| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:08 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1238/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.12.0 (landing page) Anestis Gkanogiannis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: metabinR |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2025-12-13 10:58:15 -0500 (Sat, 13 Dec 2025) |
| EndedAt: 2025-12-13 11:04:16 -0500 (Sat, 13 Dec 2025) |
| EllapsedTime: 361.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metabinR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/metabinR.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabinR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabinR’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
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 8.802 0.937 9.089
hierarchical_binning 5.221 0.690 5.134
composition_based_binning 4.627 0.718 3.424
* 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
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-arm64/Resources/library’ * installing *source* package ‘metabinR’ ... ** this is package ‘metabinR’ version ‘1.12.0’ ** 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)
metabinR.Rcheck/tests/spelling.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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)
All Done!
>
> proc.time()
user system elapsed
0.213 0.068 0.276
metabinR.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 =Thu Dec 11 15:13:24 EST 2025
cpus=10
using=1
2025/12/13 11:03:34 Using Dictionary ORIGINAL
2025/12/13 11:03:34 START of AB Counting
2025/12/13 11:03:34 FastaManager: START READ
2025/12/13 11:03:34 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2025/12/13 11:03:34 FastaManager: lines read 53328
2025/12/13 11:03:34 FastaManager: END READ
2025/12/13 11:03:34 FastaManager: FASTA
2025/12/13 11:03:36 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2025/12/13 11:03:36 END of AB Counting
2025/12/13 11:03:36 Loaded sequences: 26664
2025/12/13 11:03:36 Total kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.261
Current Free Memory=0.239
############################################
2025/12/13 11:03:36
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2025/12/13 11:03:36 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
2025/12/13 11:03:36 Runs=25
2025/12/13 11:03:36 END of EMsync
2025/12/13 11:03:36 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
2025/12/13 11:03:36 Trove size/4=18022
2025/12/13 11:03:36 Trove size/4=18022
2025/12/13 11:03:36 Cluster 1 size in kmers=65536 norm=126.50589485137961
2025/12/13 11:03:36 Cluster 2 size in kmers=65536 norm=221.81983091435748
2025/12/13 11:03:36 END of Creating AB Cluster Vectors
cpus=10
using=1
2025/12/13 11:03:36 START of AB Binning
2025/12/13 11:03:36 FastaManager: START READ
2025/12/13 11:03:36 SequenceProcessor: 0 AB_BINNING START
2025/12/13 11:03:36 FastaManager: lines read 53328
2025/12/13 11:03:36 FastaManager: END READ
2025/12/13 11:03:36 FastaManager: FASTA
2025/12/13 11:03:40 SequenceProcessor: 0 AB_BINNING EXIT
2025/12/13 11:03:40 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=0.345
Current Free Memory=0.155
############################################
version MTxCB =Thu Dec 11 15:13:24 EST 2025
cpus=10
using=1
2025/12/13 11:03:40 START of CB Counting
2025/12/13 11:03:40 FastaManager: START READ
2025/12/13 11:03:40 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2025/12/13 11:03:40 FastaManager: lines read 53328
2025/12/13 11:03:40 FastaManager: END READ
2025/12/13 11:03:40 FastaManager: FASTA
2025/12/13 11:03:41 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2025/12/13 11:03:41 END of CB Counting
2025/12/13 11:03:41 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.417
Current Free Memory=0.083
############################################
cpus=10
using=1
2025/12/13 11:03:41 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 6766
... iteration 2 moves = 2122
... iteration 3 moves = 707
... iteration 4 moves = 346
... iteration 5 moves = 148
... iteration 6 moves = 67
... iteration 7 moves = 49
... iteration 8 moves = 29
... iteration 9 moves = 21
... iteration 10 moves = 22
... iteration 11 moves = 5
... iteration 12 moves = 0
...end. 7.689 seconds.
2025/12/13 11:03:49 : kMeans cleanup.
2025/12/13 11:03:49 END of Creating CB Clusters.
cpus=10
using=1
2025/12/13 11:03:49 START of CB Binning
2025/12/13 11:03:49 FastaManager: START READ
2025/12/13 11:03:49 SequenceProcessor: 0 CB_BINNING START
2025/12/13 11:03:49 FastaManager: lines read 53328
2025/12/13 11:03:49 FastaManager: END READ
2025/12/13 11:03:49 FastaManager: FASTA
2025/12/13 11:03:49 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=0.457
Current Free Memory=0.043
############################################
version MTxABxCB =Thu Dec 11 15:13:24 EST 2025
cpus=10
using=1
2025/12/13 11:03:50 Using Dictionary ORIGINAL
2025/12/13 11:03:50 START of AB Counting
2025/12/13 11:03:50 FastaManager: START READ
2025/12/13 11:03:50 SequenceProcessor: 0 AB_KMERCOUNT START
2025/12/13 11:03:50 FastaManager: lines read 53328
2025/12/13 11:03:50 FastaManager: END READ
2025/12/13 11:03:50 FastaManager: FASTA
2025/12/13 11:03:52 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2025/12/13 11:03:52 END of AB Counting
2025/12/13 11:03:52 Loaded sequences: 26664
2025/12/13 11:03:52 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.258
Current Used Memory=0.15
Current Free Memory=0.108
############################################
2025/12/13 11:03:52
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2025/12/13 11:03:52 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
2025/12/13 11:03:52 Runs=25
2025/12/13 11:03:52 END of EMsync
2025/12/13 11:03:52 Filter before=2
2025/12/13 11:03:52 Filter after=2
2025/12/13 11:03:52 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
2025/12/13 11:03:52 Trove size/4=18022
2025/12/13 11:03:52 Trove size/4=18022
2025/12/13 11:03:52 Cluster 1 size in kmers=65536 norm=126.50589485137961
2025/12/13 11:03:52 Cluster 2 size in kmers=65536 norm=221.81983091435748
2025/12/13 11:03:52 END of Creating AB Cluster Vectors
cpus=10
using=1
2025/12/13 11:03:52 START of AB Binning
2025/12/13 11:03:52 FastaManager: START READ
2025/12/13 11:03:52 SequenceProcessor: 0 AB_BINNING START
2025/12/13 11:03:52 FastaManager: lines read 53328
2025/12/13 11:03:52 FastaManager: END READ
2025/12/13 11:03:52 FastaManager: FASTA
2025/12/13 11:03:56 SequenceProcessor: 0 AB_BINNING EXIT
2025/12/13 11:03:56 END of AB Binning
cpus=10
using=1
2025/12/13 11:03:56 START of CB Counting
2025/12/13 11:03:56 FastaManager: START READ
2025/12/13 11:03:56 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2025/12/13 11:03:56 FastaManager: lines read 53328
2025/12/13 11:03:56 FastaManager: END READ
2025/12/13 11:03:56 FastaManager: FASTA
2025/12/13 11:03:57 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2025/12/13 11:03:57 END of CB Counting
2025/12/13 11:03:57 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.416
Current Used Memory=0.277
Current Free Memory=0.139
############################################
2025/12/13 11:03:57 AB Cluster=1 Size=19871
2025/12/13 11:03:57 AB Cluster=2 Size=6793
cpus=10
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
1 19,871 241.01134 16,168 12,367 1 1
2025/12/13 11:03:57 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. 3.988 seconds.
2025/12/13 11:04:01 END of Creating CB Clusters for AB Cluster=1
2025/12/13 11:04:01 : kMeans cleanup.
cpus=10
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
2 6,793 75.53889 49,367 13,489 1 1
2025/12/13 11:04:01 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. 1.304 seconds.
2025/12/13 11:04:02 : kMeans cleanup.
2025/12/13 11:04:02 END of Creating CB Clusters for AB Cluster=2
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.425
Current Used Memory=0.291
Current Free Memory=0.134
############################################
cpus=10
using=1
2025/12/13 11:04:02 START of CB Binning
2025/12/13 11:04:02 FastaManager: START READ
2025/12/13 11:04:02 SequenceProcessor: 0 CB_BINNING START
2025/12/13 11:04:02 FastaManager: lines read 53328
2025/12/13 11:04:02 FastaManager: END READ
2025/12/13 11:04:02 FastaManager: FASTA
2025/12/13 11:04:03 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=0.45
Current Used Memory=0.264
Current Free Memory=0.186
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
35.166 0.943 30.716
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 8.802 | 0.937 | 9.089 | |
| composition_based_binning | 4.627 | 0.718 | 3.424 | |
| hierarchical_binning | 5.221 | 0.690 | 5.134 | |