Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 236/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BPRMeth 1.32.0 (landing page) Chantriolnt-Andreas Kapourani
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: BPRMeth |
Version: 1.32.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BPRMeth.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BPRMeth_1.32.0.tar.gz |
StartedAt: 2024-12-19 23:32:46 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:36:30 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 223.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BPRMeth.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BPRMeth.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BPRMeth_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BPRMeth.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BPRMeth/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BPRMeth' version '1.32.0' * 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 whether package 'BPRMeth' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 code 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 whether 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/BPRMeth/libs/x64/BPRMeth.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cluster_profiles_mle 7.13 0.14 7.28 cluster_profiles_vb 6.18 0.34 6.53 bpr_cluster_wrap 5.65 0.06 5.71 boxplot_cluster_expr 4.91 0.14 5.05 old_plot_cluster_prof 4.98 0.06 5.22 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/BPRMeth.Rcheck/00check.log' for details.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BPRMeth ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BPRMeth' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_likelihood.cpp -o model_likelihood.o g++ -shared -s -static-libgcc -o BPRMeth.dll tmp.def RcppExports.o model_likelihood.o -fopenmp -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BPRMeth/00new/BPRMeth/libs/x64 ** 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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb > > test_check("BPRMeth") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ] > > proc.time() user system elapsed 4.35 0.53 5.00
BPRMeth.Rcheck/BPRMeth-Ex.timings
name | user | system | elapsed | |
boxplot_cluster_expr | 4.91 | 0.14 | 5.05 | |
bpr_cluster_wrap | 5.65 | 0.06 | 5.71 | |
bpr_optimize | 1.55 | 0.03 | 1.58 | |
bpr_predict_wrap | 1.00 | 0.05 | 1.05 | |
cluster_profiles_mle | 7.13 | 0.14 | 7.28 | |
cluster_profiles_vb | 6.18 | 0.34 | 6.53 | |
create_anno_region | 0.05 | 0.03 | 0.08 | |
create_basis | 0 | 0 | 0 | |
create_region_object | 0 | 0 | 0 | |
design_matrix | 0 | 0 | 0 | |
eval_functions | 0 | 0 | 0 | |
impute_bulk_met | 0.66 | 0.02 | 0.69 | |
infer_profiles_gibbs | 3.06 | 0.11 | 3.19 | |
infer_profiles_mle | 1.39 | 0.00 | 1.39 | |
infer_profiles_vb | 3.44 | 0.14 | 3.57 | |
inner_predict_model_expr | 0 | 0 | 0 | |
inner_train_model_expr | 0.02 | 0.00 | 0.02 | |
old_boxplot_cluster_gex | 4.75 | 0.03 | 4.81 | |
old_plot_cluster_prof | 4.98 | 0.06 | 5.22 | |
old_plot_fitted_profiles | 1.08 | 0.02 | 1.09 | |
partition_bulk_dataset | 0.03 | 0.00 | 0.03 | |
plot_cluster_profiles | 4.24 | 0.12 | 4.36 | |
plot_infer_profiles | 2.23 | 0.05 | 2.28 | |
plot_predicted_expr | 2.52 | 0.08 | 2.60 | |
pool_bs_seq_rep | 0.37 | 0.04 | 0.43 | |
predict_expr | 2.69 | 0.02 | 2.71 | |
preprocess_bs_seq | 0.14 | 0.00 | 0.14 | |
preprocess_final_HTS_data | 0.34 | 0.00 | 0.36 | |
process_haib_caltech_wrap | 0.42 | 0.02 | 0.43 | |
read_anno | 0.05 | 0.00 | 0.05 | |
read_bs_encode_haib | 0.06 | 0.00 | 0.06 | |
read_chrom_size | 0.02 | 0.00 | 0.02 | |
read_expr | 0 | 0 | 0 | |
read_met | 0.03 | 0.00 | 0.03 | |
read_rna_encode_caltech | 0.12 | 0.00 | 0.12 | |