Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 706/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fastreeR 1.99.4  (landing page)
Anestis Gkanogiannis
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/fastreeR
git_branch: devel
git_last_commit: 815fd6f
git_last_commit_date: 2025-08-08 05:41:53 -0400 (Fri, 08 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES


CHECK results for fastreeR on nebbiolo2

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.

raw results


Summary

Package: fastreeR
Version: 1.99.4
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings fastreeR_1.99.4.tar.gz
StartedAt: 2025-08-08 22:23:01 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 22:24:10 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 69.1 seconds
RetCode: 0
Status:   OK  
CheckDir: fastreeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings fastreeR_1.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/fastreeR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘fastreeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastreeR’ version ‘1.99.4’
* 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

fastreeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL fastreeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘fastreeR’ ...
** this is package ‘fastreeR’ version ‘1.99.4’
** 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)

Tests output

fastreeR.Rcheck/tests/spelling.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  0.135   0.043   0.167 

fastreeR.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
3 5
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:26 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 5
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:26 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 5
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:26 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 5
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:26 Clusters=2

S2	0	1
S1	1	2
S3	1	2



100 1000
2025-08-08 22:23:26 Distances=100x100
hierarchical method=Complete
 ..cutHeight not given, setting it to 0.0794  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:26 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
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:26 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 5
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
100 1000
2025-08-08 22:23:26 Distances=100x100
hierarchical method=Complete
VCF2DIST
3 0
2025-08-08 22:23:26 Distances=3x3
hierarchical method=Complete
FASTA2DIST
FASTA2DIST
FASTA2DIST
FASTA2DIST
FASTA2DIST
 ..done.
2025-08-08 22:23:28 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.
2025-08-08 22:23:28 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.
2025-08-08 22:23:28 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST
3 0
2025-08-08 22:23:28 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:28 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST
3 0
2025-08-08 22:23:28 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:28 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST
3 0
2025-08-08 22:23:28 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:28 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST
3 0
2025-08-08 22:23:28 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:28 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST
100 0
2025-08-08 22:23:29 Distances=100x100
hierarchical method=Complete
 ..cutHeight not given, setting it to 0.0407  ===>  99% of the (truncated) height range in dendro.
 ..done.
2025-08-08 22:23:29 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
2025-08-08 22:23:29 Distances=3x3
hierarchical method=Complete
VCF2TREE
2025-08-08 22:23:29 Distances=100x100
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  8.119   0.661   5.132 

Example timings

fastreeR.Rcheck/fastreeR-Ex.timings

nameusersystemelapsed
dist2clusters0.9900.0440.610
dist2tree0.2040.0070.104
fasta2dist3.5590.2571.316
tree2clusters0.1340.0070.090
vcf2clusters1.3130.0350.361
vcf2dist0.2800.0530.137
vcf2istats1.0330.0530.287
vcf2tree0.2670.0170.109