Anestis Gkanogiannis
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/metabinR |
| git_branch: devel |
| git_last_commit: 611ad69 |
| git_last_commit_date: 2024-04-30 11:46:03 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 1174/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.7.0 (landing page) Anestis Gkanogiannis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.7.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabinR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metabinR_1.7.0.tar.gz |
| StartedAt: 2024-06-10 05:00:27 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 05:03:03 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 156.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metabinR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabinR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metabinR_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/metabinR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'metabinR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metabinR' version '1.7.0'
* 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 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 7.54 0.89 6.06
composition_based_binning 6.48 0.74 2.32
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL metabinR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
0.1 1.9 1.9
metabinR.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 =Sun Jun 09 15:44:00 EDT 2024
cpus=32
using=1
2024/06/10 05:02:25 Using Dictionary ORIGINAL
2024/06/10 05:02:25 START of AB Counting
2024/06/10 05:02:25 FastaManager: START READ
2024/06/10 05:02:25 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2024/06/10 05:02:25 FastaManager: lines read 53328
2024/06/10 05:02:25 FastaManager: END READ
2024/06/10 05:02:25 FastaManager: FASTA
2024/06/10 05:02:27 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/06/10 05:02:27 END of AB Counting
2024/06/10 05:02:27 Loaded sequences: 26664
2024/06/10 05:02:27 Total kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.302
Current Free Memory=0.198
############################################
2024/06/10 05:02:27
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/06/10 05:02:27 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
2024/06/10 05:02:27 Runs=25
2024/06/10 05:02:27 END of EMsync
2024/06/10 05:02:27 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
2024/06/10 05:02:27 Trove size/4=18022
2024/06/10 05:02:27 Trove size/4=18022
2024/06/10 05:02:27 Cluster 1 size in kmers=65536 norm=126.5058948513796
2024/06/10 05:02:27 Cluster 2 size in kmers=65536 norm=221.81983091435748
2024/06/10 05:02:27 END of Creating AB Cluster Vectors
cpus=32
using=1
2024/06/10 05:02:27 START of AB Binning
2024/06/10 05:02:27 FastaManager: START READ
2024/06/10 05:02:27 SequenceProcessor: 0 AB_BINNING START
2024/06/10 05:02:27 FastaManager: lines read 53328
2024/06/10 05:02:27 FastaManager: END READ
2024/06/10 05:02:27 FastaManager: FASTA
2024/06/10 05:02:29 SequenceProcessor: 0 AB_BINNING EXIT
2024/06/10 05:02:29 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=0.385
Current Free Memory=0.115
############################################
version MTxCB =Sun Jun 09 15:44:00 EDT 2024
cpus=32
using=1
2024/06/10 05:02:29 START of CB Counting
2024/06/10 05:02:29 FastaManager: START READ
2024/06/10 05:02:29 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/06/10 05:02:30 FastaManager: lines read 53328
2024/06/10 05:02:30 FastaManager: END READ
2024/06/10 05:02:30 FastaManager: FASTA
2024/06/10 05:02:30 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/06/10 05:02:30 END of CB Counting
2024/06/10 05:02:30 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.406
Current Free Memory=0.094
############################################
cpus=32
using=1
2024/06/10 05:02:30 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 5192
... iteration 2 moves = 3283
... iteration 3 moves = 1790
... iteration 4 moves = 763
... iteration 5 moves = 442
... iteration 6 moves = 313
... iteration 7 moves = 202
... iteration 8 moves = 168
... iteration 9 moves = 112
... iteration 10 moves = 89
... iteration 11 moves = 71
... iteration 12 moves = 64
... iteration 13 moves = 72
... iteration 14 moves = 73
... iteration 15 moves = 77
... iteration 16 moves = 72
... iteration 17 moves = 66
... iteration 18 moves = 44
... iteration 19 moves = 29
... iteration 20 moves = 12
... iteration 21 moves = 15
... iteration 22 moves = 10
... iteration 23 moves = 10
... iteration 24 moves = 6
... iteration 25 moves = 15
...end. 6.234 seconds.
2024/06/10 05:02:37 : kMeans cleanup.
2024/06/10 05:02:37 END of Creating CB Clusters.
cpus=32
using=1
2024/06/10 05:02:37 START of CB Binning
2024/06/10 05:02:37 FastaManager: START READ
2024/06/10 05:02:37 SequenceProcessor: 0 CB_BINNING START
2024/06/10 05:02:37 FastaManager: lines read 53328
2024/06/10 05:02:37 FastaManager: END READ
2024/06/10 05:02:37 FastaManager: FASTA
2024/06/10 05:02:37 SequenceProcessor: 0 CB_BINNING EXIT
Clustered reads:
CB Cluster 1: 19536
CB Cluster 2: 7128
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.248
Current Free Memory=0.252
############################################
version MTxABxCB =Sun Jun 09 15:44:00 EDT 2024
cpus=32
using=1
2024/06/10 05:02:37 Using Dictionary ORIGINAL
2024/06/10 05:02:37 START of AB Counting
2024/06/10 05:02:37 FastaManager: START READ
2024/06/10 05:02:37 SequenceProcessor: 0 AB_KMERCOUNT START
2024/06/10 05:02:37 FastaManager: lines read 53328
2024/06/10 05:02:37 FastaManager: END READ
2024/06/10 05:02:37 FastaManager: FASTA
2024/06/10 05:02:39 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/06/10 05:02:39 END of AB Counting
2024/06/10 05:02:39 Loaded sequences: 26664
2024/06/10 05:02:39 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.445
Current Free Memory=0.055
############################################
2024/06/10 05:02:39
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/06/10 05:02:39 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
2024/06/10 05:02:39 Runs=25
2024/06/10 05:02:39 END of EMsync
2024/06/10 05:02:39 Filter before=2
2024/06/10 05:02:39 Filter after=2
2024/06/10 05:02:39 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
2024/06/10 05:02:39 Trove size/4=18022
2024/06/10 05:02:39 Trove size/4=18022
2024/06/10 05:02:39 Cluster 2 size in kmers=65536 norm=221.81983091435748
2024/06/10 05:02:39 Cluster 1 size in kmers=65536 norm=126.5058948513796
2024/06/10 05:02:39 END of Creating AB Cluster Vectors
cpus=32
using=1
2024/06/10 05:02:39 START of AB Binning
2024/06/10 05:02:39 FastaManager: START READ
2024/06/10 05:02:39 SequenceProcessor: 0 AB_BINNING START
2024/06/10 05:02:39 FastaManager: lines read 53328
2024/06/10 05:02:39 FastaManager: END READ
2024/06/10 05:02:39 FastaManager: FASTA
2024/06/10 05:02:41 SequenceProcessor: 0 AB_BINNING EXIT
2024/06/10 05:02:41 END of AB Binning
cpus=32
using=1
2024/06/10 05:02:41 START of CB Counting
2024/06/10 05:02:41 FastaManager: START READ
2024/06/10 05:02:41 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/06/10 05:02:41 FastaManager: lines read 53328
2024/06/10 05:02:41 FastaManager: END READ
2024/06/10 05:02:41 FastaManager: FASTA
2024/06/10 05:02:42 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/06/10 05:02:42 END of CB Counting
2024/06/10 05:02:42 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.339
Current Used Memory=0.235
Current Free Memory=0.104
############################################
2024/06/10 05:02:42 AB Cluster=1 Size=19871
2024/06/10 05:02:42 AB Cluster=2 Size=6793
cpus=32
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
1 19,871 241.01134 16,168 12,367 1 1
2024/06/10 05:02:42 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. 2.13 seconds.
2024/06/10 05:02:44 : kMeans cleanup.
2024/06/10 05:02:44 END of Creating CB Clusters for AB Cluster=1
cpus=32
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
2 6,793 75.53889 49,367 13,489 1 1
2024/06/10 05:02:44 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. 0.642 seconds.
2024/06/10 05:02:45 : kMeans cleanup.
2024/06/10 05:02:45 END of Creating CB Clusters for AB Cluster=2
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.405
Current Used Memory=0.248
Current Free Memory=0.158
############################################
cpus=32
using=1
2024/06/10 05:02:45 START of CB Binning
2024/06/10 05:02:45 FastaManager: START READ
2024/06/10 05:02:45 SequenceProcessor: 0 CB_BINNING START
2024/06/10 05:02:45 FastaManager: lines read 53328
2024/06/10 05:02:45 FastaManager: END READ
2024/06/10 05:02:45 FastaManager: FASTA
2024/06/10 05:02:45 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=0.437
Current Used Memory=0.26
Current Free Memory=0.176
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
31.25 4.18 24.56
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 7.54 | 0.89 | 6.06 | |
| composition_based_binning | 6.48 | 0.74 | 2.32 | |
| hierarchical_binning | 4.48 | 0.50 | 3.42 | |