Anestis Gkanogiannis
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1192/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.9.0 (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 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.9.0 |
| 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: 2024-12-23 23:35:25 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 23:37:00 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 94.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metabinR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 8.370 1.297 6.110
hierarchical_binning 4.453 0.681 3.523
composition_based_binning 4.240 0.822 2.174
* 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
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’ ... ** 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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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
0.140 0.038 0.167
metabinR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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 =Mon Dec 23 15:04:01 EST 2024
cpus=72
using=1
2024/12/23 23:35:57 Using Dictionary ORIGINAL
2024/12/23 23:35:57 START of AB Counting
2024/12/23 23:35:57 FastaManager: START READ
2024/12/23 23:35:57 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2024/12/23 23:35:57 FastaManager: lines read 53328
2024/12/23 23:35:57 FastaManager: END READ
2024/12/23 23:35:57 FastaManager: FASTA
2024/12/23 23:35:59 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/12/23 23:35:59 END of AB Counting
2024/12/23 23:35:59 Loaded sequences: 26664
2024/12/23 23:35:59 Total kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.292
Current Free Memory=0.208
############################################
2024/12/23 23:35:59
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/12/23 23:35:59 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
2024/12/23 23:35:59 Runs=25
2024/12/23 23:35:59 END of EMsync
2024/12/23 23:35:59 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
2024/12/23 23:35:59 Trove size/4=18022
2024/12/23 23:35:59 Trove size/4=18022
2024/12/23 23:35:59 Cluster 2 size in kmers=65536 norm=221.81983091435748
2024/12/23 23:35:59 Cluster 1 size in kmers=65536 norm=126.5058948513796
2024/12/23 23:35:59 END of Creating AB Cluster Vectors
cpus=72
using=1
2024/12/23 23:35:59 START of AB Binning
2024/12/23 23:35:59 FastaManager: START READ
2024/12/23 23:35:59 SequenceProcessor: 0 AB_BINNING START
2024/12/23 23:35:59 FastaManager: lines read 53328
2024/12/23 23:35:59 FastaManager: END READ
2024/12/23 23:35:59 FastaManager: FASTA
2024/12/23 23:36:01 SequenceProcessor: 0 AB_BINNING EXIT
2024/12/23 23:36:01 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=0.375
Current Free Memory=0.125
############################################
version MTxCB =Mon Dec 23 15:04:01 EST 2024
cpus=72
using=1
2024/12/23 23:36:02 START of CB Counting
2024/12/23 23:36:02 FastaManager: START READ
2024/12/23 23:36:02 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/12/23 23:36:02 FastaManager: lines read 53328
2024/12/23 23:36:02 FastaManager: END READ
2024/12/23 23:36:02 FastaManager: FASTA
2024/12/23 23:36:03 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/12/23 23:36:03 END of CB Counting
2024/12/23 23:36:03 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.375
Current Free Memory=0.125
############################################
cpus=72
using=1
2024/12/23 23:36:03 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 6390
... iteration 2 moves = 1581
... iteration 3 moves = 538
... iteration 4 moves = 413
... iteration 5 moves = 480
... iteration 6 moves = 516
... iteration 7 moves = 441
... iteration 8 moves = 361
... iteration 9 moves = 324
... iteration 10 moves = 297
... iteration 11 moves = 272
... iteration 12 moves = 234
... iteration 13 moves = 191
... iteration 14 moves = 115
... iteration 15 moves = 62
... iteration 16 moves = 61
... iteration 17 moves = 28
... iteration 18 moves = 14
... iteration 19 moves = 15
... iteration 20 moves = 6
... iteration 21 moves = 2
... iteration 22 moves = 2
... iteration 23 moves = 0
...end. 6.082 seconds.
2024/12/23 23:36:09 : kMeans cleanup.
2024/12/23 23:36:09 END of Creating CB Clusters.
cpus=72
using=1
2024/12/23 23:36:09 START of CB Binning
2024/12/23 23:36:09 FastaManager: START READ
2024/12/23 23:36:09 SequenceProcessor: 0 CB_BINNING START
2024/12/23 23:36:09 FastaManager: lines read 53328
2024/12/23 23:36:09 FastaManager: END READ
2024/12/23 23:36:09 FastaManager: FASTA
2024/12/23 23:36:09 SequenceProcessor: 0 CB_BINNING EXIT
Clustered reads:
CB Cluster 1: 17349
CB Cluster 2: 9315
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.479
Current Free Memory=0.021
############################################
version MTxABxCB =Mon Dec 23 15:04:01 EST 2024
cpus=72
using=1
2024/12/23 23:36:09 Using Dictionary ORIGINAL
2024/12/23 23:36:09 START of AB Counting
2024/12/23 23:36:09 FastaManager: START READ
2024/12/23 23:36:09 SequenceProcessor: 0 AB_KMERCOUNT START
2024/12/23 23:36:09 FastaManager: lines read 53328
2024/12/23 23:36:09 FastaManager: END READ
2024/12/23 23:36:09 FastaManager: FASTA
2024/12/23 23:36:11 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/12/23 23:36:11 END of AB Counting
2024/12/23 23:36:11 Loaded sequences: 26664
2024/12/23 23:36:11 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.318
Current Free Memory=0.182
############################################
2024/12/23 23:36:11
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/12/23 23:36:11 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
2024/12/23 23:36:11 Runs=25
2024/12/23 23:36:11 END of EMsync
2024/12/23 23:36:11 Filter before=2
2024/12/23 23:36:11 Filter after=2
2024/12/23 23:36:11 START of Creating AB Cluster Vectors
Cluster 1 Abundance=75.53888858729701 Length=49367.826262240575 LowLimit=32 HighLimit=118
Cluster 2 Abundance=241.01134335779187 Length=16168.173737759438 LowLimit=163 HighLimit=318
2024/12/23 23:36:11 Trove size/4=18022
2024/12/23 23:36:11 Trove size/4=18022
2024/12/23 23:36:11 Cluster 2 size in kmers=65536 norm=126.5058948513796
2024/12/23 23:36:11 Cluster 1 size in kmers=65536 norm=221.81983091435748
2024/12/23 23:36:11 END of Creating AB Cluster Vectors
cpus=72
using=1
2024/12/23 23:36:11 START of AB Binning
2024/12/23 23:36:11 FastaManager: START READ
2024/12/23 23:36:11 SequenceProcessor: 0 AB_BINNING START
2024/12/23 23:36:11 FastaManager: lines read 53328
2024/12/23 23:36:11 FastaManager: END READ
2024/12/23 23:36:11 FastaManager: FASTA
2024/12/23 23:36:13 SequenceProcessor: 0 AB_BINNING EXIT
2024/12/23 23:36:13 END of AB Binning
cpus=72
using=1
2024/12/23 23:36:13 START of CB Counting
2024/12/23 23:36:13 FastaManager: START READ
2024/12/23 23:36:13 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/12/23 23:36:13 FastaManager: lines read 53328
2024/12/23 23:36:13 FastaManager: END READ
2024/12/23 23:36:13 FastaManager: FASTA
2024/12/23 23:36:14 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/12/23 23:36:14 END of CB Counting
2024/12/23 23:36:14 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.43
Current Used Memory=0.249
Current Free Memory=0.181
############################################
2024/12/23 23:36:14 AB Cluster=1 Size=6793
2024/12/23 23:36:14 AB Cluster=2 Size=19871
cpus=72
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
1 6,793 75.53889 49,367 13,489 1 1
2024/12/23 23:36:14 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. 0.75 seconds.
2024/12/23 23:36:14 : kMeans cleanup.
2024/12/23 23:36:14 END of Creating CB Clusters for AB Cluster=1
cpus=72
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
2 19,871 241.01134 16,168 12,367 1 1
2024/12/23 23:36:14 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. 2.14 seconds.
2024/12/23 23:36:17 : kMeans cleanup.
2024/12/23 23:36:17 END of Creating CB Clusters for AB Cluster=2
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.43
Current Used Memory=0.273
Current Free Memory=0.157
############################################
cpus=72
using=1
2024/12/23 23:36:17 START of CB Binning
2024/12/23 23:36:17 FastaManager: START READ
2024/12/23 23:36:17 SequenceProcessor: 0 CB_BINNING START
2024/12/23 23:36:17 FastaManager: lines read 53328
2024/12/23 23:36:17 FastaManager: END READ
2024/12/23 23:36:17 FastaManager: FASTA
2024/12/23 23:36:17 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=0.452
Current Used Memory=0.263
Current Free Memory=0.189
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
31.538 1.277 21.132
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 8.370 | 1.297 | 6.110 | |
| composition_based_binning | 4.240 | 0.822 | 2.174 | |
| hierarchical_binning | 4.453 | 0.681 | 3.523 | |