Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1223/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metabinR 1.11.0 (landing page) Anestis Gkanogiannis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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: 1.11.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings metabinR_1.11.0.tar.gz |
StartedAt: 2025-09-20 01:27:35 -0400 (Sat, 20 Sep 2025) |
EndedAt: 2025-09-20 01:29:08 -0400 (Sat, 20 Sep 2025) |
EllapsedTime: 93.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metabinR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings metabinR_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/metabinR.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘metabinR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metabinR’ version ‘1.11.0’ * 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 loading without being on the library search path ... 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 8.362 0.820 5.956 composition_based_binning 6.519 0.399 1.841 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
metabinR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL metabinR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘metabinR’ ... ** this is package ‘metabinR’ version ‘1.11.0’ ** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.136 0.038 0.163
metabinR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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. > library(testthat) > library(metabinR) > > test_check("metabinR") version MTxAB =Fri Sep 19 15:04:32 EDT 2025 cpus=72 using=1 2025/09/20 01:28:06 Using Dictionary ORIGINAL 2025/09/20 01:28:06 START of AB Counting 2025/09/20 01:28:07 FastaManager: START READ 2025/09/20 01:28:07 SequenceProcessor: 0 AB_KMERCOUNT START CHUNK_SIZE=67108864 2025/09/20 01:28:07 FastaManager: lines read 53328 2025/09/20 01:28:07 FastaManager: END READ 2025/09/20 01:28:07 FastaManager: FASTA 2025/09/20 01:28:08 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2025/09/20 01:28:08 END of AB Counting 2025/09/20 01:28:08 Loaded sequences: 26664 2025/09/20 01:28:08 Total kmers(before remove): 65536 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.294 Current Free Memory=0.206 ############################################ 2025/09/20 01:28:08 Unique: 0 Distinct: 65536 Total: 7625904 MaxCount: 1574 2025/09/20 01:28:08 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 2025/09/20 01:28:08 Runs=25 2025/09/20 01:28:08 END of EMsync 2025/09/20 01:28:08 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 2025/09/20 01:28:08 Trove size/4=18022 2025/09/20 01:28:08 Trove size/4=18022 2025/09/20 01:28:08 Cluster 2 size in kmers=65536 norm=221.81983091435748 2025/09/20 01:28:08 Cluster 1 size in kmers=65536 norm=126.5058948513796 2025/09/20 01:28:08 END of Creating AB Cluster Vectors cpus=72 using=1 2025/09/20 01:28:08 START of AB Binning 2025/09/20 01:28:08 FastaManager: START READ 2025/09/20 01:28:08 SequenceProcessor: 0 AB_BINNING START 2025/09/20 01:28:08 FastaManager: lines read 53328 2025/09/20 01:28:08 FastaManager: END READ 2025/09/20 01:28:08 FastaManager: FASTA 2025/09/20 01:28:10 SequenceProcessor: 0 AB_BINNING EXIT 2025/09/20 01:28:10 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=0.376 Current Free Memory=0.124 ############################################ version MTxCB =Fri Sep 19 15:04:32 EDT 2025 cpus=72 using=1 2025/09/20 01:28:11 START of CB Counting 2025/09/20 01:28:11 FastaManager: START READ 2025/09/20 01:28:11 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2025/09/20 01:28:11 FastaManager: lines read 53328 2025/09/20 01:28:11 FastaManager: END READ 2025/09/20 01:28:11 FastaManager: FASTA 2025/09/20 01:28:12 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2025/09/20 01:28:12 END of CB Counting 2025/09/20 01:28:12 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.372 Current Free Memory=0.128 ############################################ cpus=72 using=1 2025/09/20 01:28:12 START of Creating CB Clusters Size=26664 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 7583 ... iteration 2 moves = 3173 ... iteration 3 moves = 1236 ... iteration 4 moves = 484 ... iteration 5 moves = 224 ... iteration 6 moves = 142 ... iteration 7 moves = 42 ... iteration 8 moves = 32 ... iteration 9 moves = 0 ...end. 4.107 seconds. 2025/09/20 01:28:16 : kMeans cleanup. 2025/09/20 01:28:16 END of Creating CB Clusters. cpus=72 using=1 2025/09/20 01:28:16 START of CB Binning 2025/09/20 01:28:16 FastaManager: START READ 2025/09/20 01:28:16 SequenceProcessor: 0 CB_BINNING START 2025/09/20 01:28:16 FastaManager: lines read 53328 2025/09/20 01:28:16 FastaManager: END READ 2025/09/20 01:28:16 FastaManager: FASTA 2025/09/20 01:28:16 SequenceProcessor: 0 CB_BINNING EXIT Clustered reads: CB Cluster 1: 7144 CB Cluster 2: 19520 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.454 Current Free Memory=0.046 ############################################ version MTxABxCB =Fri Sep 19 15:04:32 EDT 2025 cpus=72 using=1 2025/09/20 01:28:16 Using Dictionary ORIGINAL 2025/09/20 01:28:16 START of AB Counting 2025/09/20 01:28:16 FastaManager: START READ 2025/09/20 01:28:16 SequenceProcessor: 0 AB_KMERCOUNT START 2025/09/20 01:28:16 FastaManager: lines read 53328 2025/09/20 01:28:16 FastaManager: END READ 2025/09/20 01:28:16 FastaManager: FASTA 2025/09/20 01:28:17 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2025/09/20 01:28:17 END of AB Counting 2025/09/20 01:28:17 Loaded sequences: 26664 2025/09/20 01:28:17 Distinct kmers(before remove): 65536 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.312 Current Free Memory=0.188 ############################################ 2025/09/20 01:28:17 Unique: 0 Distinct: 65536 Total: 7625904 MaxCount: 1574 2025/09/20 01:28:17 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 2025/09/20 01:28:18 Runs=25 2025/09/20 01:28:18 END of EMsync 2025/09/20 01:28:18 Filter before=2 2025/09/20 01:28:18 Filter after=2 2025/09/20 01:28:18 START of Creating AB Cluster Vectors Cluster 1 Abundance=75.53888858729701 Length=49367.826262240575 LowLimit=32 HighLimit=118 Cluster 2 Abundance=241.01134335779187 Length=16168.173737759438 LowLimit=163 HighLimit=318 2025/09/20 01:28:18 Trove size/4=18022 2025/09/20 01:28:18 Trove size/4=18022 2025/09/20 01:28:18 Cluster 1 size in kmers=65536 norm=221.81983091435748 2025/09/20 01:28:18 Cluster 2 size in kmers=65536 norm=126.5058948513796 2025/09/20 01:28:18 END of Creating AB Cluster Vectors cpus=72 using=1 2025/09/20 01:28:18 START of AB Binning 2025/09/20 01:28:18 FastaManager: START READ 2025/09/20 01:28:18 SequenceProcessor: 0 AB_BINNING START 2025/09/20 01:28:18 FastaManager: lines read 53328 2025/09/20 01:28:18 FastaManager: END READ 2025/09/20 01:28:18 FastaManager: FASTA 2025/09/20 01:28:20 SequenceProcessor: 0 AB_BINNING EXIT 2025/09/20 01:28:20 END of AB Binning cpus=72 using=1 2025/09/20 01:28:20 START of CB Counting 2025/09/20 01:28:20 FastaManager: START READ 2025/09/20 01:28:20 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2025/09/20 01:28:20 FastaManager: lines read 53328 2025/09/20 01:28:20 FastaManager: END READ 2025/09/20 01:28:20 FastaManager: FASTA 2025/09/20 01:28:20 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2025/09/20 01:28:20 END of CB Counting 2025/09/20 01:28:20 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.297 Current Free Memory=0.203 ############################################ 2025/09/20 01:28:20 AB Cluster=1 Size=6793 2025/09/20 01:28:20 AB Cluster=2 Size=19871 cpus=72 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 1 6,793 75.53889 49,367 13,489 1 1 2025/09/20 01:28:20 START of Creating CB Clusters for AB Cluster=1 Size=6793 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 0 ...end. 0.757 seconds. 2025/09/20 01:28:21 : kMeans cleanup. 2025/09/20 01:28:21 END of Creating CB Clusters for AB Cluster=1 cpus=72 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 2 19,871 241.01134 16,168 12,367 1 1 2025/09/20 01:28:21 START of Creating CB Clusters for AB Cluster=2 Size=19871 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 0 ...end. 2.154 seconds. 2025/09/20 01:28:23 : kMeans cleanup. 2025/09/20 01:28:23 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=0.405 Current Free Memory=0.095 ############################################ cpus=72 using=1 2025/09/20 01:28:23 START of CB Binning 2025/09/20 01:28:23 FastaManager: START READ 2025/09/20 01:28:23 SequenceProcessor: 0 CB_BINNING START 2025/09/20 01:28:23 FastaManager: lines read 53328 2025/09/20 01:28:23 FastaManager: END READ 2025/09/20 01:28:23 FastaManager: FASTA 2025/09/20 01:28:24 SequenceProcessor: 0 CB_BINNING EXIT Clustered reads: ABxCB Cluster 1: 6793 ABxCB Cluster 2: 19871 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.5 Current Used Memory=0.444 Current Free Memory=0.056 ############################################ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ] > > proc.time() user system elapsed 26.881 1.037 18.227
metabinR.Rcheck/metabinR-Ex.timings
name | user | system | elapsed | |
abundance_based_binning | 8.362 | 0.820 | 5.956 | |
composition_based_binning | 6.519 | 0.399 | 1.841 | |
hierarchical_binning | 4.633 | 0.186 | 3.094 | |