Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:13 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 934/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiCDCPlus 1.13.0 (landing page) Merve Sahin
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the HiCDCPlus 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: HiCDCPlus |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCDCPlus_1.13.0.tar.gz |
StartedAt: 2024-05-19 15:54:59 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 16:01:49 -0400 (Sun, 19 May 2024) |
EllapsedTime: 410.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiCDCPlus.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCDCPlus_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/HiCDCPlus.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiCDCPlus/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HiCDCPlus’ version ‘1.13.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘HiCDCPlus’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * 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 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 dependencies in R code ... OK * 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 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 construct_features 13.178 2.276 15.582 construct_features_chr 8.717 2.550 11.342 HTClist2gi_list 9.097 0.425 9.725 HiCDCPlus_parallel 0.548 0.040 17.882 construct_features_parallel 0.015 0.012 27.792 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/HiCDCPlus.Rcheck/00check.log’ for details.
HiCDCPlus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCDCPlus ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘HiCDCPlus’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ 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/4.4-arm64/Resources/library/Rcpp/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/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c straw.cpp -o straw.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o HiCDCPlus.so RcppExports.o straw.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-HiCDCPlus/00new/HiCDCPlus/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (HiCDCPlus)
HiCDCPlus.Rcheck/tests/runTests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > BiocGenerics:::testPackage("HiCDCPlus") Loading required package: BSgenome 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 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 Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat RUNIT TEST PROTOCOL -- Sun May 19 16:01:38 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : HiCDCPlus RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 14.009 0.551 14.872
HiCDCPlus.Rcheck/HiCDCPlus-Ex.timings
name | user | system | elapsed | |
HTClist2gi_list | 9.097 | 0.425 | 9.725 | |
HiCDCPlus | 4.275 | 0.067 | 4.404 | |
HiCDCPlus_chr | 2.486 | 0.052 | 2.543 | |
HiCDCPlus_parallel | 0.548 | 0.040 | 17.882 | |
add_1D_features | 0.090 | 0.001 | 0.096 | |
add_2D_features | 0.445 | 0.019 | 0.472 | |
add_hic_counts | 0.553 | 0.033 | 0.603 | |
construct_features | 13.178 | 2.276 | 15.582 | |
construct_features_chr | 8.717 | 2.550 | 11.342 | |
construct_features_parallel | 0.015 | 0.012 | 27.792 | |
expand_1D_features | 0.100 | 0.002 | 0.112 | |
extract_hic_eigenvectors | 2.837 | 0.287 | 2.928 | |
generate_binned_gi_list | 0.312 | 0.016 | 0.329 | |
generate_bintolen_gi_list | 0.508 | 0.033 | 0.542 | |
generate_df_gi_list | 0.309 | 0.016 | 0.326 | |
get_chr_sizes | 0.283 | 0.016 | 0.299 | |
get_chrs | 0.280 | 0.020 | 0.306 | |
get_enzyme_cutsites | 2.662 | 0.082 | 2.781 | |
gi_list2HTClist | 0.549 | 0.025 | 0.574 | |
gi_list_Dthreshold.detect | 0.303 | 0.016 | 0.319 | |
gi_list_binsize_detect | 0.318 | 0.017 | 0.335 | |
gi_list_read | 0.428 | 0.037 | 0.464 | |
gi_list_topdom | 2.136 | 0.351 | 2.495 | |
gi_list_validate | 0.316 | 0.017 | 0.334 | |
gi_list_write | 0.330 | 0.018 | 0.350 | |
hic2icenorm_gi_list | 1.463 | 0.418 | 1.888 | |
hicdc2hic | 2.949 | 0.255 | 2.656 | |
hicdcdiff | 3.209 | 0.124 | 3.400 | |