Chantriolnt-Andreas Kapourani
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BPRMeth |
| Branch: RELEASE_3_9 |
| Last Commit: b4db474 |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:59:09 -0400 (Wed, 16 Oct 2019).
| Package 181/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BPRMeth 1.10.0 Chantriolnt-Andreas Kapourani
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BPRMeth |
| Version: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2019-10-16 01:01:26 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:05:27 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 240.9 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BPRMeth.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 ... 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
old_boxplot_cluster_gex 8.598 0.457 9.057
bpr_cluster_wrap 7.855 1.141 8.375
old_plot_cluster_prof 8.062 0.470 8.534
cluster_profiles_mle 7.603 0.441 8.044
cluster_profiles_vb 6.790 0.724 7.514
boxplot_cluster_expr 5.326 0.737 5.826
plot_cluster_profiles 5.111 0.502 5.612
* 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
‘/Users/biocbuild/bbs-3.9-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/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)
BPRMeth.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
5.828 0.697 6.479
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 5.326 | 0.737 | 5.826 | |
| bpr_cluster_wrap | 7.855 | 1.141 | 8.375 | |
| bpr_optimize | 2.298 | 0.066 | 2.365 | |
| bpr_predict_wrap | 1.500 | 0.016 | 1.516 | |
| cluster_profiles_mle | 7.603 | 0.441 | 8.044 | |
| cluster_profiles_vb | 6.790 | 0.724 | 7.514 | |
| create_anno_region | 0.295 | 0.182 | 0.128 | |
| create_basis | 0.009 | 0.007 | 0.004 | |
| create_region_object | 0.002 | 0.002 | 0.001 | |
| design_matrix | 0.012 | 0.009 | 0.005 | |
| eval_functions | 0.018 | 0.013 | 0.008 | |
| infer_profiles_gibbs | 4.560 | 0.210 | 4.598 | |
| infer_profiles_mle | 2.413 | 0.046 | 2.460 | |
| infer_profiles_vb | 4.385 | 0.306 | 4.691 | |
| inner_predict_model_expr | 0.014 | 0.001 | 0.016 | |
| inner_train_model_expr | 0.040 | 0.002 | 0.043 | |
| old_boxplot_cluster_gex | 8.598 | 0.457 | 9.057 | |
| old_plot_cluster_prof | 8.062 | 0.470 | 8.534 | |
| old_plot_fitted_profiles | 1.529 | 0.042 | 1.572 | |
| plot_cluster_profiles | 5.111 | 0.502 | 5.612 | |
| plot_infer_profiles | 2.320 | 0.242 | 2.563 | |
| plot_predicted_expr | 2.853 | 0.406 | 3.087 | |
| pool_bs_seq_rep | 0.992 | 0.557 | 0.467 | |
| predict_expr | 2.388 | 0.276 | 2.585 | |
| preprocess_bs_seq | 0.489 | 0.302 | 0.195 | |
| preprocess_final_HTS_data | 1.432 | 0.977 | 0.509 | |
| process_haib_caltech_wrap | 2.160 | 0.550 | 0.576 | |
| read_anno | 0.113 | 0.074 | 0.039 | |
| read_bs_encode_haib | 0.232 | 0.160 | 0.080 | |
| read_chrom_size | 0.029 | 0.024 | 0.010 | |
| read_expr | 0.010 | 0.009 | 0.004 | |
| read_met | 0.104 | 0.074 | 0.035 | |
| read_rna_encode_caltech | 0.602 | 0.419 | 0.199 | |