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CHECK report for BPRMeth on merida1

This page was generated on 2020-04-15 12:44:35 -0400 (Wed, 15 Apr 2020).

Package 191/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.12.0
Chantriolnt-Andreas Kapourani
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BPRMeth
Branch: RELEASE_3_10
Last Commit: ddd4beb
Last Changed Date: 2019-10-29 13:10:14 -0400 (Tue, 29 Oct 2019)
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 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BPRMeth
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BPRMeth_1.12.0.tar.gz
StartedAt: 2020-04-15 00:49:11 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:52:27 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 195.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BPRMeth_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BPRMeth.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
bpr_cluster_wrap        7.760  0.327   7.927
cluster_profiles_mle    7.882  0.182   8.337
old_plot_cluster_prof   5.973  0.118   6.143
cluster_profiles_vb     5.851  0.174   6.154
old_boxplot_cluster_gex 5.632  0.082   5.762
boxplot_cluster_expr    5.132  0.332   5.481
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.



Installation output

BPRMeth.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BPRMeth
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BPRMeth’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp  -fPIC  -Wall -g -O2  -c model_likelihood.cpp -o model_likelihood.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BPRMeth/00new/BPRMeth/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BPRMeth)

Tests output

BPRMeth.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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: 70 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  6.567   0.394   6.989 

Example timings

BPRMeth.Rcheck/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr5.1320.3325.481
bpr_cluster_wrap7.7600.3277.927
bpr_optimize2.3680.0092.472
bpr_predict_wrap1.5800.0061.608
cluster_profiles_mle7.8820.1828.337
cluster_profiles_vb5.8510.1746.154
create_anno_region1.3020.0570.150
create_basis0.0080.0100.003
create_region_object0.0010.0020.000
design_matrix0.0110.0080.005
eval_functions0.0170.0160.007
impute_bulk_met0.9790.1150.925
infer_profiles_gibbs3.1350.0193.195
infer_profiles_mle1.8310.0121.876
infer_profiles_vb2.9120.0542.990
inner_predict_model_expr0.0110.0010.011
inner_train_model_expr0.0340.0010.036
old_boxplot_cluster_gex5.6320.0825.762
old_plot_cluster_prof5.9730.1186.143
old_plot_fitted_profiles1.3110.0031.327
partition_bulk_dataset0.0470.0000.048
plot_cluster_profiles4.2650.1414.436
plot_infer_profiles2.0630.0662.143
plot_predicted_expr2.1300.2102.134
pool_bs_seq_rep1.2731.2370.499
predict_expr2.2830.1052.319
preprocess_bs_seq0.6040.6440.193
preprocess_final_HTS_data3.0140.9850.554
process_haib_caltech_wrap1.4121.3060.580
read_anno0.1910.1680.058
read_bs_encode_haib0.3210.2980.092
read_chrom_size0.0260.0210.007
read_expr0.0110.0100.003
read_met0.1800.1710.053
read_rna_encode_caltech0.6380.4960.198