| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:55 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 fastreeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fastreeR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 648/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fastreeR 1.0.0 (landing page) Anestis Gkanogiannis
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: fastreeR |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fastreeR_1.0.0.tar.gz |
| StartedAt: 2022-10-19 02:21:34 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 02:22:32 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 58.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fastreeR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fastreeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/fastreeR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fastreeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastreeR’ version ‘1.0.0’
* 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 ‘fastreeR’ 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 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
fasta2dist 5.193 0.354 1.812
* 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
fastreeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fastreeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘fastreeR’ ... ** 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 (fastreeR)
fastreeR.Rcheck/tests/spelling.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.335 0.078 0.391
fastreeR.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(fastreeR)
>
> test_check("fastreeR")
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:20 VCFManager: START READ
16777216
2022/10/19 02:22:20 VCFManager: END READ
Processed variants : 4
VCF2TREE : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:20 VCFManager: START READ
2022/10/19 02:22:20 VCFManager: END READ
Processed variants : 4
2022/10/19 02:22:20 Distances=3x3
hierarchical method=Complete
3 4
2022/10/19 02:22:20 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:21 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/19 02:22:21 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:21 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/19 02:22:21 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:21 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/19 02:22:21 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:21 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/19 02:22:21 Distances=3x3
hierarchical method=Complete
FASTA2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:21 FastaManager: START READ
2022/10/19 02:22:21 FastaManager: Chunk with 6 lines.
2022/10/19 02:22:21 FastaManager: END READ
2022/10/19 02:22:21 FastaManager: FASTA
2 S1
2 S2
3 S3
FASTA2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:22 FastaManager: START READ
2022/10/19 02:22:22 FastaManager: Chunk with 6 lines.
1 S1
2 S2
2022/10/19 02:22:22 FastaManager: END READ
2022/10/19 02:22:22 FastaManager: FASTA
3 S3
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:22 Clusters=2
S2 0 1
S1 1 2
S3 1 2
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:22 Clusters=2
S2 0 1
S1 1 2
S3 1 2
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:22 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:22 VCFManager: START READ
2022/10/19 02:22:22 VCFManager: END READ
Processed variants : 4
3 0
2022/10/19 02:22:22 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:22 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:22 VCFManager: START READ
2022/10/19 02:22:22 VCFManager: END READ
Processed variants : 4
3 0
2022/10/19 02:22:22 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:22 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:22 VCFManager: START READ
2022/10/19 02:22:22 VCFManager: END READ
Processed variants : 4
3 0
2022/10/19 02:22:22 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:22 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:22 VCFManager: START READ
2022/10/19 02:22:22 VCFManager: END READ
Processed variants : 4
3 0
2022/10/19 02:22:22 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/19 02:22:23 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:23 VCFManager: START READ
2022/10/19 02:22:23 VCFManager: END READ
Processed variants : 4
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:23 VCFManager: START READ
2022/10/19 02:22:23 VCFManager: END READ
Processed variants : 4
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:23 VCFManager: START READ
2022/10/19 02:22:23 VCFManager: END READ
Processed variants : 4
VCF2DIST : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:23 VCFManager: START READ
2022/10/19 02:22:23 VCFManager: END READ
Processed variants : 4
VCF2ISTATS : Tue Oct 18 15:23:49 EDT 2022
Num of Ind = 3
VCF2ISTATS : Tue Oct 18 15:23:49 EDT 2022
Num of Ind = 3
VCF2TREE : Tue Oct 18 15:23:49 EDT 2022
cpus=24
using=2
2022/10/19 02:22:23 VCFManager: START READ
2022/10/19 02:22:23 VCFManager: END READ
Processed variants : 4
2022/10/19 02:22:23 Distances=3x3
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
6.471 0.381 5.987
fastreeR.Rcheck/fastreeR-Ex.timings
| name | user | system | elapsed | |
| dist2clusters | 1.497 | 0.110 | 1.239 | |
| dist2tree | 0.308 | 0.022 | 0.176 | |
| fasta2dist | 5.193 | 0.354 | 1.812 | |
| tree2clusters | 0.282 | 0.014 | 0.162 | |
| vcf2clusters | 3.829 | 0.139 | 0.978 | |
| vcf2dist | 1.682 | 0.088 | 0.467 | |
| vcf2istats | 0.680 | 0.065 | 0.402 | |
| vcf2tree | 0.395 | 0.013 | 0.141 | |