| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:13 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1196/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabinR 1.4.0 (landing page) Anestis Gkanogiannis
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the metabinR package: - 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2024-04-17 18:41:29 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 18:42:49 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 79.4 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/metabinR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabinR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabinR’ version ‘1.4.0’
* 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 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 9.146 0.780 7.682
hierarchical_binning 5.942 0.551 4.988
composition_based_binning 4.556 0.571 2.590
* 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 ... 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/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
0.235 0.059 0.279
metabinR.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 =Tue Apr 16 10:10:47 EDT 2024
cpus=10
using=1
2024/04/17 18:42:09 Using Dictionary ORIGINAL
2024/04/17 18:42:09 START of AB Counting
2024/04/17 18:42:09 FastaManager: START READ
2024/04/17 18:42:09 SequenceProcessor: 0 AB_KMERCOUNT START
CHUNK_SIZE=67108864
2024/04/17 18:42:09 FastaManager: lines read 53328
2024/04/17 18:42:09 FastaManager: END READ
2024/04/17 18:42:09 FastaManager: FASTA
2024/04/17 18:42:11 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/04/17 18:42:11 END of AB Counting
2024/04/17 18:42:11 Loaded sequences: 26664
2024/04/17 18:42:11 Total kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.5
Current Used Memory=0.295
Current Free Memory=0.205
############################################
2024/04/17 18:42:11
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/04/17 18:42:11 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
2024/04/17 18:42:11 Runs=25
2024/04/17 18:42:11 END of EMsync
2024/04/17 18:42:11 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
2024/04/17 18:42:11 Trove size/4=18022
2024/04/17 18:42:11 Trove size/4=18022
2024/04/17 18:42:11 Cluster 1 size in kmers=65536 norm=126.50589485137961
2024/04/17 18:42:11 Cluster 2 size in kmers=65536 norm=221.81983091435748
2024/04/17 18:42:11 END of Creating AB Cluster Vectors
cpus=10
using=1
2024/04/17 18:42:11 START of AB Binning
2024/04/17 18:42:11 FastaManager: START READ
2024/04/17 18:42:11 SequenceProcessor: 0 AB_BINNING START
2024/04/17 18:42:11 FastaManager: lines read 53328
2024/04/17 18:42:11 FastaManager: END READ
2024/04/17 18:42:11 FastaManager: FASTA
2024/04/17 18:42:14 SequenceProcessor: 0 AB_BINNING EXIT
2024/04/17 18:42:14 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=0.277
Current Free Memory=0.223
############################################
version MTxCB =Tue Apr 16 10:10:47 EDT 2024
cpus=10
using=1
2024/04/17 18:42:15 START of CB Counting
2024/04/17 18:42:15 FastaManager: START READ
2024/04/17 18:42:15 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/04/17 18:42:15 FastaManager: lines read 53328
2024/04/17 18:42:15 FastaManager: END READ
2024/04/17 18:42:15 FastaManager: FASTA
2024/04/17 18:42:16 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/04/17 18:42:16 END of CB Counting
2024/04/17 18:42:16 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.376
Current Used Memory=0.248
Current Free Memory=0.128
############################################
cpus=10
using=1
2024/04/17 18:42:16 START of Creating CB Clusters Size=26664
K-Means clustering started
... centers initialized
... concurrent processing mode with 1 subtask threads
... iteration 1 moves = 6837
... iteration 2 moves = 3759
... iteration 3 moves = 1508
... iteration 4 moves = 564
... iteration 5 moves = 323
... iteration 6 moves = 194
... iteration 7 moves = 108
... iteration 8 moves = 101
... iteration 9 moves = 69
... iteration 10 moves = 91
... iteration 11 moves = 84
... iteration 12 moves = 115
... iteration 13 moves = 115
... iteration 14 moves = 141
... iteration 15 moves = 234
... iteration 16 moves = 254
... iteration 17 moves = 257
... iteration 18 moves = 317
... iteration 19 moves = 311
... iteration 20 moves = 371
... iteration 21 moves = 485
... iteration 22 moves = 491
... iteration 23 moves = 418
... iteration 24 moves = 378
... iteration 25 moves = 312
...end. 10.679 seconds.
2024/04/17 18:42:26 : kMeans cleanup.
2024/04/17 18:42:26 END of Creating CB Clusters.
cpus=10
using=1
2024/04/17 18:42:26 START of CB Binning
2024/04/17 18:42:26 FastaManager: START READ
2024/04/17 18:42:26 SequenceProcessor: 0 CB_BINNING START
2024/04/17 18:42:27 FastaManager: lines read 53328
2024/04/17 18:42:27 FastaManager: END READ
2024/04/17 18:42:27 FastaManager: FASTA
2024/04/17 18:42:27 SequenceProcessor: 0 CB_BINNING EXIT
Clustered reads:
CB Cluster 1: 16127
CB Cluster 2: 10537
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.405
Current Used Memory=0.093
Current Free Memory=0.312
############################################
version MTxABxCB =Tue Apr 16 10:10:47 EDT 2024
cpus=10
using=1
2024/04/17 18:42:27 Using Dictionary ORIGINAL
2024/04/17 18:42:27 START of AB Counting
2024/04/17 18:42:27 FastaManager: START READ
2024/04/17 18:42:27 SequenceProcessor: 0 AB_KMERCOUNT START
2024/04/17 18:42:27 FastaManager: lines read 53328
2024/04/17 18:42:27 FastaManager: END READ
2024/04/17 18:42:27 FastaManager: FASTA
2024/04/17 18:42:29 SequenceProcessor: 0 AB_KMERCOUNT EXIT
2024/04/17 18:42:29 END of AB Counting
2024/04/17 18:42:29 Loaded sequences: 26664
2024/04/17 18:42:29 Distinct kmers(before remove): 65536
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.405
Current Used Memory=0.18
Current Free Memory=0.225
############################################
2024/04/17 18:42:29
Unique: 0
Distinct: 65536
Total: 7625904
MaxCount: 1574
2024/04/17 18:42:29 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
2024/04/17 18:42:29 Runs=25
2024/04/17 18:42:29 END of EMsync
2024/04/17 18:42:29 Filter before=2
2024/04/17 18:42:29 Filter after=2
2024/04/17 18:42:29 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
2024/04/17 18:42:29 Trove size/4=18022
2024/04/17 18:42:29 Trove size/4=18022
2024/04/17 18:42:29 Cluster 1 size in kmers=65536 norm=221.81983091435748
2024/04/17 18:42:29 Cluster 2 size in kmers=65536 norm=126.50589485137961
2024/04/17 18:42:29 END of Creating AB Cluster Vectors
cpus=10
using=1
2024/04/17 18:42:29 START of AB Binning
2024/04/17 18:42:29 FastaManager: START READ
2024/04/17 18:42:29 SequenceProcessor: 0 AB_BINNING START
2024/04/17 18:42:29 FastaManager: lines read 53328
2024/04/17 18:42:29 FastaManager: END READ
2024/04/17 18:42:29 FastaManager: FASTA
2024/04/17 18:42:32 SequenceProcessor: 0 AB_BINNING EXIT
2024/04/17 18:42:32 END of AB Binning
cpus=10
using=1
2024/04/17 18:42:32 START of CB Counting
2024/04/17 18:42:32 FastaManager: START READ
2024/04/17 18:42:32 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD START
2024/04/17 18:42:32 FastaManager: lines read 53328
2024/04/17 18:42:32 FastaManager: END READ
2024/04/17 18:42:32 FastaManager: FASTA
2024/04/17 18:42:33 SequenceProcessor: 0 CB_SEQUENCEVECTORBUILD EXIT
2024/04/17 18:42:33 END of CB Counting
2024/04/17 18:42:33 Loaded sequences: 26664
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.449
Current Used Memory=0.292
Current Free Memory=0.158
############################################
2024/04/17 18:42:33 AB Cluster=1 Size=6793
2024/04/17 18:42:33 AB Cluster=2 Size=19871
cpus=10
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
1 6,793 75.53889 49,367 13,489 1 1
2024/04/17 18:42:33 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. 1.261 seconds.
2024/04/17 18:42:34 : kMeans cleanup.
2024/04/17 18:42:34 END of Creating CB Clusters for AB Cluster=1
cpus=10
using=1
ABid size abundance EMLength newLength EMspecies newspecies
----- ---- --------- -------- --------- --------- ----------
2 19,871 241.01134 16,168 12,367 1 1
2024/04/17 18:42:34 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. 2.809 seconds.
2024/04/17 18:42:37 : kMeans cleanup.
2024/04/17 18:42:37 END of Creating CB Clusters for AB Cluster=2
##### Heap utilization statistics [GB] #####
Max Memory=0.5
Current Total Memory=0.449
Current Used Memory=0.262
Current Free Memory=0.188
############################################
cpus=10
using=1
2024/04/17 18:42:37 START of CB Binning
2024/04/17 18:42:37 FastaManager: START READ
2024/04/17 18:42:37 SequenceProcessor: 0 CB_BINNING START
2024/04/17 18:42:37 FastaManager: lines read 53328
2024/04/17 18:42:37 FastaManager: END READ
2024/04/17 18:42:37 FastaManager: FASTA
2024/04/17 18:42:38 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=0.449
Current Used Memory=0.436
Current Free Memory=0.013
############################################
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
36.703 0.892 30.404
metabinR.Rcheck/metabinR-Ex.timings
| name | user | system | elapsed | |
| abundance_based_binning | 9.146 | 0.780 | 7.682 | |
| composition_based_binning | 4.556 | 0.571 | 2.590 | |
| hierarchical_binning | 5.942 | 0.551 | 4.988 | |