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) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:12:06 -0400 (Wed, 15 Apr 2020).
| Package 191/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BPRMeth 1.12.0 Chantriolnt-Andreas Kapourani
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### /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
###
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* 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.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 5.700 | 0.028 | 5.334 | |
| bpr_cluster_wrap | 5.860 | 0.016 | 5.921 | |
| bpr_optimize | 1.904 | 0.000 | 1.914 | |
| bpr_predict_wrap | 1.312 | 0.000 | 1.317 | |
| cluster_profiles_mle | 6.952 | 0.004 | 6.995 | |
| cluster_profiles_vb | 5.704 | 0.000 | 5.729 | |
| create_anno_region | 0.524 | 0.000 | 0.207 | |
| create_basis | 0.000 | 0.000 | 0.002 | |
| create_region_object | 0 | 0 | 0 | |
| design_matrix | 0.000 | 0.000 | 0.003 | |
| eval_functions | 0.004 | 0.000 | 0.004 | |
| impute_bulk_met | 0.840 | 0.000 | 0.845 | |
| infer_profiles_gibbs | 3.132 | 0.000 | 3.199 | |
| infer_profiles_mle | 2.020 | 0.004 | 2.035 | |
| infer_profiles_vb | 3.072 | 0.004 | 3.094 | |
| inner_predict_model_expr | 0.012 | 0.000 | 0.010 | |
| inner_train_model_expr | 0.032 | 0.000 | 0.029 | |
| old_boxplot_cluster_gex | 6.164 | 0.000 | 6.272 | |
| old_plot_cluster_prof | 6.144 | 0.004 | 6.189 | |
| old_plot_fitted_profiles | 1.420 | 0.000 | 1.424 | |
| partition_bulk_dataset | 0.040 | 0.000 | 0.039 | |
| plot_cluster_profiles | 4.376 | 0.012 | 4.464 | |
| plot_infer_profiles | 2.228 | 0.000 | 2.245 | |
| plot_predicted_expr | 3.460 | 0.012 | 3.092 | |
| pool_bs_seq_rep | 1.116 | 0.004 | 0.695 | |
| predict_expr | 3.200 | 0.000 | 2.625 | |
| preprocess_bs_seq | 0.452 | 0.000 | 0.254 | |
| preprocess_final_HTS_data | 1.132 | 0.004 | 0.717 | |
| process_haib_caltech_wrap | 1.144 | 0.008 | 0.671 | |
| read_anno | 0.484 | 0.004 | 0.164 | |
| read_bs_encode_haib | 0.396 | 0.004 | 0.166 | |
| read_chrom_size | 0.216 | 0.000 | 0.058 | |
| read_expr | 0.004 | 0.000 | 0.012 | |
| read_met | 0.272 | 0.000 | 0.109 | |
| read_rna_encode_caltech | 0.552 | 0.004 | 0.328 | |