| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1223/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.10.0 (landing page) Anestis Gkanogiannis
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.10.0 |
| 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: 2025-04-21 20:12:15 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:12:45 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 29.4 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/metabinR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 Ventura 13.7.1
* 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
* 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 ‘1.10.0’ ** 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)
metabinR.Rcheck/tests/spelling.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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)
NULL
>
> proc.time()
user system elapsed
0.071 0.022 0.087
metabinR.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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 =Mon Apr 21 15:01:52 EDT 2025
cpus=24
using=1
2025/04/21 20:12:31 Using Dictionary ORIGINAL
2025/04/21 20:12:31 START of AB Counting
2025/04/21 20:12:31 FastaManager: START READ
2025/04/21 20:12:31 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2025/04/21 20:12:31 FastaManager: lines read 53328
2025/04/21 20:12:31 FastaManager: END READ
2025/04/21 20:12:31 FastaManager: FASTA
2025/04/21 20:12:32 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2025/04/21 20:12:32 END of AB Counting
2025/04/21 20:12:32 Loaded sequences: 26664
2025/04/21 20:12:32 Total kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.293
Current Free Memory=0.207
############################################
2025/04/21 20:12:32
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2025/04/21 20:12:32 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
2025/04/21 20:12:32 Runs=25
2025/04/21 20:12:32 END of EMsync
2025/04/21 20:12:32 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
2025/04/21 20:12:32 Trove size/4=18022
2025/04/21 20:12:32 Trove size/4=18022
2025/04/21 20:12:32 Cluster 1 size in kmers=65536 norm=126.50589485137961
2025/04/21 20:12:32 Cluster 2 size in kmers=65536 norm=221.81983091435748
2025/04/21 20:12:32 END of Creating AB Cluster Vectors
cpus=24
using=1
2025/04/21 20:12:32 START of AB Binning
2025/04/21 20:12:32 FastaManager: START READ
2025/04/21 20:12:32 SequenceProcessor: 0 AB_BINNING START
2025/04/21 20:12:32 FastaManager: lines read 53328
2025/04/21 20:12:32 FastaManager: END READ
2025/04/21 20:12:32 FastaManager: FASTA
2025/04/21 20:12:33 SequenceProcessor: 0 AB_BINNING EXIT
2025/04/21 20:12:33 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=0.378
Current Free Memory=0.122
############################################
version MTxCB =Mon Apr 21 15:01:52 EDT 2025
cpus=24
using=1
2025/04/21 20:12:33 START of CB Counting
2025/04/21 20:12:33 FastaManager: START READ
2025/04/21 20:12:33 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2025/04/21 20:12:33 FastaManager: lines read 53328
2025/04/21 20:12:33 FastaManager: END READ
2025/04/21 20:12:33 FastaManager: FASTA
2025/04/21 20:12:34 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2025/04/21 20:12:34 END of CB Counting
2025/04/21 20:12:34 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.395
Current Free Memory=0.105
############################################
cpus=24
using=1
2025/04/21 20:12:34 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 3633
... iteration 2 moves = 537
... iteration 3 moves = 217
... iteration 4 moves = 146
... iteration 5 moves = 92
... iteration 6 moves = 55
... iteration 7 moves = 39
... iteration 8 moves = 40
... iteration 9 moves = 26
... iteration 10 moves = 18
... iteration 11 moves = 14
... iteration 12 moves = 12
... iteration 13 moves = 4
... iteration 14 moves = 2
... iteration 15 moves = 8
... iteration 16 moves = 1
... iteration 17 moves = 0
...end. 2.791 seconds.
2025/04/21 20:12:36 : kMeans cleanup.
2025/04/21 20:12:36 END of Creating CB Clusters.
cpus=24
using=1
2025/04/21 20:12:36 START of CB Binning
2025/04/21 20:12:36 FastaManager: START READ
2025/04/21 20:12:36 SequenceProcessor: 0 CB_BINNING START
2025/04/21 20:12:36 FastaManager: lines read 53328
2025/04/21 20:12:36 FastaManager: END READ
2025/04/21 20:12:36 FastaManager: FASTA
2025/04/21 20:12:37 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=0.5
Current Used Memory=0.48
Current Free Memory=0.02
############################################
version MTxABxCB =Mon Apr 21 15:01:52 EDT 2025
cpus=24
using=1
2025/04/21 20:12:37 Using Dictionary ORIGINAL
2025/04/21 20:12:37 START of AB Counting
2025/04/21 20:12:37 FastaManager: START READ
2025/04/21 20:12:37 SequenceProcessor: 0 AB_KMERCOUNT START
2025/04/21 20:12:37 FastaManager: lines read 53328
2025/04/21 20:12:37 FastaManager: END READ
2025/04/21 20:12:37 FastaManager: FASTA
2025/04/21 20:12:37 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2025/04/21 20:12:37 END of AB Counting
2025/04/21 20:12:37 Loaded sequences: 26664
2025/04/21 20:12:37 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.24
Current Free Memory=0.26
############################################
2025/04/21 20:12:37
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2025/04/21 20:12:37 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
2025/04/21 20:12:37 Runs=25
2025/04/21 20:12:37 END of EMsync
2025/04/21 20:12:37 Filter before=2
2025/04/21 20:12:37 Filter after=2
2025/04/21 20:12:37 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
2025/04/21 20:12:37 Trove size/4=18022
2025/04/21 20:12:37 Trove size/4=18022
2025/04/21 20:12:37 Cluster 1 size in kmers=65536 norm=126.50589485137961
2025/04/21 20:12:37 Cluster 2 size in kmers=65536 norm=221.81983091435748
2025/04/21 20:12:37 END of Creating AB Cluster Vectors
cpus=24
using=1
2025/04/21 20:12:37 START of AB Binning
2025/04/21 20:12:37 FastaManager: START READ
2025/04/21 20:12:37 SequenceProcessor: 0 AB_BINNING START
2025/04/21 20:12:37 FastaManager: lines read 53328
2025/04/21 20:12:37 FastaManager: END READ
2025/04/21 20:12:37 FastaManager: FASTA
2025/04/21 20:12:38 SequenceProcessor: 0 AB_BINNING EXIT
2025/04/21 20:12:38 END of AB Binning
cpus=24
using=1
2025/04/21 20:12:38 START of CB Counting
2025/04/21 20:12:38 FastaManager: START READ
2025/04/21 20:12:38 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2025/04/21 20:12:38 FastaManager: lines read 53328
2025/04/21 20:12:38 FastaManager: END READ
2025/04/21 20:12:38 FastaManager: FASTA
2025/04/21 20:12:39 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2025/04/21 20:12:39 END of CB Counting
2025/04/21 20:12:39 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.38
Current Used Memory=0.236
Current Free Memory=0.144
############################################
2025/04/21 20:12:39 AB Cluster=1 Size=19871
2025/04/21 20:12:39 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
2025/04/21 20:12:39 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. 1.19 seconds.
2025/04/21 20:12:40 : kMeans cleanup.
2025/04/21 20:12:40 END of Creating CB Clusters for AB Cluster=1
cpus=24
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
2 6,793 75.53889 49,367 13,489 1 1
2025/04/21 20:12:40 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. 0.4 seconds.
2025/04/21 20:12:40 : kMeans cleanup.
2025/04/21 20:12:40 END of Creating CB Clusters for AB Cluster=2
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.415
Current Used Memory=0.261
Current Free Memory=0.155
############################################
cpus=24
using=1
2025/04/21 20:12:40 START of CB Binning
2025/04/21 20:12:40 FastaManager: START READ
2025/04/21 20:12:40 SequenceProcessor: 0 CB_BINNING START
2025/04/21 20:12:40 FastaManager: lines read 53328
2025/04/21 20:12:40 FastaManager: END READ
2025/04/21 20:12:40 FastaManager: FASTA
2025/04/21 20:12:40 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=0.425
Current Free Memory=0.075
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
13.512 0.593 9.702
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 3.087 | 0.369 | 2.358 | |
| composition_based_binning | 2.661 | 0.347 | 0.977 | |
| hierarchical_binning | 1.897 | 0.211 | 1.702 | |