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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1223/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabinR 1.10.0  (landing page)
Anestis Gkanogiannis
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/metabinR
git_branch: RELEASE_3_21
git_last_commit: f3a7794
git_last_commit_date: 2025-04-15 12:59:43 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for metabinR on merida1

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.

raw results


Summary

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: 2025-08-19 06:59:44 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 07:01:44 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 119.9 seconds
RetCode: 0
Status:   OK  
CheckDir: metabinR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.5.1 RC (2025-06-05 r88288)
* 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   12.388  2.363  11.568
composition_based_binning  8.350  1.862   4.597
hierarchical_binning       7.871  1.629   6.652
* 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


Installation output

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)

Tests output

metabinR.Rcheck/tests/spelling.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
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 
  0.349   0.113   0.438 

metabinR.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
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 Aug 18 15:49:27 EDT 2025
cpus=24
using=1
2025/08/19 07:00:57 Using Dictionary ORIGINAL
2025/08/19 07:00:57 START of AB Counting
2025/08/19 07:00:57 FastaManager: START READ
2025/08/19 07:00:57 SequenceProcessor: 0	AB_KMERCOUNT START
CHUNK_SIZE=67108864
2025/08/19 07:00:57 FastaManager: lines read 53328
2025/08/19 07:00:57 FastaManager: END READ
2025/08/19 07:00:57 FastaManager: FASTA
2025/08/19 07:01:00 SequenceProcessor: 0	AB_KMERCOUNT EXIT
2025/08/19 07:01:00 END of AB Counting
2025/08/19 07:01:00 Loaded sequences: 26664
2025/08/19 07:01:00 Total kmers(before remove):	65536


##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.305
Current Free Memory=0.195
############################################

2025/08/19 07:01:00
Unique:		0
Distinct:	65536
Total:		7625904
MaxCount:	1574

2025/08/19 07:01:00 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
2025/08/19 07:01:00	Runs=25
2025/08/19 07:01:00 END of EMsync
2025/08/19 07:01:00 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
2025/08/19 07:01:00	Trove size/4=18022
2025/08/19 07:01:00	Trove size/4=18022
2025/08/19 07:01:00	Cluster 2	size in kmers=65536	norm=221.81983091435748
2025/08/19 07:01:00	Cluster 1	size in kmers=65536	norm=126.5058948513796
2025/08/19 07:01:00 END of Creating AB Cluster Vectors
cpus=24
using=1
2025/08/19 07:01:00 START of AB Binning
2025/08/19 07:01:00 FastaManager: START READ
2025/08/19 07:01:00 SequenceProcessor: 0	AB_BINNING START
2025/08/19 07:01:00 FastaManager: lines read 53328
2025/08/19 07:01:00 FastaManager: END READ
2025/08/19 07:01:00 FastaManager: FASTA
2025/08/19 07:01:04 SequenceProcessor: 0	AB_BINNING EXIT
2025/08/19 07:01:04 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=0.391
Current Free Memory=0.109
############################################

version MTxCB =Mon Aug 18 15:49:27 EDT 2025
cpus=24
using=1
2025/08/19 07:01:05 START of CB Counting
2025/08/19 07:01:05 FastaManager: START READ
2025/08/19 07:01:05 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD START
2025/08/19 07:01:05 FastaManager: lines read 53328
2025/08/19 07:01:05 FastaManager: END READ
2025/08/19 07:01:05 FastaManager: FASTA
2025/08/19 07:01:06 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD EXIT
2025/08/19 07:01:06 END of CB Counting
2025/08/19 07:01:06 Loaded sequences: 26664

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.403
Current Free Memory=0.097
############################################

cpus=24
using=1
2025/08/19 07:01:06 START of Creating CB Clusters	Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 5492
... iteration 2 moves = 3631
... iteration 3 moves = 4614
... iteration 4 moves = 2630
... iteration 5 moves = 1118
... iteration 6 moves = 537
... iteration 7 moves = 345
... iteration 8 moves = 263
... iteration 9 moves = 289
... iteration 10 moves = 309
... iteration 11 moves = 395
... iteration 12 moves = 480
... iteration 13 moves = 464
... iteration 14 moves = 418
... iteration 15 moves = 356
... iteration 16 moves = 321
... iteration 17 moves = 297
... iteration 18 moves = 260
... iteration 19 moves = 245
... iteration 20 moves = 176
... iteration 21 moves = 109
... iteration 22 moves = 63
... iteration 23 moves = 51
... iteration 24 moves = 47
... iteration 25 moves = 18
...end.	10.035 seconds.
2025/08/19 07:01:16 : kMeans cleanup.
2025/08/19 07:01:16 END of Creating CB Clusters.
cpus=24
using=1
2025/08/19 07:01:16 START of CB Binning
2025/08/19 07:01:16 FastaManager: START READ
2025/08/19 07:01:16 SequenceProcessor: 0	CB_BINNING START
2025/08/19 07:01:16 FastaManager: lines read 53328
2025/08/19 07:01:16 FastaManager: END READ
2025/08/19 07:01:16 FastaManager: FASTA
2025/08/19 07:01:16 SequenceProcessor: 0	CB_BINNING EXIT
	Clustered reads:
		CB Cluster 1: 9339
		CB Cluster 2: 17325

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.426
Current Free Memory=0.074
############################################

version MTxABxCB =Mon Aug 18 15:49:27 EDT 2025
cpus=24
using=1
2025/08/19 07:01:17 Using Dictionary ORIGINAL
2025/08/19 07:01:17 START of AB Counting
2025/08/19 07:01:17 FastaManager: START READ
2025/08/19 07:01:17 SequenceProcessor: 0	AB_KMERCOUNT START
2025/08/19 07:01:17 FastaManager: lines read 53328
2025/08/19 07:01:17 FastaManager: END READ
2025/08/19 07:01:17 FastaManager: FASTA
2025/08/19 07:01:19 SequenceProcessor: 0	AB_KMERCOUNT EXIT
2025/08/19 07:01:19 END of AB Counting
2025/08/19 07:01:19 Loaded sequences: 26664
2025/08/19 07:01:19 Distinct kmers(before remove):	65536


##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.296
Current Free Memory=0.204
############################################

2025/08/19 07:01:19
Unique:		0
Distinct:	65536
Total:		7625904
MaxCount:	1574

2025/08/19 07:01:19 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
2025/08/19 07:01:19	Runs=25
2025/08/19 07:01:19 END of EMsync
2025/08/19 07:01:19	Filter before=2
2025/08/19 07:01:19	Filter after=2
2025/08/19 07:01:19 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
2025/08/19 07:01:19	Trove size/4=18022
2025/08/19 07:01:19	Trove size/4=18022
2025/08/19 07:01:19	Cluster 1	size in kmers=65536	norm=126.5058948513796
2025/08/19 07:01:19	Cluster 2	size in kmers=65536	norm=221.81983091435748
2025/08/19 07:01:19 END of Creating AB Cluster Vectors
cpus=24
using=1
2025/08/19 07:01:19 START of AB Binning
2025/08/19 07:01:19 FastaManager: START READ
2025/08/19 07:01:19 SequenceProcessor: 0	AB_BINNING START
2025/08/19 07:01:19 FastaManager: lines read 53328
2025/08/19 07:01:19 FastaManager: END READ
2025/08/19 07:01:19 FastaManager: FASTA
2025/08/19 07:01:23 SequenceProcessor: 0	AB_BINNING EXIT
2025/08/19 07:01:23 END of AB Binning
cpus=24
using=1
2025/08/19 07:01:23 START of CB Counting
2025/08/19 07:01:23 FastaManager: START READ
2025/08/19 07:01:23 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD START
2025/08/19 07:01:23 FastaManager: lines read 53328
2025/08/19 07:01:23 FastaManager: END READ
2025/08/19 07:01:23 FastaManager: FASTA
2025/08/19 07:01:24 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD EXIT
2025/08/19 07:01:24 END of CB Counting
2025/08/19 07:01:24 Loaded sequences: 26664

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.43
Current Free Memory=0.07
############################################

2025/08/19 07:01:24 AB Cluster=1	Size=19871
2025/08/19 07:01:24 AB Cluster=2	Size=6793

cpus=24
using=1
 ABid	    size	   abundance	  EMLength	 newLength	 EMspecies	newspecies
-----	    ----	   ---------	  --------	 ---------	 ---------	----------
    1	  19,871	   241.01134	    16,168	    12,367	    1		    1
2025/08/19 07:01:24 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.	3.481 seconds.
2025/08/19 07:01:27 END of Creating CB Clusters for AB Cluster=1
2025/08/19 07:01:27 : kMeans cleanup.
cpus=24
using=1
 ABid	    size	   abundance	  EMLength	 newLength	 EMspecies	newspecies
-----	    ----	   ---------	  --------	 ---------	 ---------	----------
    2	   6,793	    75.53889	    49,367	    13,489	    1		    1
2025/08/19 07:01:27 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.	1.128 seconds.
2025/08/19 07:01:28 : kMeans cleanup.
2025/08/19 07:01:28 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=0.349
Current Free Memory=0.151
############################################

cpus=24
using=1
2025/08/19 07:01:28 START of CB Binning
2025/08/19 07:01:28 FastaManager: START READ
2025/08/19 07:01:28 SequenceProcessor: 0	CB_BINNING START
2025/08/19 07:01:28 FastaManager: lines read 53328
2025/08/19 07:01:28 FastaManager: END READ
2025/08/19 07:01:28 FastaManager: FASTA
2025/08/19 07:01:29 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=0.473
Current Free Memory=0.027
############################################

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
> 
> proc.time()
   user  system elapsed 
 48.593   1.626  35.145 

Example timings

metabinR.Rcheck/metabinR-Ex.timings

nameusersystemelapsed
abundance_based_binning12.388 2.36311.568
composition_based_binning8.3501.8624.597
hierarchical_binning7.8711.6296.652