Chantriolnt-Andreas Kapourani
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BPRMeth |
| Branch: RELEASE_3_8 |
| Last Commit: 8e33e6c |
| Last Changed Date: 2019-01-04 13:20:50 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:28 -0400 (Tue, 16 Apr 2019).
| Package 171/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BPRMeth 1.8.1 Chantriolnt-Andreas Kapourani
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BPRMeth |
| Version: 1.8.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BPRMeth_1.8.1.tar.gz |
| StartedAt: 2019-04-15 22:34:36 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:37:09 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 152.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BPRMeth.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BPRMeth_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BPRMeth.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* 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 5.2Mb
sub-directories of 1Mb or more:
extdata 1.5Mb
libs 1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 7.312 0.020 7.349
bpr_cluster_wrap 5.412 0.020 5.436
old_plot_cluster_prof 5.348 0.000 5.368
cluster_profiles_vb 5.284 0.012 5.306
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BPRMeth ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘BPRMeth’ ... ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -L/usr/local/lib -o BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/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 * DONE (BPRMeth)
BPRMeth.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, 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: 70 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
3.832 0.100 3.940
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 4.596 | 0.032 | 3.941 | |
| bpr_cluster_wrap | 5.412 | 0.020 | 5.436 | |
| bpr_optimize | 1.620 | 0.000 | 1.625 | |
| bpr_predict_wrap | 1.18 | 0.00 | 1.18 | |
| cluster_profiles_mle | 7.312 | 0.020 | 7.349 | |
| cluster_profiles_vb | 5.284 | 0.012 | 5.306 | |
| create_anno_region | 0.524 | 0.000 | 0.177 | |
| create_basis | 0.000 | 0.000 | 0.002 | |
| create_region_object | 0.000 | 0.000 | 0.001 | |
| design_matrix | 0.004 | 0.000 | 0.003 | |
| eval_functions | 0.004 | 0.000 | 0.004 | |
| infer_profiles_gibbs | 3.828 | 0.000 | 3.829 | |
| infer_profiles_mle | 1.424 | 0.000 | 1.424 | |
| infer_profiles_vb | 2.436 | 0.000 | 2.441 | |
| inner_predict_model_expr | 0.008 | 0.000 | 0.007 | |
| inner_train_model_expr | 0.024 | 0.000 | 0.021 | |
| old_boxplot_cluster_gex | 4.192 | 0.000 | 4.197 | |
| old_plot_cluster_prof | 5.348 | 0.000 | 5.368 | |
| old_plot_fitted_profiles | 1.256 | 0.000 | 1.256 | |
| plot_cluster_profiles | 4.456 | 0.024 | 4.486 | |
| plot_infer_profiles | 2.028 | 0.004 | 2.035 | |
| plot_predicted_expr | 2.956 | 0.012 | 2.368 | |
| pool_bs_seq_rep | 0.856 | 0.004 | 0.482 | |
| predict_expr | 2.832 | 0.000 | 2.255 | |
| preprocess_bs_seq | 0.436 | 0.000 | 0.224 | |
| preprocess_final_HTS_data | 1.100 | 0.004 | 0.588 | |
| process_haib_caltech_wrap | 1.204 | 0.000 | 0.667 | |
| read_anno | 0.508 | 0.004 | 0.179 | |
| read_bs_encode_haib | 0.344 | 0.004 | 0.128 | |
| read_chrom_size | 0.224 | 0.000 | 0.066 | |
| read_expr | 0.008 | 0.000 | 0.005 | |
| read_met | 0.240 | 0.000 | 0.072 | |
| read_rna_encode_caltech | 0.516 | 0.000 | 0.221 | |