Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:40:44 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1207/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metabinR 1.6.0  (landing page)
Anestis Gkanogiannis
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/metabinR
git_branch: RELEASE_3_19
git_last_commit: 6ff415a
git_last_commit_date: 2024-04-30 11:46:03 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for metabinR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: metabinR
Version: 1.6.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings metabinR_1.6.0.tar.gz
StartedAt: 2024-05-04 09:12:25 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 09:13:27 -0000 (Sat, 04 May 2024)
EllapsedTime: 62.1 seconds
RetCode: 0
Status:   OK  
CheckDir: metabinR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings metabinR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/metabinR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabinR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabinR’ version ‘1.6.0’
* 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 8.077  0.394   5.587
* 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:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL metabinR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)

Tests output

metabinR.Rcheck/tests/spelling.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  0.202   0.034   0.222 

metabinR.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 May 03 20:06:37 UTC 2024
cpus=32
using=1
2024/05/04 09:13:03 Using Dictionary ORIGINAL
2024/05/04 09:13:03 START of AB Counting
2024/05/04 09:13:03 FastaManager: START READ
2024/05/04 09:13:03 SequenceProcessor: 0	AB_KMERCOUNT START
CHUNK_SIZE=67108864
2024/05/04 09:13:03 FastaManager: lines read 53328
2024/05/04 09:13:03 FastaManager: END READ
2024/05/04 09:13:03 FastaManager: FASTA
2024/05/04 09:13:05 SequenceProcessor: 0	AB_KMERCOUNT EXIT
2024/05/04 09:13:05 END of AB Counting
2024/05/04 09:13:05 Loaded sequences: 26664
2024/05/04 09:13:05 Total kmers(before remove):	65536


##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.288
Current Free Memory=0.212
############################################

2024/05/04 09:13:05
Unique:		0
Distinct:	65536
Total:		7625904
MaxCount:	1574

2024/05/04 09:13:05 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
2024/05/04 09:13:05	Runs=25
2024/05/04 09:13:05 END of EMsync
2024/05/04 09:13:05 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
2024/05/04 09:13:05	Trove size/4=18022
2024/05/04 09:13:05	Trove size/4=18022
2024/05/04 09:13:05	Cluster 1	size in kmers=65536	norm=126.50589485137961
2024/05/04 09:13:05	Cluster 2	size in kmers=65536	norm=221.81983091435748
2024/05/04 09:13:05 END of Creating AB Cluster Vectors
cpus=32
using=1
2024/05/04 09:13:05 START of AB Binning
2024/05/04 09:13:05 FastaManager: START READ
2024/05/04 09:13:05 SequenceProcessor: 0	AB_BINNING START
2024/05/04 09:13:05 FastaManager: lines read 53328
2024/05/04 09:13:05 FastaManager: END READ
2024/05/04 09:13:05 FastaManager: FASTA
2024/05/04 09:13:08 SequenceProcessor: 0	AB_BINNING EXIT
2024/05/04 09:13:08 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=0.29
Current Free Memory=0.21
############################################

version MTxCB =Fri May 03 20:06:37 UTC 2024
cpus=32
using=1
2024/05/04 09:13:08 START of CB Counting
2024/05/04 09:13:08 FastaManager: START READ
2024/05/04 09:13:08 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD START
2024/05/04 09:13:08 FastaManager: lines read 53328
2024/05/04 09:13:08 FastaManager: END READ
2024/05/04 09:13:08 FastaManager: FASTA
2024/05/04 09:13:09 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD EXIT
2024/05/04 09:13:09 END of CB Counting
2024/05/04 09:13:09 Loaded sequences: 26664

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.367
Current Used Memory=0.246
Current Free Memory=0.121
############################################

cpus=32
using=1
2024/05/04 09:13:09 START of Creating CB Clusters	Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 3525
... iteration 2 moves = 431
... iteration 3 moves = 79
... iteration 4 moves = 32
... iteration 5 moves = 23
... iteration 6 moves = 23
... iteration 7 moves = 15
... iteration 8 moves = 11
... iteration 9 moves = 4
... iteration 10 moves = 7
... iteration 11 moves = 1
... iteration 12 moves = 0
...end.	5.64 seconds.
2024/05/04 09:13:14 : kMeans cleanup.
2024/05/04 09:13:14 END of Creating CB Clusters.
cpus=32
using=1
2024/05/04 09:13:14 START of CB Binning
2024/05/04 09:13:14 FastaManager: START READ
2024/05/04 09:13:14 SequenceProcessor: 0	CB_BINNING START
2024/05/04 09:13:14 FastaManager: lines read 53328
2024/05/04 09:13:15 FastaManager: END READ
2024/05/04 09:13:15 FastaManager: FASTA
2024/05/04 09:13:15 SequenceProcessor: 0	CB_BINNING EXIT
	Clustered reads:
		CB Cluster 1: 9303
		CB Cluster 2: 17361

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.393
Current Used Memory=0.313
Current Free Memory=0.08
############################################

version MTxABxCB =Fri May 03 20:06:37 UTC 2024
cpus=32
using=1
2024/05/04 09:13:15 Using Dictionary ORIGINAL
2024/05/04 09:13:15 START of AB Counting
2024/05/04 09:13:15 FastaManager: START READ
2024/05/04 09:13:15 SequenceProcessor: 0	AB_KMERCOUNT START
2024/05/04 09:13:15 FastaManager: lines read 53328
2024/05/04 09:13:15 FastaManager: END READ
2024/05/04 09:13:15 FastaManager: FASTA
2024/05/04 09:13:17 SequenceProcessor: 0	AB_KMERCOUNT EXIT
2024/05/04 09:13:17 END of AB Counting
2024/05/04 09:13:17 Loaded sequences: 26664
2024/05/04 09:13:17 Distinct kmers(before remove):	65536


##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.393
Current Used Memory=0.322
Current Free Memory=0.071
############################################

2024/05/04 09:13:17
Unique:		0
Distinct:	65536
Total:		7625904
MaxCount:	1574

2024/05/04 09:13:17 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
2024/05/04 09:13:17	Runs=25
2024/05/04 09:13:17 END of EMsync
2024/05/04 09:13:17	Filter before=2
2024/05/04 09:13:17	Filter after=2
2024/05/04 09:13:17 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
2024/05/04 09:13:17	Trove size/4=18022
2024/05/04 09:13:17	Trove size/4=18022
2024/05/04 09:13:17	Cluster 1	size in kmers=65536	norm=221.81983091435748
2024/05/04 09:13:17	Cluster 2	size in kmers=65536	norm=126.50589485137961
2024/05/04 09:13:17 END of Creating AB Cluster Vectors
cpus=32
using=1
2024/05/04 09:13:17 START of AB Binning
2024/05/04 09:13:17 FastaManager: START READ
2024/05/04 09:13:17 SequenceProcessor: 0	AB_BINNING START
2024/05/04 09:13:17 FastaManager: lines read 53328
2024/05/04 09:13:17 FastaManager: END READ
2024/05/04 09:13:17 FastaManager: FASTA
2024/05/04 09:13:19 SequenceProcessor: 0	AB_BINNING EXIT
2024/05/04 09:13:19 END of AB Binning
cpus=32
using=1
2024/05/04 09:13:19 START of CB Counting
2024/05/04 09:13:19 FastaManager: START READ
2024/05/04 09:13:19 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD START
2024/05/04 09:13:19 FastaManager: lines read 53328
2024/05/04 09:13:19 FastaManager: END READ
2024/05/04 09:13:19 FastaManager: FASTA
2024/05/04 09:13:20 SequenceProcessor: 0	CB_SEQUENCEVECTORBUILD EXIT
2024/05/04 09:13:20 END of CB Counting
2024/05/04 09:13:20 Loaded sequences: 26664

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.486
Current Used Memory=0.267
Current Free Memory=0.22
############################################

2024/05/04 09:13:20 AB Cluster=1	Size=6793
2024/05/04 09:13:20 AB Cluster=2	Size=19871

cpus=32
using=1
 ABid	    size	   abundance	  EMLength	 newLength	 EMspecies	newspecies
-----	    ----	   ---------	  --------	 ---------	 ---------	----------
    1	   6,793	    75.53889	    49,367	    13,489	    1		    1
2024/05/04 09:13:20 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.	0.807 seconds.
2024/05/04 09:13:21 : kMeans cleanup.
2024/05/04 09:13:21 END of Creating CB Clusters for AB Cluster=1
cpus=32
using=1
 ABid	    size	   abundance	  EMLength	 newLength	 EMspecies	newspecies
-----	    ----	   ---------	  --------	 ---------	 ---------	----------
    2	  19,871	   241.01134	    16,168	    12,367	    1		    1
2024/05/04 09:13:21 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.	2.308 seconds.
2024/05/04 09:13:23 : kMeans cleanup.
2024/05/04 09:13:23 END of Creating CB Clusters for AB Cluster=2

##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.486
Current Used Memory=0.366
Current Free Memory=0.12
############################################

cpus=32
using=1
2024/05/04 09:13:23 START of CB Binning
2024/05/04 09:13:23 FastaManager: START READ
2024/05/04 09:13:23 SequenceProcessor: 0	CB_BINNING START
2024/05/04 09:13:23 FastaManager: lines read 53328
2024/05/04 09:13:23 FastaManager: END READ
2024/05/04 09:13:23 FastaManager: FASTA
2024/05/04 09:13:23 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=0.329
Current Free Memory=0.171
############################################

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
> 
> proc.time()
   user  system elapsed 
 30.035   0.834  22.009 

Example timings

metabinR.Rcheck/metabinR-Ex.timings

nameusersystemelapsed
abundance_based_binning8.0770.3945.587
composition_based_binning4.6720.2201.672
hierarchical_binning4.3450.1143.008