| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1198/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.8.0 (landing page) Anestis Gkanogiannis
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 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: 1.8.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metabinR_1.8.0.tar.gz |
| StartedAt: 2024-12-20 02:19:36 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 02:24:44 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 308.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metabinR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metabinR_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metabinR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/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 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 6.875 0.747 4.922
* 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-3.20-bioc/R/bin/R CMD INSTALL metabinR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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
0.130 0.029 0.150
metabinR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 =Thu Dec 19 15:06:32 EST 2024
cpus=72
using=1
2024/12/20 02:23:46 Using Dictionary ORIGINAL
2024/12/20 02:23:46 START of AB Counting
2024/12/20 02:23:46 FastaManager: START READ
2024/12/20 02:23:46 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2024/12/20 02:23:46 FastaManager: lines read 53328
2024/12/20 02:23:47 FastaManager: END READ
2024/12/20 02:23:47 FastaManager: FASTA
2024/12/20 02:23:48 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/12/20 02:23:48 END of AB Counting
2024/12/20 02:23:48 Loaded sequences: 26664
2024/12/20 02:23:48 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
############################################
2024/12/20 02:23:48
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/12/20 02:23:48 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
2024/12/20 02:23:48 Runs=25
2024/12/20 02:23:48 END of EMsync
2024/12/20 02:23:48 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
2024/12/20 02:23:48 Trove size/4=18022
2024/12/20 02:23:48 Trove size/4=18022
2024/12/20 02:23:48 Cluster 2 size in kmers=65536 norm=221.81983091435748
2024/12/20 02:23:48 Cluster 1 size in kmers=65536 norm=126.5058948513796
2024/12/20 02:23:48 END of Creating AB Cluster Vectors
cpus=72
using=1
2024/12/20 02:23:48 START of AB Binning
2024/12/20 02:23:48 FastaManager: START READ
2024/12/20 02:23:48 SequenceProcessor: 0 AB_BINNING START
2024/12/20 02:23:48 FastaManager: lines read 53328
2024/12/20 02:23:48 FastaManager: END READ
2024/12/20 02:23:48 FastaManager: FASTA
2024/12/20 02:23:50 SequenceProcessor: 0 AB_BINNING EXIT
2024/12/20 02:23:50 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=0.377
Current Free Memory=0.123
############################################
version MTxCB =Thu Dec 19 15:06:32 EST 2024
cpus=72
using=1
2024/12/20 02:23:51 START of CB Counting
2024/12/20 02:23:51 FastaManager: START READ
2024/12/20 02:23:51 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/12/20 02:23:51 FastaManager: lines read 53328
2024/12/20 02:23:51 FastaManager: END READ
2024/12/20 02:23:51 FastaManager: FASTA
2024/12/20 02:23:51 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/12/20 02:23:51 END of CB Counting
2024/12/20 02:23:51 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.374
Current Free Memory=0.126
############################################
cpus=72
using=1
2024/12/20 02:23:51 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 7123
... iteration 2 moves = 1536
... iteration 3 moves = 413
... iteration 4 moves = 266
... iteration 5 moves = 264
... iteration 6 moves = 197
... iteration 7 moves = 133
... iteration 8 moves = 80
... iteration 9 moves = 55
... iteration 10 moves = 49
... iteration 11 moves = 24
... iteration 12 moves = 8
... iteration 13 moves = 13
... iteration 14 moves = 5
... iteration 15 moves = 3
... iteration 16 moves = 2
... iteration 17 moves = 0
...end. 5.252 seconds.
2024/12/20 02:23:57 : kMeans cleanup.
2024/12/20 02:23:57 END of Creating CB Clusters.
cpus=72
using=1
2024/12/20 02:23:57 START of CB Binning
2024/12/20 02:23:57 FastaManager: START READ
2024/12/20 02:23:57 SequenceProcessor: 0 CB_BINNING START
2024/12/20 02:23:57 FastaManager: lines read 53328
2024/12/20 02:23:57 FastaManager: END READ
2024/12/20 02:23:57 FastaManager: FASTA
2024/12/20 02:23:57 SequenceProcessor: 0 CB_BINNING EXIT
Clustered reads:
CB Cluster 1: 9315
CB Cluster 2: 17349
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.45
Current Free Memory=0.05
############################################
version MTxABxCB =Thu Dec 19 15:06:32 EST 2024
cpus=72
using=1
2024/12/20 02:23:57 Using Dictionary ORIGINAL
2024/12/20 02:23:57 START of AB Counting
2024/12/20 02:23:57 FastaManager: START READ
2024/12/20 02:23:57 SequenceProcessor: 0 AB_KMERCOUNT START
2024/12/20 02:23:57 FastaManager: lines read 53328
2024/12/20 02:23:57 FastaManager: END READ
2024/12/20 02:23:57 FastaManager: FASTA
2024/12/20 02:23:58 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/12/20 02:23:58 END of AB Counting
2024/12/20 02:23:58 Loaded sequences: 26664
2024/12/20 02:23:58 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.492
Current Used Memory=0.31
Current Free Memory=0.182
############################################
2024/12/20 02:23:58
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/12/20 02:23:58 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
2024/12/20 02:23:58 Runs=25
2024/12/20 02:23:58 END of EMsync
2024/12/20 02:23:58 Filter before=2
2024/12/20 02:23:58 Filter after=2
2024/12/20 02:23:58 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
2024/12/20 02:23:58 Trove size/4=18022
2024/12/20 02:23:58 Trove size/4=18022
2024/12/20 02:23:59 Cluster 1 size in kmers=65536 norm=221.81983091435748
2024/12/20 02:23:59 Cluster 2 size in kmers=65536 norm=126.5058948513796
2024/12/20 02:23:59 END of Creating AB Cluster Vectors
cpus=72
using=1
2024/12/20 02:23:59 START of AB Binning
2024/12/20 02:23:59 FastaManager: START READ
2024/12/20 02:23:59 SequenceProcessor: 0 AB_BINNING START
2024/12/20 02:23:59 FastaManager: lines read 53328
2024/12/20 02:23:59 FastaManager: END READ
2024/12/20 02:23:59 FastaManager: FASTA
2024/12/20 02:24:00 SequenceProcessor: 0 AB_BINNING EXIT
2024/12/20 02:24:00 END of AB Binning
cpus=72
using=1
2024/12/20 02:24:00 START of CB Counting
2024/12/20 02:24:00 FastaManager: START READ
2024/12/20 02:24:00 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/12/20 02:24:00 FastaManager: lines read 53328
2024/12/20 02:24:00 FastaManager: END READ
2024/12/20 02:24:00 FastaManager: FASTA
2024/12/20 02:24:01 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/12/20 02:24:01 END of CB Counting
2024/12/20 02:24:01 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.296
Current Free Memory=0.204
############################################
2024/12/20 02:24:01 AB Cluster=1 Size=6793
2024/12/20 02:24:01 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
2024/12/20 02:24:01 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. 0.738 seconds.
2024/12/20 02:24:02 : kMeans cleanup.
2024/12/20 02:24:02 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
2024/12/20 02:24:02 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. 2.134 seconds.
2024/12/20 02:24:04 : kMeans cleanup.
2024/12/20 02:24:04 END of Creating CB Clusters for AB Cluster=2
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.415
Current Free Memory=0.085
############################################
cpus=72
using=1
2024/12/20 02:24:04 START of CB Binning
2024/12/20 02:24:04 FastaManager: START READ
2024/12/20 02:24:04 SequenceProcessor: 0 CB_BINNING START
2024/12/20 02:24:04 FastaManager: lines read 53328
2024/12/20 02:24:04 FastaManager: END READ
2024/12/20 02:24:04 FastaManager: FASTA
2024/12/20 02:24:04 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=0.442
Current Free Memory=0.058
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
29.522 1.665 19.155
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 6.875 | 0.747 | 4.922 | |
| composition_based_binning | 4.489 | 0.312 | 1.559 | |
| hierarchical_binning | 4.433 | 0.184 | 2.928 | |