Anestis Gkanogiannis
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/fastreeR |
| git_branch: devel |
| git_last_commit: 1ed9d1b |
| git_last_commit_date: 2025-06-02 15:44:38 -0400 (Mon, 02 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:06 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 705/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fastreeR 1.99.1 (landing page) Anestis Gkanogiannis
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the fastreeR package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: fastreeR |
| Version: 1.99.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fastreeR_1.99.1.tar.gz |
| StartedAt: 2025-06-17 07:22:31 -0000 (Tue, 17 Jun 2025) |
| EndedAt: 2025-06-17 07:23:08 -0000 (Tue, 17 Jun 2025) |
| EllapsedTime: 37.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: fastreeR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fastreeR_1.99.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/fastreeR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fastreeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastreeR’ version ‘1.99.1’
* 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 ... WARNING
Non-standard license specification:
GPL-3.0-only
Standardizable: FALSE
* 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.22-bioc/meat/fastreeR.Rcheck/00check.log’
for details.
fastreeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL fastreeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘fastreeR’ ... ** this is package ‘fastreeR’ version ‘1.99.1’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.161 0.047 0.195
fastreeR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(fastreeR)
>
> test_check("fastreeR")
VCF2DIST
VCF2TREE
2025-06-17 07:23:01 Distances=3x3
hierarchical method=Complete
3 5
2025-06-17 07:23:01 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:01 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 5
2025-06-17 07:23:01 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:01 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 5
2025-06-17 07:23:01 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:01 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 5
2025-06-17 07:23:02 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:02 Clusters=2
S2 0 1
S1 1 2
S3 1 2
100 1000
2025-06-17 07:23:02 Distances=100x100
hierarchical method=Complete
..cutHeight not given, setting it to 0.0794 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:02 Clusters=36
HG00126 1 5
HG00149 1 5
HG00182 1 5
HG00233 1 5
HG00262 1 5
HG00100 2 5
HG00101 2 5
HG00106 2 5
HG00107 2 5
HG00125 2 5
HG00096 3 5
HG00128 3 5
HG00154 3 5
HG00173 3 5
HG00242 3 5
HG00108 4 4
HG00129 4 4
HG00232 4 4
HG00253 4 4
HG00110 5 4
HG00121 5 4
HG00123 5 4
HG00256 5 4
HG00185 6 4
HG00189 6 4
HG00258 6 4
HG00261 6 4
HG00114 7 3
HG00133 7 3
HG00234 7 3
HG00120 8 3
HG00136 8 3
HG00236 8 3
HG00141 9 3
HG00187 9 3
HG00254 9 3
HG00142 10 3
HG00146 10 3
HG00160 10 3
HG00118 11 3
HG00138 11 3
HG00157 11 3
HG00158 12 3
HG00177 12 3
HG00178 12 3
HG00115 13 3
HG00130 13 3
HG00155 13 3
HG00111 14 3
HG00137 14 3
HG00150 14 3
HG00112 15 3
HG00132 15 3
HG00148 15 3
HG00140 16 3
HG00151 16 3
HG00237 16 3
HG00231 17 3
HG00238 17 3
HG00243 17 3
HG00180 18 3
HG00252 18 3
HG00260 18 3
HG00116 19 3
HG00122 19 3
HG00139 19 3
HG00097 20 2
HG00102 20 2
HG00145 21 2
HG00244 21 2
HG00113 22 2
HG00259 22 2
HG00099 23 2
HG00174 23 2
HG00171 24 2
HG00255 24 2
HG00176 25 2
HG00235 25 2
HG00179 26 2
HG00250 26 2
HG00103 27 2
HG00257 27 2
HG00188 28 2
HG00245 28 2
HG00127 29 2
HG00186 29 2
HG00105 30 2
HG00183 30 2
HG00119 31 2
HG00190 31 2
HG00131 32 2
HG00159 32 2
HG00109 33 2
HG00246 33 2
HG00117 34 2
HG00240 34 2
HG00143 35 2
HG00251 35 2
HG00181 36 2
HG00239 36 2
VCF2DIST
3 0
2025-06-17 07:23:02 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:02 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 5
2025-06-17 07:23:02 Distances=3x3
hierarchical method=Complete
100 1000
2025-06-17 07:23:02 Distances=100x100
hierarchical method=Complete
VCF2DIST
3 0
2025-06-17 07:23:02 Distances=3x3
hierarchical method=Complete
FASTA2DIST
FASTA2DIST
FASTA2DIST
FASTA2DIST
FASTA2DIST
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
..cutHeight not given, setting it to 1.73 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
..cutHeight not given, setting it to 1.73 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST
3 0
2025-06-17 07:23:04 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST
3 0
2025-06-17 07:23:04 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST
3 0
2025-06-17 07:23:04 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST
3 0
2025-06-17 07:23:04 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST
100 0
2025-06-17 07:23:04 Distances=100x100
hierarchical method=Complete
..cutHeight not given, setting it to 0.0407 ===> 99% of the (truncated) height range in dendro.
..done.
2025-06-17 07:23:04 Clusters=34
HG00118 1 7
HG00138 1 7
HG00142 1 7
HG00143 1 7
HG00146 1 7
HG00157 1 7
HG00160 1 7
HG00185 2 5
HG00189 2 5
HG00251 2 5
HG00258 2 5
HG00261 2 5
HG00126 3 5
HG00149 3 5
HG00182 3 5
HG00233 3 5
HG00262 3 5
HG00108 4 4
HG00129 4 4
HG00232 4 4
HG00253 4 4
HG00097 5 4
HG00099 5 4
HG00102 5 4
HG00174 5 4
HG00113 6 4
HG00158 6 4
HG00178 6 4
HG00259 6 4
HG00121 7 4
HG00123 7 4
HG00173 7 4
HG00256 7 4
HG00100 8 4
HG00101 8 4
HG00107 8 4
HG00125 8 4
HG00114 9 3
HG00133 9 3
HG00234 9 3
HG00120 10 3
HG00136 10 3
HG00236 10 3
HG00177 11 3
HG00242 11 3
HG00244 11 3
HG00141 12 3
HG00187 12 3
HG00254 12 3
HG00115 13 3
HG00130 13 3
HG00155 13 3
HG00096 14 3
HG00128 14 3
HG00145 14 3
HG00140 15 3
HG00151 15 3
HG00237 15 3
HG00106 16 3
HG00132 16 3
HG00148 16 3
HG00180 17 3
HG00252 17 3
HG00260 17 3
HG00116 18 3
HG00122 18 3
HG00139 18 3
HG00112 19 3
HG00150 19 3
HG00231 19 3
HG00171 20 2
HG00255 20 2
HG00103 21 2
HG00257 21 2
HG00179 22 2
HG00250 22 2
HG00176 23 2
HG00235 23 2
HG00188 24 2
HG00245 24 2
HG00111 25 2
HG00137 25 2
HG00127 26 2
HG00186 26 2
HG00110 27 2
HG00154 27 2
HG00105 28 2
HG00183 28 2
HG00238 29 2
HG00243 29 2
HG00119 30 2
HG00190 30 2
HG00131 31 2
HG00159 31 2
HG00109 32 2
HG00246 32 2
HG00117 33 2
HG00240 33 2
HG00181 34 2
HG00239 34 2
VCF2DIST
VCF2DIST
VCF2DIST
VCF2ISTATS
Num of Ind = 3
VCF2ISTATS
Num of Ind = 3
VCF2ISTATS
Num of Ind = 3
VCF2TREE
2025-06-17 07:23:05 Distances=3x3
hierarchical method=Complete
VCF2TREE
2025-06-17 07:23:05 Distances=100x100
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
>
> proc.time()
user system elapsed
9.550 0.471 6.063
fastreeR.Rcheck/fastreeR-Ex.timings
| name | user | system | elapsed | |
| dist2clusters | 1.123 | 0.062 | 0.801 | |
| dist2tree | 0.204 | 0.012 | 0.112 | |
| fasta2dist | 3.411 | 0.204 | 1.443 | |
| tree2clusters | 0.145 | 0.020 | 0.123 | |
| vcf2clusters | 1.243 | 0.045 | 0.358 | |
| vcf2dist | 0.594 | 0.040 | 0.222 | |
| vcf2istats | 0.960 | 0.045 | 0.355 | |
| vcf2tree | 0.367 | 0.017 | 0.129 | |