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CHECK report for BPRMeth on malbec1

This page was generated on 2020-04-15 12:12:06 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BPRMeth_1.12.0.tar.gz
StartedAt: 2020-04-15 04:22:49 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:25:57 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 188.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BPRMeth_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BPRMeth.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ... NOTE
  installed size is  5.4Mb
  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
* 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
cluster_profiles_mle    6.952  0.004   6.995
old_boxplot_cluster_gex 6.164  0.000   6.272
old_plot_cluster_prof   6.144  0.004   6.189
bpr_cluster_wrap        5.860  0.016   5.921
boxplot_cluster_expr    5.700  0.028   5.334
cluster_profiles_vb     5.704  0.000   5.729
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.



Installation output

BPRMeth.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BPRMeth
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘BPRMeth’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c model_likelihood.cpp -o model_likelihood.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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-pc-linux-gnu (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 
  6.176   0.180   6.374 

Example timings

BPRMeth.Rcheck/BPRMeth-Ex.timings

nameusersystemelapsed
boxplot_cluster_expr5.7000.0285.334
bpr_cluster_wrap5.8600.0165.921
bpr_optimize1.9040.0001.914
bpr_predict_wrap1.3120.0001.317
cluster_profiles_mle6.9520.0046.995
cluster_profiles_vb5.7040.0005.729
create_anno_region0.5240.0000.207
create_basis0.0000.0000.002
create_region_object000
design_matrix0.0000.0000.003
eval_functions0.0040.0000.004
impute_bulk_met0.8400.0000.845
infer_profiles_gibbs3.1320.0003.199
infer_profiles_mle2.0200.0042.035
infer_profiles_vb3.0720.0043.094
inner_predict_model_expr0.0120.0000.010
inner_train_model_expr0.0320.0000.029
old_boxplot_cluster_gex6.1640.0006.272
old_plot_cluster_prof6.1440.0046.189
old_plot_fitted_profiles1.4200.0001.424
partition_bulk_dataset0.0400.0000.039
plot_cluster_profiles4.3760.0124.464
plot_infer_profiles2.2280.0002.245
plot_predicted_expr3.4600.0123.092
pool_bs_seq_rep1.1160.0040.695
predict_expr3.2000.0002.625
preprocess_bs_seq0.4520.0000.254
preprocess_final_HTS_data1.1320.0040.717
process_haib_caltech_wrap1.1440.0080.671
read_anno0.4840.0040.164
read_bs_encode_haib0.3960.0040.166
read_chrom_size0.2160.0000.058
read_expr0.0040.0000.012
read_met0.2720.0000.109
read_rna_encode_caltech0.5520.0040.328