Chantriolnt-Andreas Kapourani
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BPRMeth |
| Branch: master |
| Last Commit: abc23bd |
| Last Changed Date: 2019-02-16 06:30:29 -0400 (Sat, 16 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:47:06 -0400 (Tue, 09 Apr 2019).
| Package 178/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BPRMeth 1.9.4 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: BPRMeth |
| Version: 1.9.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BPRMeth_1.9.4.tar.gz |
| StartedAt: 2019-04-08 23:06:57 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:09:32 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 155.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BPRMeth.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BPRMeth_1.9.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BPRMeth.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.4’
* 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
bpr_cluster_wrap 5.911 0.023 5.936
cluster_profiles_mle 5.840 0.003 5.852
old_boxplot_cluster_gex 5.576 0.000 5.576
* 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-3.9-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BPRMeth ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘BPRMeth’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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
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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, 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
4.934 0.179 5.100
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 3.809 | 0.028 | 3.215 | |
| bpr_cluster_wrap | 5.911 | 0.023 | 5.936 | |
| bpr_optimize | 2.063 | 0.000 | 2.063 | |
| bpr_predict_wrap | 1.547 | 0.004 | 1.551 | |
| cluster_profiles_mle | 5.840 | 0.003 | 5.852 | |
| cluster_profiles_vb | 4.412 | 0.000 | 4.412 | |
| create_anno_region | 0.461 | 0.001 | 0.157 | |
| create_basis | 0.002 | 0.000 | 0.002 | |
| create_region_object | 0.001 | 0.000 | 0.000 | |
| design_matrix | 0.004 | 0.000 | 0.004 | |
| eval_functions | 0.005 | 0.000 | 0.004 | |
| infer_profiles_gibbs | 3.214 | 0.000 | 3.215 | |
| infer_profiles_mle | 1.621 | 0.000 | 1.621 | |
| infer_profiles_vb | 2.309 | 0.008 | 2.317 | |
| inner_predict_model_expr | 0.007 | 0.000 | 0.007 | |
| inner_train_model_expr | 0.021 | 0.000 | 0.021 | |
| old_boxplot_cluster_gex | 5.576 | 0.000 | 5.576 | |
| old_plot_cluster_prof | 3.832 | 0.000 | 3.832 | |
| old_plot_fitted_profiles | 0.924 | 0.000 | 0.924 | |
| plot_cluster_profiles | 3.346 | 0.048 | 3.395 | |
| plot_infer_profiles | 1.834 | 0.000 | 1.835 | |
| plot_predicted_expr | 2.403 | 0.000 | 2.346 | |
| pool_bs_seq_rep | 0.790 | 0.011 | 0.588 | |
| predict_expr | 2.460 | 0.004 | 1.981 | |
| preprocess_bs_seq | 0.418 | 0.004 | 0.201 | |
| preprocess_final_HTS_data | 0.840 | 0.003 | 0.476 | |
| process_haib_caltech_wrap | 0.863 | 0.004 | 0.500 | |
| read_anno | 0.346 | 0.000 | 0.089 | |
| read_bs_encode_haib | 0.320 | 0.004 | 0.109 | |
| read_chrom_size | 0.165 | 0.000 | 0.030 | |
| read_expr | 0.002 | 0.000 | 0.007 | |
| read_met | 0.235 | 0.000 | 0.064 | |
| read_rna_encode_caltech | 0.409 | 0.000 | 0.187 | |