Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:13 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
To the developers/maintainers of the metabinR package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1126/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metabinR 1.1.0 (landing page) Anestis Gkanogiannis
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: metabinR |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metabinR_1.1.0.tar.gz |
StartedAt: 2023-02-07 07:22:21 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 07:24:23 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 122.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: metabinR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metabinR_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metabinR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘metabinR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metabinR’ version ‘1.1.0’ * 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 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 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 9.487 0.493 7.656 * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘metabinR_vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘metabinR_vignette.Rmd’ using rmarkdown version MTxAB =Mon Feb 06 01:55:16 UTC 2023 cpus=8 using=1 2023/02/07 07:23:41 Using Dictionary ORIGINAL 2023/02/07 07:23:41 START of AB Counting 2023/02/07 07:23:41 FastaManager: START READ 2023/02/07 07:23:41 SequenceProcessor: 0 AB_KMERCOUNT START CHUNK_SIZE=98304000 2023/02/07 07:23:41 FastaManager: lines read 53328 2023/02/07 07:23:41 FastaManager: END READ 2023/02/07 07:23:41 FastaManager: FASTA 2023/02/07 07:23:45 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2023/02/07 07:23:45 END of AB Counting 2023/02/07 07:23:45 Loaded sequences: 26664 2023/02/07 07:23:45 Total kmers(before remove): 999455 ##### Heap utilization statistics [GB] ##### Max Memory=1.465 Current Total Memory=0.602 Current Used Memory=0.223 Current Free Memory=0.379 ############################################ 2023/02/07 07:23:45 Unique: 94114 Distinct: 999455 Total: 7519248 MaxCount: 234 2023/02/07 07:23:45 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 2023/02/07 07:23:45 Runs=25 2023/02/07 07:23:45 END of EMsync 2023/02/07 07:23:45 START of Creating AB Cluster Vectors Cluster 1 Abundance=21.142433100553692 Length=160404.35424822773 LowLimit=1 HighLimit=44 Cluster 2 Abundance=4.919738387866692 Length=839050.6457517716 LowLimit=1 HighLimit=16 2023/02/07 07:23:45 Trove size/4=274849 2023/02/07 07:23:45 Trove size/4=274849 2023/02/07 07:23:46 Cluster 1 size in kmers=999455 norm=379.88718733030714 2023/02/07 07:23:46 Cluster 2 size in kmers=999455 norm=907.2167335611609 2023/02/07 07:23:46 END of Creating AB Cluster Vectors cpus=8 using=1 2023/02/07 07:23:46 START of AB Binning 2023/02/07 07:23:46 FastaManager: START READ 2023/02/07 07:23:46 SequenceProcessor: 0 AB_BINNING START 2023/02/07 07:23:46 FastaManager: lines read 53328 2023/02/07 07:23:46 FastaManager: END READ 2023/02/07 07:23:46 FastaManager: FASTA 2023/02/07 07:23:50 SequenceProcessor: 0 AB_BINNING EXIT 2023/02/07 07:23:50 END of AB Binning Clustered reads: AB Cluster 1: 19761 AB Cluster 2: 6903 ##### Heap utilization statistics [GB] ##### Max Memory=1.465 Current Total Memory=0.602 Current Used Memory=0.46 Current Free Memory=0.142 ############################################ The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/metabinR.Rcheck/vign_test/metabinR/vignettes/metabinR_vignette_files/figure-html/unnamed-chunk-7-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/metabinR.Rcheck/vign_test/metabinR/vignettes/metabinR_vignette_files/figure-html/unnamed-chunk-8-1.png" but not available. version MTxCB =Mon Feb 06 01:55:16 UTC 2023 cpus=8 using=1 2023/02/07 07:23:53 START of CB Counting 2023/02/07 07:23:53 FastaManager: START READ 2023/02/07 07:23:53 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2023/02/07 07:23:53 FastaManager: lines read 53328 2023/02/07 07:23:53 FastaManager: END READ 2023/02/07 07:23:53 FastaManager: FASTA 2023/02/07 07:23:53 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2023/02/07 07:23:53 END of CB Counting 2023/02/07 07:23:53 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=1.465 Current Total Memory=0.602 Current Used Memory=0.479 Current Free Memory=0.122 ############################################ cpus=8 using=1 2023/02/07 07:23:53 START of Creating CB Clusters Size=26664 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 13419 ... iteration 2 moves = 7590 ... iteration 3 moves = 5948 ... iteration 4 moves = 4100 ... iteration 5 moves = 3021 ... iteration 6 moves = 2092 ... iteration 7 moves = 1587 ... iteration 8 moves = 1273 ... iteration 9 moves = 1009 ... iteration 10 moves = 887 ... iteration 11 moves = 757 ... iteration 12 moves = 680 ... iteration 13 moves = 669 ... iteration 14 moves = 704 ... iteration 15 moves = 720 ... iteration 16 moves = 630 ... iteration 17 moves = 630 ... iteration 18 moves = 692 ... iteration 19 moves = 740 ... iteration 20 moves = 722 ... iteration 21 moves = 666 ... iteration 22 moves = 701 ... iteration 23 moves = 683 ... iteration 24 moves = 749 ... iteration 25 moves = 703 ...end. 11.707 seconds. 2023/02/07 07:24:05 : kMeans cleanup. 2023/02/07 07:24:05 END of Creating CB Clusters. cpus=8 using=1 2023/02/07 07:24:05 START of CB Binning 2023/02/07 07:24:05 FastaManager: START READ 2023/02/07 07:24:05 SequenceProcessor: 0 CB_BINNING START 2023/02/07 07:24:05 FastaManager: lines read 53328 2023/02/07 07:24:05 FastaManager: END READ 2023/02/07 07:24:05 FastaManager: FASTA 2023/02/07 07:24:06 SequenceProcessor: 0 CB_BINNING EXIT Clustered reads: CB Cluster 1: 3395 CB Cluster 2: 2612 CB Cluster 3: 743 CB Cluster 4: 1697 CB Cluster 5: 874 CB Cluster 6: 564 CB Cluster 7: 7556 CB Cluster 8: 1782 CB Cluster 9: 1679 CB Cluster 10: 5762 ##### Heap utilization statistics [GB] ##### Max Memory=1.465 Current Total Memory=0.709 Current Used Memory=0.398 Current Free Memory=0.311 ############################################ version MTxABxCB =Mon Feb 06 01:55:16 UTC 2023 cpus=8 using=1 2023/02/07 07:24:07 Using Dictionary ORIGINAL 2023/02/07 07:24:07 START of AB Counting 2023/02/07 07:24:07 FastaManager: START READ 2023/02/07 07:24:07 SequenceProcessor: 0 AB_KMERCOUNT START 2023/02/07 07:24:07 FastaManager: lines read 53328 2023/02/07 07:24:07 FastaManager: END READ 2023/02/07 07:24:07 FastaManager: FASTA 2023/02/07 07:24:10 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2023/02/07 07:24:10 END of AB Counting 2023/02/07 07:24:10 Loaded sequences: 26664 2023/02/07 07:24:10 Distinct kmers(before remove): 999455 ##### Heap utilization statistics [GB] ##### Max Memory=1.465 Current Total Memory=0.709 Current Used Memory=0.427 Current Free Memory=0.282 ############################################ 2023/02/07 07:24:10 Unique: 94114 Distinct: 999455 Total: 7519248 MaxCount: 234 2023/02/07 07:24:10 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 2023/02/07 07:24:10 Runs=25 2023/02/07 07:24:10 END of EMsync 2023/02/07 07:24:10 Filter before=2 2023/02/07 07:24:10 Filter after=2 2023/02/07 07:24:10 START of Creating AB Cluster Vectors Cluster 1 Abundance=21.142433100553692 Length=160404.35424822773 LowLimit=1 HighLimit=44 Cluster 2 Abundance=4.919738387866692 Length=839050.6457517716 LowLimit=1 HighLimit=16 2023/02/07 07:24:10 Trove size/4=274849 2023/02/07 07:24:10 Trove size/4=274849 2023/02/07 07:24:10 Cluster 1 size in kmers=999455 norm=379.88718733030714 2023/02/07 07:24:10 Cluster 2 size in kmers=999455 norm=907.2167335611609 2023/02/07 07:24:10 END of Creating AB Cluster Vectors cpus=8 using=1 2023/02/07 07:24:10 START of AB Binning 2023/02/07 07:24:10 FastaManager: START READ 2023/02/07 07:24:10 SequenceProcessor: 0 AB_BINNING START 2023/02/07 07:24:10 FastaManager: lines read 53328 2023/02/07 07:24:10 FastaManager: END READ 2023/02/07 07:24:10 FastaManager: FASTA 2023/02/07 07:24:13 SequenceProcessor: 0 AB_BINNING EXIT 2023/02/07 07:24:13 END of AB Binning cpus=8 using=1 2023/02/07 07:24:13 START of CB Counting 2023/02/07 07:24:13 FastaManager: START READ 2023/02/07 07:24:13 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2023/02/07 07:24:14 FastaManager: lines read 53328 2023/02/07 07:24:14 FastaManager: END READ 2023/02/07 07:24:14 FastaManager: FASTA 2023/02/07 07:24:14 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2023/02/07 07:24:14 END of CB Counting 2023/02/07 07:24:14 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=1.465 Current Total Memory=0.709 Current Used Memory=0.357 Current Free Memory=0.352 ############################################ 2023/02/07 07:24:14 AB Cluster=1 Size=19761 2023/02/07 07:24:14 AB Cluster=2 Size=6903 cpus=8 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 1 19,761 21.14243 160,404 140,199 1 1 2023/02/07 07:24:14 START of Creating CB Clusters for AB Cluster=1 Size=19761 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 0 ...end. 2.289 seconds. 2023/02/07 07:24:17 : kMeans cleanup. 2023/02/07 07:24:17 END of Creating CB Clusters for AB Cluster=1 cpus=8 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 2 6,903 4.91974 839,050 210,468 1 1 2023/02/07 07:24:17 START of Creating CB Clusters for AB Cluster=2 Size=6903 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads Killed * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/metabinR.Rcheck/00check.log’ for details.
metabinR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metabinR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘metabinR’ ... ** 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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.197 0.031 0.218
metabinR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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(metabinR) > > test_check("metabinR") version MTxAB =Mon Feb 06 01:55:16 UTC 2023 cpus=8 using=1 2023/02/07 07:23:04 Using Dictionary ORIGINAL 2023/02/07 07:23:04 START of AB Counting 2023/02/07 07:23:04 FastaManager: START READ 2023/02/07 07:23:04 SequenceProcessor: 0 AB_KMERCOUNT START CHUNK_SIZE=67108864 2023/02/07 07:23:04 FastaManager: lines read 53328 2023/02/07 07:23:05 FastaManager: END READ 2023/02/07 07:23:05 FastaManager: FASTA 2023/02/07 07:23:06 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2023/02/07 07:23:06 END of AB Counting 2023/02/07 07:23:06 Loaded sequences: 26664 2023/02/07 07:23:06 Total kmers(before remove): 65536 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.244 Current Used Memory=0.109 Current Free Memory=0.135 ############################################ 2023/02/07 07:23:06 Unique: 0 Distinct: 65536 Total: 7625904 MaxCount: 1574 2023/02/07 07:23:06 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 2023/02/07 07:23:06 Runs=25 2023/02/07 07:23:06 END of EMsync 2023/02/07 07:23:06 START of Creating AB Cluster Vectors Cluster 1 Abundance=241.01134335779187 Length=16168.173737759447 LowLimit=163 HighLimit=318 Cluster 2 Abundance=75.538888587297 Length=49367.82626224055 LowLimit=32 HighLimit=118 2023/02/07 07:23:06 Trove size/4=18022 2023/02/07 07:23:06 Trove size/4=18022 2023/02/07 07:23:07 Cluster 1 size in kmers=65536 norm=126.50589485137961 2023/02/07 07:23:07 Cluster 2 size in kmers=65536 norm=221.81983091435748 2023/02/07 07:23:07 END of Creating AB Cluster Vectors cpus=8 using=1 2023/02/07 07:23:07 START of AB Binning 2023/02/07 07:23:07 FastaManager: START READ 2023/02/07 07:23:07 SequenceProcessor: 0 AB_BINNING START 2023/02/07 07:23:07 FastaManager: lines read 53328 2023/02/07 07:23:07 FastaManager: END READ 2023/02/07 07:23:07 FastaManager: FASTA 2023/02/07 07:23:09 SequenceProcessor: 0 AB_BINNING EXIT 2023/02/07 07:23:09 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=0.267 Current Used Memory=0.153 Current Free Memory=0.113 ############################################ version MTxCB =Mon Feb 06 01:55:16 UTC 2023 cpus=8 using=1 2023/02/07 07:23:10 START of CB Counting 2023/02/07 07:23:10 FastaManager: START READ 2023/02/07 07:23:10 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2023/02/07 07:23:10 FastaManager: lines read 53328 2023/02/07 07:23:10 FastaManager: END READ 2023/02/07 07:23:10 FastaManager: FASTA 2023/02/07 07:23:11 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2023/02/07 07:23:11 END of CB Counting 2023/02/07 07:23:11 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.283 Current Used Memory=0.223 Current Free Memory=0.06 ############################################ cpus=8 using=1 2023/02/07 07:23:11 START of Creating CB Clusters Size=26664 K-Means clustering started ... centers initialized ... concurrent processing mode with 1 subtask threads ... iteration 1 moves = 6252 ... iteration 2 moves = 5312 ... iteration 3 moves = 2114 ... iteration 4 moves = 767 ... iteration 5 moves = 361 ... iteration 6 moves = 147 ... iteration 7 moves = 56 ... iteration 8 moves = 60 ... iteration 9 moves = 30 ... iteration 10 moves = 16 ... iteration 11 moves = 6 ... iteration 12 moves = 0 ...end. 6.169 seconds. 2023/02/07 07:23:17 : kMeans cleanup. 2023/02/07 07:23:17 END of Creating CB Clusters. cpus=8 using=1 2023/02/07 07:23:17 START of CB Binning 2023/02/07 07:23:17 FastaManager: START READ 2023/02/07 07:23:17 SequenceProcessor: 0 CB_BINNING START 2023/02/07 07:23:17 FastaManager: lines read 53328 2023/02/07 07:23:17 FastaManager: END READ 2023/02/07 07:23:17 FastaManager: FASTA 2023/02/07 07:23:18 SequenceProcessor: 0 CB_BINNING EXIT Clustered reads: CB Cluster 1: 10620 CB Cluster 2: 16044 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.347 Current Used Memory=0.117 Current Free Memory=0.23 ############################################ version MTxABxCB =Mon Feb 06 01:55:16 UTC 2023 cpus=8 using=1 2023/02/07 07:23:18 Using Dictionary ORIGINAL 2023/02/07 07:23:18 START of AB Counting 2023/02/07 07:23:18 FastaManager: START READ 2023/02/07 07:23:18 SequenceProcessor: 0 AB_KMERCOUNT START 2023/02/07 07:23:18 FastaManager: lines read 53328 2023/02/07 07:23:18 FastaManager: END READ 2023/02/07 07:23:18 FastaManager: FASTA 2023/02/07 07:23:20 SequenceProcessor: 0 AB_KMERCOUNT EXIT 2023/02/07 07:23:20 END of AB Counting 2023/02/07 07:23:20 Loaded sequences: 26664 2023/02/07 07:23:20 Distinct kmers(before remove): 65536 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.347 Current Used Memory=0.181 Current Free Memory=0.165 ############################################ 2023/02/07 07:23:20 Unique: 0 Distinct: 65536 Total: 7625904 MaxCount: 1574 2023/02/07 07:23:20 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 2023/02/07 07:23:20 Runs=25 2023/02/07 07:23:20 END of EMsync 2023/02/07 07:23:20 Filter before=2 2023/02/07 07:23:20 Filter after=2 2023/02/07 07:23:20 START of Creating AB Cluster Vectors Cluster 1 Abundance=75.538888587297 Length=49367.82626224055 LowLimit=32 HighLimit=118 Cluster 2 Abundance=241.01134335779187 Length=16168.173737759447 LowLimit=163 HighLimit=318 2023/02/07 07:23:20 Trove size/4=18022 2023/02/07 07:23:20 Trove size/4=18022 2023/02/07 07:23:20 Cluster 1 size in kmers=65536 norm=221.81983091435748 2023/02/07 07:23:20 Cluster 2 size in kmers=65536 norm=126.50589485137961 2023/02/07 07:23:20 END of Creating AB Cluster Vectors cpus=8 using=1 2023/02/07 07:23:20 START of AB Binning 2023/02/07 07:23:20 FastaManager: START READ 2023/02/07 07:23:20 SequenceProcessor: 0 AB_BINNING START 2023/02/07 07:23:20 FastaManager: lines read 53328 2023/02/07 07:23:20 FastaManager: END READ 2023/02/07 07:23:20 FastaManager: FASTA 2023/02/07 07:23:22 SequenceProcessor: 0 AB_BINNING EXIT 2023/02/07 07:23:22 END of AB Binning cpus=8 using=1 2023/02/07 07:23:22 START of CB Counting 2023/02/07 07:23:22 FastaManager: START READ 2023/02/07 07:23:22 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START 2023/02/07 07:23:23 FastaManager: lines read 53328 2023/02/07 07:23:23 FastaManager: END READ 2023/02/07 07:23:23 FastaManager: FASTA 2023/02/07 07:23:23 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT 2023/02/07 07:23:23 END of CB Counting 2023/02/07 07:23:23 Loaded sequences: 26664 ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.378 Current Used Memory=0.325 Current Free Memory=0.053 ############################################ 2023/02/07 07:23:23 AB Cluster=1 Size=6793 2023/02/07 07:23:23 AB Cluster=2 Size=19871 cpus=8 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 1 6,793 75.53889 49,367 13,489 1 1 2023/02/07 07:23:23 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. 0.942 seconds. 2023/02/07 07:23:24 : kMeans cleanup. 2023/02/07 07:23:24 END of Creating CB Clusters for AB Cluster=1 cpus=8 using=1 ABid size abundance EMLength newLength EMspecies newspecies ----- ---- --------- -------- --------- --------- ---------- 2 19,871 241.01134 16,168 12,367 1 1 2023/02/07 07:23:24 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. 2.485 seconds. 2023/02/07 07:23:27 END of Creating CB Clusters for AB Cluster=2 2023/02/07 07:23:27 : kMeans cleanup. ##### Heap utilization statistics [GB] ##### Max Memory=0.5 Current Total Memory=0.378 Current Used Memory=0.305 Current Free Memory=0.073 ############################################ cpus=8 using=1 2023/02/07 07:23:27 START of CB Binning 2023/02/07 07:23:27 FastaManager: START READ 2023/02/07 07:23:27 SequenceProcessor: 0 CB_BINNING START 2023/02/07 07:23:27 FastaManager: lines read 53328 2023/02/07 07:23:27 FastaManager: END READ 2023/02/07 07:23:27 FastaManager: FASTA 2023/02/07 07:23:27 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=0.441 Current Used Memory=0.32 Current Free Memory=0.121 ############################################ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ] > > proc.time() user system elapsed 31.186 0.689 25.126
metabinR.Rcheck/metabinR-Ex.timings
name | user | system | elapsed | |
abundance_based_binning | 9.487 | 0.493 | 7.656 | |
composition_based_binning | 3.831 | 0.259 | 2.614 | |
hierarchical_binning | 4.573 | 0.254 | 3.767 | |