Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 964/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiCDCPlus 1.12.0 (landing page) Merve Sahin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the HiCDCPlus package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCDCPlus.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: HiCDCPlus |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings HiCDCPlus_1.12.0.tar.gz |
StartedAt: 2024-06-09 23:49:41 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:56:13 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 391.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiCDCPlus.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings HiCDCPlus_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HiCDCPlus.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘HiCDCPlus/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HiCDCPlus’ version ‘1.12.0’ * 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 loading without being on the library search path ... 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 7.410 2.504 9.914 construct_features_chr 4.964 2.444 7.408 HTClist2gi_list 6.655 0.512 7.168 HiCDCPlus_parallel 0.395 0.025 13.525 construct_features_parallel 0.019 0.009 24.889 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/HiCDCPlus.Rcheck/00check.log’ for details.
HiCDCPlus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL HiCDCPlus ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘HiCDCPlus’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c straw.cpp -o straw.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o HiCDCPlus.so RcppExports.o straw.o -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 Jun 9 23:55:04 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 10.381 0.555 10.926
HiCDCPlus.Rcheck/HiCDCPlus-Ex.timings
name | user | system | elapsed | |
HTClist2gi_list | 6.655 | 0.512 | 7.168 | |
HiCDCPlus | 3.109 | 0.176 | 3.285 | |
HiCDCPlus_chr | 1.872 | 0.060 | 1.932 | |
HiCDCPlus_parallel | 0.395 | 0.025 | 13.525 | |
add_1D_features | 0.08 | 0.00 | 0.08 | |
add_2D_features | 0.334 | 0.000 | 0.334 | |
add_hic_counts | 0.385 | 0.028 | 0.412 | |
construct_features | 7.410 | 2.504 | 9.914 | |
construct_features_chr | 4.964 | 2.444 | 7.408 | |
construct_features_parallel | 0.019 | 0.009 | 24.889 | |
expand_1D_features | 0.100 | 0.056 | 0.155 | |
extract_hic_eigenvectors | 2.472 | 0.222 | 1.529 | |
generate_binned_gi_list | 0.206 | 0.028 | 0.233 | |
generate_bintolen_gi_list | 0.392 | 0.032 | 0.424 | |
generate_df_gi_list | 0.283 | 0.032 | 0.314 | |
get_chr_sizes | 0.171 | 0.012 | 0.182 | |
get_chrs | 0.184 | 0.020 | 0.204 | |
get_enzyme_cutsites | 1.484 | 0.108 | 1.592 | |
gi_list2HTClist | 0.358 | 0.056 | 0.414 | |
gi_list_Dthreshold.detect | 0.188 | 0.020 | 0.208 | |
gi_list_binsize_detect | 0.202 | 0.008 | 0.210 | |
gi_list_read | 0.317 | 0.040 | 0.356 | |
gi_list_topdom | 1.961 | 0.146 | 2.092 | |
gi_list_validate | 0.216 | 0.016 | 0.231 | |
gi_list_write | 0.261 | 0.016 | 0.277 | |
hic2icenorm_gi_list | 1.111 | 0.480 | 1.592 | |
hicdc2hic | 2.333 | 0.221 | 1.508 | |
hicdcdiff | 2.356 | 0.352 | 2.710 | |