Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
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 1223/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metabinR 1.10.0 (landing page) Anestis Gkanogiannis
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the metabinR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metabinR.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: metabinR |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabinR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabinR_1.10.0.tar.gz |
StartedAt: 2025-04-21 21:44:25 -0400 (Mon, 21 Apr 2025) |
EndedAt: 2025-04-21 21:45:38 -0400 (Mon, 21 Apr 2025) |
EllapsedTime: 73.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metabinR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabinR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabinR_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/metabinR.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metabinR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metabinR’ version ‘1.10.0’ * 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 ‘metabinR’ can be installed ... OK * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed abundance_based_binning 8.234 1.018 7.045 composition_based_binning 4.715 0.752 2.192 hierarchical_binning 4.747 0.560 3.847 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ 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: OK
metabinR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metabinR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘metabinR’ ... ** this is package ‘metabinR’ version ‘1.10.0’ ** using staged installation ** R ** 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 (metabinR)
metabinR.Rcheck/tests/spelling.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.190 0.069 0.251
metabinR.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(metabinR) > > test_check("metabinR") version MTxAB =Mon Apr 21 15:04:03 EDT 2025 cpus=48 using=1 2025/04/21 21:45:07 Using Dictionary ORIGINAL 2025/04/21 21:45:07 START of AB Counting 2025/04/21 21:45:07 FastaManager: START READ 2025/04/21 21:45:07 SequenceProcessor: 0 AB_KMERCOUNT START CHUNK_SIZE=67108864 2025/04/21 21:45:07 FastaManager: lines read 53328 2025/04/21 21:45:07 FastaManager: END READ 2025/04/21 21:45:07 FastaManager: FASTA 2025/04/21 21:45:09 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2025/04/21 21:45:09 END of AB Counting 2025/04/21 21:45:09 Loaded sequences: 26664 2025/04/21 21:45:09 Total kmers(before remove): 65536 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.286 Current Free Memory=0.214 ############################################ 2025/04/21 21:45:09 Unique: 0 Distinct: 65536 Total: 7625904 MaxCount: 1574 2025/04/21 21:45:09 START of EMsync Run=1 Run=2 Run=3 Run=4 Run=5 Run=6 Run=7 Run=8 Run=9 Run=10 Run=11 Run=12 Run=13 Run=14 Run=15 Run=16 Run=17 Run=18 Run=19 Run=20 Run=21 Run=22 Run=23 Run=24 Run=25 2025/04/21 21:45:09 Runs=25 2025/04/21 21:45:09 END of EMsync 2025/04/21 21:45:09 START of Creating AB Cluster Vectors Cluster 1 Abundance=241.01134335779187 Length=16168.173737759438 LowLimit=163 HighLimit=318 Cluster 2 Abundance=75.53888858729701 Length=49367.826262240575 LowLimit=32 HighLimit=118 2025/04/21 21:45:09 Trove size/4=18022 2025/04/21 21:45:09 Trove size/4=18022 2025/04/21 21:45:10 Cluster 2 size in kmers=65536 norm=221.81983091435748 2025/04/21 21:45:10 Cluster 1 size in kmers=65536 norm=126.5058948513796 2025/04/21 21:45:10 END of Creating AB Cluster Vectors cpus=48 using=1 2025/04/21 21:45:10 START of AB Binning 2025/04/21 21:45:10 FastaManager: START READ 2025/04/21 21:45:10 SequenceProcessor: 0 AB_BINNING START 2025/04/21 21:45:10 FastaManager: lines read 53328 2025/04/21 21:45:10 FastaManager: END READ 2025/04/21 21:45:10 FastaManager: FASTA 2025/04/21 21:45:12 SequenceProcessor: 0 AB_BINNING EXIT 2025/04/21 21:45:12 END of AB Binning Clustered reads: AB Cluster 1: 19871 AB Cluster 2: 6793 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.37 Current Free Memory=0.13 ############################################ version MTxCB =Mon Apr 21 15:04:03 EDT 2025 cpus=48 using=1 2025/04/21 21:45:12 START of CB Counting 2025/04/21 21:45:12 FastaManager: START READ 2025/04/21 21:45:12 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2025/04/21 21:45:12 FastaManager: lines read 53328 2025/04/21 21:45:12 FastaManager: END READ 2025/04/21 21:45:12 FastaManager: FASTA 2025/04/21 21:45:13 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2025/04/21 21:45:13 END of CB Counting 2025/04/21 21:45:13 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.376 Current Free Memory=0.124 ############################################ cpus=48 using=1 2025/04/21 21:45:13 START of Creating CB Clusters Size=26664 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 6848 ... iteration 2 moves = 3541 ... iteration 3 moves = 1289 ... iteration 4 moves = 547 ... iteration 5 moves = 239 ... iteration 6 moves = 151 ... iteration 7 moves = 103 ... iteration 8 moves = 49 ... iteration 9 moves = 28 ... iteration 10 moves = 19 ... iteration 11 moves = 13 ... iteration 12 moves = 14 ... iteration 13 moves = 7 ... iteration 14 moves = 3 ... iteration 15 moves = 0 ...end. 5.267 seconds. 2025/04/21 21:45:19 : kMeans cleanup. 2025/04/21 21:45:19 END of Creating CB Clusters. cpus=48 using=1 2025/04/21 21:45:19 START of CB Binning 2025/04/21 21:45:19 FastaManager: START READ 2025/04/21 21:45:19 SequenceProcessor: 0 CB_BINNING START 2025/04/21 21:45:19 FastaManager: lines read 53328 2025/04/21 21:45:19 FastaManager: END READ 2025/04/21 21:45:19 FastaManager: FASTA 2025/04/21 21:45:19 SequenceProcessor: 0 CB_BINNING EXIT Clustered reads: CB Cluster 1: 10628 CB Cluster 2: 16036 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.447 Current Free Memory=0.053 ############################################ version MTxABxCB =Mon Apr 21 15:04:03 EDT 2025 cpus=48 using=1 2025/04/21 21:45:19 Using Dictionary ORIGINAL 2025/04/21 21:45:19 START of AB Counting 2025/04/21 21:45:19 FastaManager: START READ 2025/04/21 21:45:19 SequenceProcessor: 0 AB_KMERCOUNT START 2025/04/21 21:45:19 FastaManager: lines read 53328 2025/04/21 21:45:19 FastaManager: END READ 2025/04/21 21:45:19 FastaManager: FASTA 2025/04/21 21:45:21 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2025/04/21 21:45:21 END of AB Counting 2025/04/21 21:45:21 Loaded sequences: 26664 2025/04/21 21:45:21 Distinct kmers(before remove): 65536 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.318 Current Free Memory=0.182 ############################################ 2025/04/21 21:45:21 Unique: 0 Distinct: 65536 Total: 7625904 MaxCount: 1574 2025/04/21 21:45:21 START of EMsync Run=1 Run=2 Run=3 Run=4 Run=5 Run=6 Run=7 Run=8 Run=9 Run=10 Run=11 Run=12 Run=13 Run=14 Run=15 Run=16 Run=17 Run=18 Run=19 Run=20 Run=21 Run=22 Run=23 Run=24 Run=25 2025/04/21 21:45:21 Runs=25 2025/04/21 21:45:21 END of EMsync 2025/04/21 21:45:21 Filter before=2 2025/04/21 21:45:21 Filter after=2 2025/04/21 21:45:21 START of Creating AB Cluster Vectors Cluster 1 Abundance=241.01134335779187 Length=16168.173737759438 LowLimit=163 HighLimit=318 Cluster 2 Abundance=75.53888858729701 Length=49367.826262240575 LowLimit=32 HighLimit=118 2025/04/21 21:45:21 Trove size/4=18022 2025/04/21 21:45:21 Trove size/4=18022 2025/04/21 21:45:21 Cluster 2 size in kmers=65536 norm=221.81983091435748 2025/04/21 21:45:21 Cluster 1 size in kmers=65536 norm=126.5058948513796 2025/04/21 21:45:21 END of Creating AB Cluster Vectors cpus=48 using=1 2025/04/21 21:45:21 START of AB Binning 2025/04/21 21:45:21 FastaManager: START READ 2025/04/21 21:45:21 SequenceProcessor: 0 AB_BINNING START 2025/04/21 21:45:21 FastaManager: lines read 53328 2025/04/21 21:45:21 FastaManager: END READ 2025/04/21 21:45:21 FastaManager: FASTA 2025/04/21 21:45:23 SequenceProcessor: 0 AB_BINNING EXIT 2025/04/21 21:45:23 END of AB Binning cpus=48 using=1 2025/04/21 21:45:23 START of CB Counting 2025/04/21 21:45:23 FastaManager: START READ 2025/04/21 21:45:23 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2025/04/21 21:45:24 FastaManager: lines read 53328 2025/04/21 21:45:24 FastaManager: END READ 2025/04/21 21:45:24 FastaManager: FASTA 2025/04/21 21:45:24 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2025/04/21 21:45:24 END of CB Counting 2025/04/21 21:45:24 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.294 Current Free Memory=0.206 ############################################ 2025/04/21 21:45:24 AB Cluster=1 Size=19871 2025/04/21 21:45:24 AB Cluster=2 Size=6793 cpus=48 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 1 19,871 241.01134 16,168 12,367 1 1 2025/04/21 21:45:24 START of Creating CB Clusters for AB Cluster=1 Size=19871 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 0 ...end. 2.246 seconds. 2025/04/21 21:45:26 : kMeans cleanup. 2025/04/21 21:45:26 END of Creating CB Clusters for AB Cluster=1 cpus=48 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 2 6,793 75.53889 49,367 13,489 1 1 2025/04/21 21:45:26 START of Creating CB Clusters for AB Cluster=2 Size=6793 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 0 ...end. 0.743 seconds. 2025/04/21 21:45:27 : kMeans cleanup. 2025/04/21 21:45:27 END of Creating CB Clusters for AB Cluster=2 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.404 Current Free Memory=0.096 ############################################ cpus=48 using=1 2025/04/21 21:45:27 START of CB Binning 2025/04/21 21:45:27 FastaManager: START READ 2025/04/21 21:45:27 SequenceProcessor: 0 CB_BINNING START 2025/04/21 21:45:27 FastaManager: lines read 53328 2025/04/21 21:45:27 FastaManager: END READ 2025/04/21 21:45:27 FastaManager: FASTA 2025/04/21 21:45:27 SequenceProcessor: 0 CB_BINNING EXIT Clustered reads: ABxCB Cluster 1: 19871 ABxCB Cluster 2: 6793 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.443 Current Free Memory=0.057 ############################################ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ] > > proc.time() user system elapsed 29.760 1.375 22.058
metabinR.Rcheck/metabinR-Ex.timings
name | user | system | elapsed | |
abundance_based_binning | 8.234 | 1.018 | 7.045 | |
composition_based_binning | 4.715 | 0.752 | 2.192 | |
hierarchical_binning | 4.747 | 0.560 | 3.847 | |