| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 232/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BPRMeth 1.26.1 (landing page) Chantriolnt-Andreas Kapourani
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the BPRMeth package: - 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: 1.26.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BPRMeth_1.26.1.tar.gz |
| StartedAt: 2023-10-17 06:32:41 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 06:37:01 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 260.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BPRMeth.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BPRMeth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BPRMeth_1.26.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BPRMeth.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BPRMeth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BPRMeth’ version ‘1.26.1’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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
cluster_profiles_mle 5.080 0.126 7.991
bpr_cluster_wrap 4.346 0.092 6.840
old_plot_cluster_prof 4.182 0.092 6.531
old_boxplot_cluster_gex 4.076 0.088 6.375
cluster_profiles_vb 3.970 0.070 6.180
boxplot_cluster_expr 3.694 0.130 5.889
* 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-3.17-bioc-mac-arm64/meat/BPRMeth.Rcheck/00check.log’
for details.
BPRMeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BPRMeth ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘BPRMeth’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c model_likelihood.cpp -o model_likelihood.o clang++ -arch arm64 -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/opt/R/arm64/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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
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 object is masked from 'package:utils':
findMatches
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
4.712 0.312 7.749
BPRMeth.Rcheck/BPRMeth-Ex.timings
| name | user | system | elapsed | |
| boxplot_cluster_expr | 3.694 | 0.130 | 5.889 | |
| bpr_cluster_wrap | 4.346 | 0.092 | 6.840 | |
| bpr_optimize | 1.403 | 0.029 | 2.193 | |
| bpr_predict_wrap | 1.037 | 0.019 | 1.636 | |
| cluster_profiles_mle | 5.080 | 0.126 | 7.991 | |
| cluster_profiles_vb | 3.97 | 0.07 | 6.18 | |
| create_anno_region | 0.090 | 0.003 | 0.150 | |
| create_basis | 0.001 | 0.001 | 0.002 | |
| create_region_object | 0 | 0 | 0 | |
| design_matrix | 0.002 | 0.000 | 0.002 | |
| eval_functions | 0.003 | 0.000 | 0.003 | |
| impute_bulk_met | 0.661 | 0.007 | 1.024 | |
| infer_profiles_gibbs | 3.002 | 0.041 | 4.665 | |
| infer_profiles_mle | 1.517 | 0.027 | 2.376 | |
| infer_profiles_vb | 2.326 | 0.045 | 3.647 | |
| inner_predict_model_expr | 0.007 | 0.001 | 0.012 | |
| inner_train_model_expr | 0.024 | 0.003 | 0.039 | |
| old_boxplot_cluster_gex | 4.076 | 0.088 | 6.375 | |
| old_plot_cluster_prof | 4.182 | 0.092 | 6.531 | |
| old_plot_fitted_profiles | 0.980 | 0.018 | 1.528 | |
| partition_bulk_dataset | 0.027 | 0.000 | 0.042 | |
| plot_cluster_profiles | 2.789 | 0.091 | 4.410 | |
| plot_infer_profiles | 1.761 | 0.022 | 2.756 | |
| plot_predicted_expr | 1.792 | 0.020 | 2.754 | |
| pool_bs_seq_rep | 0.318 | 0.009 | 0.497 | |
| predict_expr | 1.796 | 0.019 | 2.798 | |
| preprocess_bs_seq | 0.131 | 0.003 | 0.208 | |
| preprocess_final_HTS_data | 0.347 | 0.008 | 0.542 | |
| process_haib_caltech_wrap | 0.377 | 0.007 | 0.596 | |
| read_anno | 0.042 | 0.002 | 0.067 | |
| read_bs_encode_haib | 0.059 | 0.003 | 0.097 | |
| read_chrom_size | 0.005 | 0.001 | 0.007 | |
| read_expr | 0.003 | 0.001 | 0.006 | |
| read_met | 0.025 | 0.002 | 0.042 | |
| read_rna_encode_caltech | 0.116 | 0.003 | 0.181 | |