Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-03-19 11:41 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1210/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabinR 1.9.0  (landing page)
Anestis Gkanogiannis
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/metabinR
git_branch: devel
git_last_commit: e7264a2
git_last_commit_date: 2024-10-29 11:16:18 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

CHECK results for metabinR on nebbiolo1

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: 1.9.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings metabinR_1.9.0.tar.gz
StartedAt: 2025-03-18 23:44:57 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 23:46:30 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 93.1 seconds
RetCode: 0
Status:   OK  
CheckDir: metabinR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings metabinR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/metabinR.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘metabinR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabinR’ version ‘1.9.0’
* 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   7.824  1.243   5.877
composition_based_binning 5.446  0.849   2.110
hierarchical_binning      4.877  0.692   3.600
* 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

Installation output

metabinR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL metabinR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘metabinR’ ...
** this is package ‘metabinR’ version ‘1.9.0’
** 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 Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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)
NULL
> 
> proc.time()
   user  system elapsed 
  0.148   0.035   0.172

metabinR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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 =Tue Mar 18 15:04:49 EDT 2025
cpus=72
using=1
2025/03/18 23:45:30 Using Dictionary ORIGINAL
2025/03/18 23:45:30 START of AB Counting
2025/03/18 23:45:30 FastaManager: START READ
2025/03/18 23:45:30 SequenceProcessor: 0	AB_KMERCOUNT START
CHUNK_SIZE=67108864
2025/03/18 23:45:30 FastaManager: lines read 53328
2025/03/18 23:45:30 FastaManager: END READ
2025/03/18 23:45:30 FastaManager: FASTA
2025/03/18 23:45:31 SequenceProcessor: 0	AB_KMERCOUNT EXIT
2025/03/18 23:45:31 END of AB Counting
2025/03/18 23:45:31 Loaded sequences: 26664
2025/03/18 23:45:31 Total kmers(before remove):	65536


##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.291
Current Free Memory=0.209
############################################

2025/03/18 23:45:31
Unique:		0
Distinct:	65536
Total:		7625904
MaxCount:	1574

2025/03/18 23:45:31 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
2025/03/18 23:45:31	Runs=25
2025/03/18 23:45:31 END of EMsync
2025/03/18 23:45:31 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
2025/03/18 23:45:31	Trove size/4=18022
2025/03/18 23:45:31	Trove size/4=18022
2025/03/18 23:45:31	Cluster 1	size in kmers=65536	norm=126.5058948513796
2025/03/18 23:45:31	Cluster 2	size in kmers=65536	norm=221.81983091435748
2025/03/18 23:45:31 END of Creating AB Cluster Vectors
cpus=72
using=1
2025/03/18 23:45:31 START of AB Binning
2025/03/18 23:45:31 FastaManager: START READ
2025/03/18 23:45:31 SequenceProcessor: 0	AB_BINNING START
2025/03/18 23:45:32 FastaManager: lines read 53328
2025/03/18 23:45:32 FastaManager: END READ
2025/03/18 23:45:32 FastaManager: FASTA
2025/03/18 23:45:34 SequenceProcessor: 0	AB_BINNING EXIT
2025/03/18 23:45:34 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=0.374
Current Free Memory=0.126
############################################

version MTxCB =Tue Mar 18 15:04:49 EDT 2025
cpus=72
using=1
2025/03/18 23:45:34 START of CB Counting
2025/03/18 23:45:34 FastaManager: START READ
2025/03/18 23:45:34 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD START
2025/03/18 23:45:34 FastaManager: lines read 53328
2025/03/18 23:45:34 FastaManager: END READ
2025/03/18 23:45:34 FastaManager: FASTA
2025/03/18 23:45:35 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD EXIT
2025/03/18 23:45:35 END of CB Counting
2025/03/18 23:45:35 Loaded sequences: 26664

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.384
Current Free Memory=0.116
############################################

cpus=72
using=1
2025/03/18 23:45:35 START of Creating CB Clusters	Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 2657
... iteration 2 moves = 389
... iteration 3 moves = 182
... iteration 4 moves = 126
... iteration 5 moves = 78
... iteration 6 moves = 50
... iteration 7 moves = 34
... iteration 8 moves = 40
... iteration 9 moves = 30
... iteration 10 moves = 15
... iteration 11 moves = 8
... iteration 12 moves = 16
... iteration 13 moves = 4
... iteration 14 moves = 0
...end.	4.684 seconds.
2025/03/18 23:45:40 : kMeans cleanup.
2025/03/18 23:45:40 END of Creating CB Clusters.
cpus=72
using=1
2025/03/18 23:45:40 START of CB Binning
2025/03/18 23:45:40 FastaManager: START READ
2025/03/18 23:45:40 SequenceProcessor: 0	CB_BINNING START
2025/03/18 23:45:40 FastaManager: lines read 53328
2025/03/18 23:45:40 FastaManager: END READ
2025/03/18 23:45:40 FastaManager: FASTA
2025/03/18 23:45:40 SequenceProcessor: 0	CB_BINNING EXIT
	Clustered reads:
		CB Cluster 1: 9294
		CB Cluster 2: 17370

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.485
Current Free Memory=0.015
############################################

version MTxABxCB =Tue Mar 18 15:04:49 EDT 2025
cpus=72
using=1
2025/03/18 23:45:40 Using Dictionary ORIGINAL
2025/03/18 23:45:40 START of AB Counting
2025/03/18 23:45:40 FastaManager: START READ
2025/03/18 23:45:40 SequenceProcessor: 0	AB_KMERCOUNT START
2025/03/18 23:45:40 FastaManager: lines read 53328
2025/03/18 23:45:40 FastaManager: END READ
2025/03/18 23:45:40 FastaManager: FASTA
2025/03/18 23:45:41 SequenceProcessor: 0	AB_KMERCOUNT EXIT
2025/03/18 23:45:41 END of AB Counting
2025/03/18 23:45:41 Loaded sequences: 26664
2025/03/18 23:45:41 Distinct kmers(before remove):	65536


##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.327
Current Free Memory=0.173
############################################

2025/03/18 23:45:41
Unique:		0
Distinct:	65536
Total:		7625904
MaxCount:	1574

2025/03/18 23:45:41 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
2025/03/18 23:45:41	Runs=25
2025/03/18 23:45:41 END of EMsync
2025/03/18 23:45:41	Filter before=2
2025/03/18 23:45:41	Filter after=2
2025/03/18 23:45:41 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
2025/03/18 23:45:41	Trove size/4=18022
2025/03/18 23:45:41	Trove size/4=18022
2025/03/18 23:45:41	Cluster 2	size in kmers=65536	norm=221.81983091435748
2025/03/18 23:45:41	Cluster 1	size in kmers=65536	norm=126.5058948513796
2025/03/18 23:45:41 END of Creating AB Cluster Vectors
cpus=72
using=1
2025/03/18 23:45:41 START of AB Binning
2025/03/18 23:45:41 FastaManager: START READ
2025/03/18 23:45:41 SequenceProcessor: 0	AB_BINNING START
2025/03/18 23:45:42 FastaManager: lines read 53328
2025/03/18 23:45:42 FastaManager: END READ
2025/03/18 23:45:42 FastaManager: FASTA
2025/03/18 23:45:43 SequenceProcessor: 0	AB_BINNING EXIT
2025/03/18 23:45:43 END of AB Binning
cpus=72
using=1
2025/03/18 23:45:43 START of CB Counting
2025/03/18 23:45:43 FastaManager: START READ
2025/03/18 23:45:43 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD START
2025/03/18 23:45:43 FastaManager: lines read 53328
2025/03/18 23:45:44 FastaManager: END READ
2025/03/18 23:45:44 FastaManager: FASTA
2025/03/18 23:45:44 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD EXIT
2025/03/18 23:45:44 END of CB Counting
2025/03/18 23:45:44 Loaded sequences: 26664

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.441
Current Free Memory=0.059
############################################

2025/03/18 23:45:44 AB Cluster=1	Size=19871
2025/03/18 23:45:44 AB Cluster=2	Size=6793

cpus=72
using=1
 ABid	    size	   abundance	  EMLength	 newLength	 EMspecies	newspecies
-----	    ----	   ---------	  --------	 ---------	 ---------	----------
    1	  19,871	   241.01134	    16,168	    12,367	    1		    1
2025/03/18 23:45:44 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.	2.186 seconds.
2025/03/18 23:45:46 : kMeans cleanup.
2025/03/18 23:45:46 END of Creating CB Clusters for AB Cluster=1
cpus=72
using=1
 ABid	    size	   abundance	  EMLength	 newLength	 EMspecies	newspecies
-----	    ----	   ---------	  --------	 ---------	 ---------	----------
    2	   6,793	    75.53889	    49,367	    13,489	    1		    1
2025/03/18 23:45:46 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.	0.729 seconds.
2025/03/18 23:45:47 : kMeans cleanup.
2025/03/18 23:45:47 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=0.396
Current Free Memory=0.104
############################################

cpus=72
using=1
2025/03/18 23:45:47 START of CB Binning
2025/03/18 23:45:47 FastaManager: START READ
2025/03/18 23:45:47 SequenceProcessor: 0	CB_BINNING START
2025/03/18 23:45:47 FastaManager: lines read 53328
2025/03/18 23:45:47 FastaManager: END READ
2025/03/18 23:45:47 FastaManager: FASTA
2025/03/18 23:45:47 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=0.295
Current Free Memory=0.205
############################################

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
> 
> proc.time()
   user  system elapsed 
 28.089   1.087  19.174

Example timings

metabinR.Rcheck/metabinR-Ex.timings

nameusersystemelapsed
abundance_based_binning7.8241.2435.877
composition_based_binning5.4460.8492.110
hierarchical_binning4.8770.6923.600