35
cluster_profiles_vb     5.67   0.09    5.76
boxplot_cluster_expr    5.06   0.19    5.25
plot_cluster_profiles   5.05   0.14    5.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
cluster_profiles_mle    8.46   0.02    8.48
old_boxplot_cluster_gex 7.53   0.00    7.53
old_plot_cluster_prof   7.39   0.02    7.40
cluster_profiles_vb     6.92   0.04    6.96
bpr_cluster_wrap        5.70   0.01    5.72
plot_cluster_profiles   5.58   0.00    5.58
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BPRMeth.Rcheck/00check.log'
for details.



Installation output

BPRMeth.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BPRMeth_1.15.3.tar.gz && rm -rf BPRMeth.buildbin-libdir && mkdir BPRMeth.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BPRMeth.buildbin-libdir BPRMeth_1.15.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BPRMeth_1.15.3.zip && rm BPRMeth_1.15.3.tar.gz BPRMeth_1.15.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3346k  100 3346k    0     0  28.7M      0 --:--:-- --:--:-- --:--:-- 29.7M

install for i386

* installing *source* package 'BPRMeth' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c model_likelihood.cpp -o model_likelihood.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BPRMeth.dll tmp.def RcppExports.o model_likelihood.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BPRMeth.buildbin-libdir/00LOCK-BPRMeth/00new/BPRMeth/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BPRMeth'
    finding HTML links ... done
    BPRMeth                                 html  
    bernoulli_data                          html  
    beta_data                               html  
    binomial_data                           html  
    boxplot_cluster_expr                    html  
    bpr_cluster_wrap                        html  
    bpr_optimize                            html  
    bpr_predict_wrap                        html  
    cluster_profiles_mle                    html  
    cluster_profiles_vb                     html  
    create_anno_region                      html  
    create_basis                            html  
    create_region_object                    html  
    design_matrix                           html  
    encode_expr                             html  
    encode_met                              html  
    eval_functions                          html  
    gaussian_data                           html  
    gex_data                                html  
    impute_bulk_met                         html  
    infer_profiles_gibbs                    html  
    infer_profiles_mle                      html  
    infer_profiles_vb                       html  
    inner_predict_model_expr                html  
    inner_train_model_expr                  html  
    meth_data                               html  
    model_log_likelihood                    html  
    old_boxplot_cluster_gex                 html  
    old_plot_cluster_prof                   html  
    old_plot_fitted_profiles                html  
    partition_bulk_dataset                  html  
    plot_cluster_profiles                   html  
    plot_infer_profiles                     html  
    finding level-2 HTML links ... done

    plot_predicted_expr                     html  
    pool_bs_seq_rep                         html  
    predict_expr                            html  
    preprocess_bs_seq                       html  
    preprocess_final_HTS_data               html  
    process_haib_caltech_wrap               html  
    read_anno                               html  
    read_bs_encode_haib                     html  
    read_chrom_size                         html  
    read_expr                               html  
    read_met                                html  
    read_rna_encode_caltech                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BPRMeth' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c model_likelihood.cpp -o model_likelihood.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BPRMeth.dll tmp.def RcppExports.o model_likelihood.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BPRMeth.buildbin-libdir/BPRMeth/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BPRMeth' as BPRMeth_1.15.3.zip
* DONE (BPRMeth)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BPRMeth' successfully unpacked and MD5 sums checked

Tests output

BPRMeth.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("BPRMeth")
== testthat results  ===========================================================
[ OK: 70 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   5.89    0.32    6.20 

BPRMeth.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("BPRMeth")
== testthat results  ===========================================================
[ OK: 70 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   5.92    0.14    6.06 

Example timings

BPRMeth.Rcheck/examples_i386/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr5.060.195.25
bpr_cluster_wrap6.550.056.59
bpr_optimize1.330.001.33
bpr_predict_wrap101
cluster_profiles_mle9.110.069.17
cluster_profiles_vb5.670.095.76
create_anno_region0.130.000.13
create_basis000
create_region_object000
design_matrix000
eval_functions000
impute_bulk_met1.090.001.09
infer_profiles_gibbs3.060.003.06
infer_profiles_mle1.820.001.81
infer_profiles_vb4.600.004.61
inner_predict_model_expr000
inner_train_model_expr0.040.000.03
old_boxplot_cluster_gex6.340.006.35
old_plot_cluster_prof7.750.007.78
old_plot_fitted_profiles1.140.001.14
partition_bulk_dataset0.030.000.03
plot_cluster_profiles5.050.145.19
plot_infer_profiles3.490.003.49
plot_predicted_expr3.30.03.3
pool_bs_seq_rep0.430.000.64
predict_expr3.350.033.37
preprocess_bs_seq0.150.000.16
preprocess_final_HTS_data0.470.000.50
process_haib_caltech_wrap0.600.020.58
read_anno0.050.000.05
read_bs_encode_haib0.080.010.09
read_chrom_size000
read_expr0.010.000.02
read_met0.030.000.03
read_rna_encode_caltech0.190.000.19

BPRMeth.Rcheck/examples_x64/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr4.550.054.59
bpr_cluster_wrap5.700.015.72
bpr_optimize1.390.001.39
bpr_predict_wrap1.040.001.04
cluster_profiles_mle8.460.028.48
cluster_profiles_vb6.920.046.96
create_anno_region0.10.00.1
create_basis000
create_region_object000
design_matrix000
eval_functions000
impute_bulk_met1.020.001.02
infer_profiles_gibbs4.110.004.11
infer_profiles_mle2.390.002.40
infer_profiles_vb4.490.004.48
inner_predict_model_expr000
inner_train_model_expr0.030.000.03
old_boxplot_cluster_gex7.530.007.53
old_plot_cluster_prof7.390.027.40
old_plot_fitted_profiles1.180.001.19
partition_bulk_dataset0.050.000.05
plot_cluster_profiles5.580.005.58
plot_infer_profiles2.280.002.28
plot_predicted_expr3.030.013.04
pool_bs_seq_rep0.420.000.43
predict_expr3.070.003.06
preprocess_bs_seq0.120.000.12
preprocess_final_HTS_data0.280.020.30
process_haib_caltech_wrap0.440.000.44
read_anno0.050.000.05
read_bs_encode_haib0.040.000.04
read_chrom_size0.020.000.02
read_expr000
read_met0.030.000.03
read_rna_encode_caltech0.090.000.09