| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:37 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1151/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.3.0 (landing page) Anestis Gkanogiannis
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: metabinR |
| Version: 1.3.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings metabinR_1.3.0.tar.gz |
| StartedAt: 2023-05-30 11:28:20 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 11:30:03 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 103.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metabinR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:metabinR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings metabinR_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/metabinR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘metabinR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabinR’ version ‘1.3.0’
* 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 R 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 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 8.296 1.011 6.318
hierarchical_binning 5.334 0.394 3.539
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘metabinR_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
metabinR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL metabinR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
0.217 0.021 0.221
metabinR.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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 May 29 12:20:38 UTC 2023
cpus=32
using=1
2023/05/30 11:28:54 Using Dictionary ORIGINAL
2023/05/30 11:28:54 START of AB Counting
2023/05/30 11:28:54 FastaManager: START READ
2023/05/30 11:28:54 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2023/05/30 11:28:54 FastaManager: lines read 53328
2023/05/30 11:28:54 FastaManager: END READ
2023/05/30 11:28:54 FastaManager: FASTA
2023/05/30 11:28:56 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2023/05/30 11:28:56 END of AB Counting
2023/05/30 11:28:56 Loaded sequences: 26664
2023/05/30 11:28:56 Total kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.113
Current Free Memory=0.387
############################################
2023/05/30 11:28:56
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2023/05/30 11:28:56 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
2023/05/30 11:28:56 Runs=25
2023/05/30 11:28:56 END of EMsync
2023/05/30 11:28:56 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
2023/05/30 11:28:56 Trove size/4=18022
2023/05/30 11:28:56 Trove size/4=18022
2023/05/30 11:28:56 Cluster 1 size in kmers=65536 norm=126.50589485137961
2023/05/30 11:28:56 Cluster 2 size in kmers=65536 norm=221.81983091435748
2023/05/30 11:28:56 END of Creating AB Cluster Vectors
cpus=32
using=1
2023/05/30 11:28:56 START of AB Binning
2023/05/30 11:28:56 FastaManager: START READ
2023/05/30 11:28:56 SequenceProcessor: 0 AB_BINNING START
2023/05/30 11:28:56 FastaManager: lines read 53328
2023/05/30 11:28:56 FastaManager: END READ
2023/05/30 11:28:56 FastaManager: FASTA
2023/05/30 11:28:58 SequenceProcessor: 0 AB_BINNING EXIT
2023/05/30 11:28:58 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=0.291
Current Free Memory=0.209
############################################
version MTxCB =Mon May 29 12:20:38 UTC 2023
cpus=32
using=1
2023/05/30 11:28:58 START of CB Counting
2023/05/30 11:28:58 FastaManager: START READ
2023/05/30 11:28:58 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2023/05/30 11:28:59 FastaManager: lines read 53328
2023/05/30 11:28:59 FastaManager: END READ
2023/05/30 11:28:59 FastaManager: FASTA
2023/05/30 11:28:59 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2023/05/30 11:28:59 END of CB Counting
2023/05/30 11:28:59 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.266
Current Free Memory=0.234
############################################
cpus=32
using=1
2023/05/30 11:28:59 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 2434
... iteration 2 moves = 476
... iteration 3 moves = 213
... iteration 4 moves = 151
... iteration 5 moves = 91
... iteration 6 moves = 61
... iteration 7 moves = 39
... iteration 8 moves = 35
... iteration 9 moves = 30
... iteration 10 moves = 19
... iteration 11 moves = 9
... iteration 12 moves = 8
... iteration 13 moves = 8
... iteration 14 moves = 2
... iteration 15 moves = 2
... iteration 16 moves = 2
... iteration 17 moves = 0
...end. 6.37 seconds.
2023/05/30 11:29:06 : kMeans cleanup.
2023/05/30 11:29:06 END of Creating CB Clusters.
cpus=32
using=1
2023/05/30 11:29:06 START of CB Binning
2023/05/30 11:29:06 FastaManager: START READ
2023/05/30 11:29:06 SequenceProcessor: 0 CB_BINNING START
2023/05/30 11:29:06 FastaManager: lines read 53328
2023/05/30 11:29:06 FastaManager: END READ
2023/05/30 11:29:06 FastaManager: FASTA
2023/05/30 11:29:06 SequenceProcessor: 0 CB_BINNING EXIT
Clustered reads:
CB Cluster 1: 9293
CB Cluster 2: 17371
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.303
Current Free Memory=0.197
############################################
version MTxABxCB =Mon May 29 12:20:38 UTC 2023
cpus=32
using=1
2023/05/30 11:29:06 Using Dictionary ORIGINAL
2023/05/30 11:29:06 START of AB Counting
2023/05/30 11:29:06 FastaManager: START READ
2023/05/30 11:29:06 SequenceProcessor: 0 AB_KMERCOUNT START
2023/05/30 11:29:06 FastaManager: lines read 53328
2023/05/30 11:29:06 FastaManager: END READ
2023/05/30 11:29:06 FastaManager: FASTA
2023/05/30 11:29:08 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2023/05/30 11:29:08 END of AB Counting
2023/05/30 11:29:08 Loaded sequences: 26664
2023/05/30 11:29:08 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.219
Current Free Memory=0.281
############################################
2023/05/30 11:29:08
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2023/05/30 11:29:08 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
2023/05/30 11:29:08 Runs=25
2023/05/30 11:29:08 END of EMsync
2023/05/30 11:29:08 Filter before=2
2023/05/30 11:29:08 Filter after=2
2023/05/30 11:29:08 START of Creating AB Cluster Vectors
Cluster 1 Abundance=75.538888587297 Length=49367.82626224055 LowLimit=32 HighLimit=118
Cluster 2 Abundance=241.01134335779187 Length=16168.173737759447 LowLimit=163 HighLimit=318
2023/05/30 11:29:08 Trove size/4=18022
2023/05/30 11:29:08 Trove size/4=18022
2023/05/30 11:29:08 Cluster 1 size in kmers=65536 norm=221.81983091435748
2023/05/30 11:29:08 Cluster 2 size in kmers=65536 norm=126.50589485137961
2023/05/30 11:29:08 END of Creating AB Cluster Vectors
cpus=32
using=1
2023/05/30 11:29:08 START of AB Binning
2023/05/30 11:29:08 FastaManager: START READ
2023/05/30 11:29:08 SequenceProcessor: 0 AB_BINNING START
2023/05/30 11:29:08 FastaManager: lines read 53328
2023/05/30 11:29:08 FastaManager: END READ
2023/05/30 11:29:08 FastaManager: FASTA
2023/05/30 11:29:10 SequenceProcessor: 0 AB_BINNING EXIT
2023/05/30 11:29:10 END of AB Binning
cpus=32
using=1
2023/05/30 11:29:10 START of CB Counting
2023/05/30 11:29:10 FastaManager: START READ
2023/05/30 11:29:10 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2023/05/30 11:29:10 FastaManager: lines read 53328
2023/05/30 11:29:10 FastaManager: END READ
2023/05/30 11:29:10 FastaManager: FASTA
2023/05/30 11:29:11 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2023/05/30 11:29:11 END of CB Counting
2023/05/30 11:29:11 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.264
Current Free Memory=0.236
############################################
2023/05/30 11:29:11 AB Cluster=1 Size=6793
2023/05/30 11:29:11 AB Cluster=2 Size=19871
cpus=32
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
1 6,793 75.53889 49,367 13,489 1 1
2023/05/30 11:29:11 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. 0.801 seconds.
2023/05/30 11:29:12 : kMeans cleanup.
2023/05/30 11:29:12 END of Creating CB Clusters for AB Cluster=1
cpus=32
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
2 19,871 241.01134 16,168 12,367 1 1
2023/05/30 11:29:12 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. 2.293 seconds.
2023/05/30 11:29:14 END of Creating CB Clusters for AB Cluster=2
2023/05/30 11:29:14 : kMeans cleanup.
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.276
Current Free Memory=0.224
############################################
cpus=32
using=1
2023/05/30 11:29:14 START of CB Binning
2023/05/30 11:29:14 FastaManager: START READ
2023/05/30 11:29:14 SequenceProcessor: 0 CB_BINNING START
2023/05/30 11:29:14 FastaManager: lines read 53328
2023/05/30 11:29:14 FastaManager: END READ
2023/05/30 11:29:14 FastaManager: FASTA
2023/05/30 11:29:14 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=0.438
Current Free Memory=0.062
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
30.946 1.361 22.001
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 8.296 | 1.011 | 6.318 | |
| composition_based_binning | 4.124 | 0.305 | 1.838 | |
| hierarchical_binning | 5.334 | 0.394 | 3.539 | |