Chantriolnt-Andreas Kapourani
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BPRMeth |
| Branch: RELEASE_3_11 |
| Last Commit: 451cdaf |
| Last Changed Date: 2020-07-16 17:39:39 -0400 (Thu, 16 Jul 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:08 -0400 (Sat, 17 Oct 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 196/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BPRMeth 1.14.1 Chantriolnt-Andreas Kapourani
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BPRMeth |
| Version: 1.14.1 |
| 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_1.14.1.tar.gz |
| StartedAt: 2020-10-16 23:12:31 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:16:37 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 245.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BPRMeth.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BPRMeth.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.1’
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cluster_profiles_mle 6.938 0.152 7.104
bpr_cluster_wrap 6.986 0.102 7.095
old_boxplot_cluster_gex 6.389 0.116 6.508
old_plot_cluster_prof 6.367 0.108 6.482
cluster_profiles_vb 5.811 0.138 5.955
* 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-3.11-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BPRMeth ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘BPRMeth’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c model_likelihood.cpp -o model_likelihood.o clang++ -mmacosx-version-min=10.13 -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 -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-darwin18/8.2.0 -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/4.0/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)
BPRMeth.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
7.503 0.498 8.065
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 4.445 | 0.296 | 4.746 | |
| bpr_cluster_wrap | 6.986 | 0.102 | 7.095 | |
| bpr_optimize | 1.876 | 0.008 | 1.885 | |
| bpr_predict_wrap | 1.286 | 0.005 | 1.291 | |
| cluster_profiles_mle | 6.938 | 0.152 | 7.104 | |
| cluster_profiles_vb | 5.811 | 0.138 | 5.955 | |
| create_anno_region | 0.117 | 0.001 | 0.119 | |
| create_basis | 0.003 | 0.001 | 0.003 | |
| create_region_object | 0.000 | 0.000 | 0.001 | |
| design_matrix | 0.003 | 0.001 | 0.004 | |
| eval_functions | 0.004 | 0.001 | 0.004 | |
| impute_bulk_met | 1.078 | 0.003 | 1.081 | |
| infer_profiles_gibbs | 3.373 | 0.023 | 3.398 | |
| infer_profiles_mle | 2.335 | 0.011 | 2.349 | |
| infer_profiles_vb | 3.131 | 0.052 | 3.188 | |
| inner_predict_model_expr | 0.007 | 0.001 | 0.008 | |
| inner_train_model_expr | 0.037 | 0.002 | 0.039 | |
| old_boxplot_cluster_gex | 6.389 | 0.116 | 6.508 | |
| old_plot_cluster_prof | 6.367 | 0.108 | 6.482 | |
| old_plot_fitted_profiles | 1.377 | 0.013 | 1.393 | |
| partition_bulk_dataset | 0.042 | 0.000 | 0.042 | |
| plot_cluster_profiles | 4.206 | 0.188 | 4.414 | |
| plot_infer_profiles | 2.575 | 0.066 | 2.668 | |
| plot_predicted_expr | 2.278 | 0.065 | 2.371 | |
| pool_bs_seq_rep | 0.461 | 0.013 | 0.479 | |
| predict_expr | 2.382 | 0.052 | 2.458 | |
| preprocess_bs_seq | 0.187 | 0.004 | 0.192 | |
| preprocess_final_HTS_data | 0.518 | 0.013 | 0.539 | |
| process_haib_caltech_wrap | 0.592 | 0.016 | 0.615 | |
| read_anno | 0.055 | 0.002 | 0.056 | |
| read_bs_encode_haib | 0.080 | 0.003 | 0.084 | |
| read_chrom_size | 0.005 | 0.001 | 0.006 | |
| read_expr | 0.003 | 0.000 | 0.003 | |
| read_met | 0.042 | 0.001 | 0.044 | |
| read_rna_encode_caltech | 0.183 | 0.004 | 0.188 | |