| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:15 -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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings fastreeR_1.0.0.tar.gz |
| StartedAt: 2022-10-18 19:42:50 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 19:43:21 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 30.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fastreeR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings fastreeR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/fastreeR.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (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 * 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: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL fastreeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-pc-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
0.136 0.057 0.178
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-pc-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(fastreeR)
>
> test_check("fastreeR")
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:16 VCFManager: START READ
16777216
2022/10/18 19:43:16 VCFManager: END READ
Processed variants : 4
VCF2TREE : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:16 VCFManager: START READ
2022/10/18 19:43:16 VCFManager: END READ
Processed variants : 4
2022/10/18 19:43:16 Distances=3x3
hierarchical method=Complete
3 4
2022/10/18 19:43:16 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:16 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/18 19:43:16 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:16 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/18 19:43:16 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:16 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/18 19:43:16 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:16 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2022/10/18 19:43:16 Distances=3x3
hierarchical method=Complete
FASTA2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:16 FastaManager: START READ
2022/10/18 19:43:16 FastaManager: Chunk with 6 lines.
2022/10/18 19:43:16 FastaManager: END READ
2022/10/18 19:43:16 FastaManager: FASTA
2 S1
2 S2
3 S3
FASTA2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 FastaManager: START READ
2022/10/18 19:43:17 FastaManager: Chunk with 6 lines.
2 S1
2022/10/18 19:43:17 FastaManager: END READ
2 S2
2022/10/18 19:43:17 FastaManager: FASTA
3 S3
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:17 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.
2022/10/18 19:43:17 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.
2022/10/18 19:43:17 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
3 0
2022/10/18 19:43:17 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:17 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
3 0
2022/10/18 19:43:17 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:17 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
3 0
2022/10/18 19:43:17 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:17 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
3 0
2022/10/18 19:43:17 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2022/10/18 19:43:17 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
VCF2DIST : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
VCF2ISTATS : Tue Oct 18 15:16:38 EDT 2022
Num of Ind = 3
VCF2ISTATS : Tue Oct 18 15:16:38 EDT 2022
Num of Ind = 3
VCF2TREE : Tue Oct 18 15:16:38 EDT 2022
cpus=72
using=2
2022/10/18 19:43:17 VCFManager: START READ
2022/10/18 19:43:17 VCFManager: END READ
Processed variants : 4
2022/10/18 19:43:17 Distances=3x3
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
3.374 0.241 2.879
fastreeR.Rcheck/fastreeR-Ex.timings
| name | user | system | elapsed | |
| dist2clusters | 0.851 | 0.057 | 0.548 | |
| dist2tree | 0.181 | 0.009 | 0.082 | |
| fasta2dist | 3.332 | 0.134 | 1.031 | |
| tree2clusters | 0.370 | 0.016 | 0.105 | |
| vcf2clusters | 2.371 | 0.071 | 0.519 | |
| vcf2dist | 1.335 | 0.032 | 0.239 | |
| vcf2istats | 0.920 | 0.033 | 0.240 | |
| vcf2tree | 0.248 | 0.028 | 0.099 | |