| Back to Build/check report for BioC 3.17 |
|
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
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Run=3
Run=4
Run=5
Run=6
Run=7
Run=8
Run=9
Run=10
Run=11
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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
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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
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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 | |