| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:27 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BPRMeth package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BPRMeth.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 228/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BPRMeth 1.27.1 (landing page) Chantriolnt-Andreas Kapourani
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: BPRMeth |
| Version: 1.27.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BPRMeth_1.27.1.tar.gz |
| StartedAt: 2023-05-09 10:24:04 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 10:28:26 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 262.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BPRMeth.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BPRMeth_1.27.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BPRMeth.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BPRMeth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BPRMeth’ version ‘1.27.1’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 1.5Mb
libs 2.0Mb
* 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 startup messages can be suppressed ... 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 LazyData ... 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
bpr_cluster_wrap 5.897 0.152 6.049
cluster_profiles_mle 5.891 0.112 6.003
old_plot_cluster_prof 5.521 0.016 5.537
old_boxplot_cluster_gex 5.429 0.028 5.457
cluster_profiles_vb 5.127 0.164 5.291
* 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 ...
‘BPRMeth_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BPRMeth ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘BPRMeth’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c model_likelihood.cpp -o model_likelihood.o g++ -std=gnu++11 -shared -L/usr/local/lib -o BPRMeth.so RcppExports.o model_likelihood.o -fopenmp -llapack -L/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/lib -lRblas -lgfortran -lm installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
> test_check("BPRMeth")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ]
>
> proc.time()
user system elapsed
4.993 0.252 5.225
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 4.578 | 0.188 | 4.765 | |
| bpr_cluster_wrap | 5.897 | 0.152 | 6.049 | |
| bpr_optimize | 1.673 | 0.052 | 1.726 | |
| bpr_predict_wrap | 1.163 | 0.008 | 1.171 | |
| cluster_profiles_mle | 5.891 | 0.112 | 6.003 | |
| cluster_profiles_vb | 5.127 | 0.164 | 5.291 | |
| create_anno_region | 0.096 | 0.004 | 0.101 | |
| create_basis | 0.000 | 0.000 | 0.002 | |
| create_region_object | 0.000 | 0.000 | 0.001 | |
| design_matrix | 0.001 | 0.001 | 0.003 | |
| eval_functions | 0.003 | 0.000 | 0.003 | |
| impute_bulk_met | 0.828 | 0.000 | 0.827 | |
| infer_profiles_gibbs | 2.990 | 0.016 | 3.005 | |
| infer_profiles_mle | 1.780 | 0.012 | 1.792 | |
| infer_profiles_vb | 2.709 | 0.027 | 2.736 | |
| inner_predict_model_expr | 0.008 | 0.000 | 0.009 | |
| inner_train_model_expr | 0.022 | 0.003 | 0.026 | |
| old_boxplot_cluster_gex | 5.429 | 0.028 | 5.457 | |
| old_plot_cluster_prof | 5.521 | 0.016 | 5.537 | |
| old_plot_fitted_profiles | 1.141 | 0.003 | 1.144 | |
| partition_bulk_dataset | 0.037 | 0.000 | 0.037 | |
| plot_cluster_profiles | 4.355 | 0.052 | 4.407 | |
| plot_infer_profiles | 1.931 | 0.008 | 1.939 | |
| plot_predicted_expr | 1.998 | 0.020 | 2.018 | |
| pool_bs_seq_rep | 0.320 | 0.023 | 0.342 | |
| predict_expr | 1.988 | 0.000 | 1.988 | |
| preprocess_bs_seq | 0.130 | 0.000 | 0.129 | |
| preprocess_final_HTS_data | 0.312 | 0.000 | 0.311 | |
| process_haib_caltech_wrap | 0.336 | 0.004 | 0.337 | |
| read_anno | 0.06 | 0.00 | 0.06 | |
| read_bs_encode_haib | 0.056 | 0.000 | 0.054 | |
| read_chrom_size | 0.002 | 0.003 | 0.006 | |
| read_expr | 0.002 | 0.000 | 0.004 | |
| read_met | 0.033 | 0.000 | 0.034 | |
| read_rna_encode_caltech | 0.123 | 0.000 | 0.124 | |