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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 683/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fastreeR 1.4.0  (landing page)
Anestis Gkanogiannis
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/fastreeR
git_branch: RELEASE_3_17
git_last_commit: 534a1ca
git_last_commit_date: 2023-04-25 11:36:45 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for fastreeR on kjohnson2


To the developers/maintainers of the fastreeR 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.

raw results


Summary

Package: fastreeR
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-10-17 19:15:54 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 19:17:13 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 78.5 seconds
RetCode: 0
Status:   OK  
CheckDir: fastreeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/fastreeR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fastreeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastreeR’ version ‘1.4.0’
* 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 ‘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 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 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


Installation output

fastreeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fastreeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

fastreeR.Rcheck/tests/spelling.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
  0.213   0.067   0.438 

fastreeR.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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(fastreeR)
> 
> test_check("fastreeR")
VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:52 VCFManager: START READ
16777216
2023/10/17 19:16:52 VCFManager: END READ

Processed variants : 	       4
VCF2TREE : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:52 VCFManager: START READ
2023/10/17 19:16:52 VCFManager: END READ

Processed variants : 	       4
2023/10/17 19:16:52 Distances=3x3
hierarchical method=Complete
3 4
2023/10/17 19:16:53 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:53 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2023/10/17 19:16:53 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:53 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2023/10/17 19:16:53 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:53 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2023/10/17 19:16:53 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:53 Clusters=2

S2	0	1
S1	1	2
S3	1	2



100 1000
2023/10/17 19:16:54 Distances=100x100
hierarchical method=Complete
 ..cutHeight not given, setting it to 0.0794  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:54 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 : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:54 VCFManager: START READ
2023/10/17 19:16:54 VCFManager: END READ

Processed variants : 	       4
3 0
2023/10/17 19:16:54 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:54 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2023/10/17 19:16:54 Distances=3x3
hierarchical method=Complete
100 1000
2023/10/17 19:16:54 Distances=100x100
hierarchical method=Complete
VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:54 VCFManager: START READ
2023/10/17 19:16:54 VCFManager: END READ

Processed variants : 	       4
3 0
2023/10/17 19:16:54 Distances=3x3
hierarchical method=Complete
FASTA2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:55 FastaManager: START READ
CHUNK_SIZE=16777216
2023/10/17 19:16:55 FastaManager: Chunk with 7 lines.
2023/10/17 19:16:55 FastaManager: END READ
2023/10/17 19:16:55 FastaManager: FASTA
2	null
3	null
2	null
FASTA2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:55 FastaManager: START READ
2023/10/17 19:16:55 FastaManager: Chunk with 7 lines.
2023/10/17 19:16:55 FastaManager: END READ
2023/10/17 19:16:55 FastaManager: FASTA
1	null
2	null
3	null
FASTA2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:55 FastaManager: START READ
2023/10/17 19:16:55 FastaManager: Chunk with 7 lines.
2023/10/17 19:16:55 FastaManager: END READ
2023/10/17 19:16:55 FastaManager: FASTA
1	null
2	null
3	null
FASTA2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:56 FastaManager: START READ
2023/10/17 19:16:56 FastaManager: Chunk with 7 lines.
2023/10/17 19:16:56 FastaManager: END READ
2023/10/17 19:16:56 FastaManager: FASTA
1	null
2	null
3	null
FASTA2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:56 FastaManager: START READ
2023/10/17 19:16:56 FastaManager: Chunk with 96 lines.
2023/10/17 19:16:56 FastaManager: END READ
2023/10/17 19:16:56 FastaManager: FASTA
2	null
3	null
4	null
5	null
6	null
7	null
8	null
9	null
10	null
11	null
12	null
13	null
14	null
15	null
16	null
17	null
18	null
19	null
20	null
21	null
22	null
23	null
24	null
25	null
26	null
27	null
28	null
29	null
30	null
31	null
32	null
33	null
34	null
35	null
35	null
37	null
38	null
39	null
38	null
41	null
40	null
43	null
44	null
42	null
46	null
47	null
48	null
48	null
2023/10/17 19:16:57 CalculateD2ChildTask(51): 	50
 ..done.
2023/10/17 19:16:57 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.
2023/10/17 19:16:58 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.
2023/10/17 19:16:58 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:58 VCFManager: START READ
2023/10/17 19:16:58 VCFManager: END READ

Processed variants : 	       4
3 0
2023/10/17 19:16:58 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:58 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:58 VCFManager: START READ
2023/10/17 19:16:58 VCFManager: END READ

Processed variants : 	       4
3 0
2023/10/17 19:16:58 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:58 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:58 VCFManager: START READ
2023/10/17 19:16:58 VCFManager: END READ

Processed variants : 	       4
3 0
2023/10/17 19:16:58 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:58 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:58 VCFManager: START READ
2023/10/17 19:16:58 VCFManager: END READ

Processed variants : 	       4
3 0
2023/10/17 19:16:58 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:58 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:58 VCFManager: START READ
2023/10/17 19:16:58 VCFManager: END READ

Processed variants : 	    1000
2023/10/17 19:16:58 CalculateDistancesChildTask(42): 	50
2023/10/17 19:16:59 CalculateDistancesChildTask(71): 	100
100 0
2023/10/17 19:16:59 Distances=100x100
hierarchical method=Complete
 ..cutHeight not given, setting it to 0.0794  ===>  99% of the (truncated) height range in dendro.
 ..done.
2023/10/17 19:16:59 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 : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:59 VCFManager: START READ
2023/10/17 19:16:59 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:59 VCFManager: START READ
2023/10/17 19:16:59 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:59 VCFManager: START READ
2023/10/17 19:16:59 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:16:59 VCFManager: START READ
2023/10/17 19:16:59 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:17:00 VCFManager: START READ
2023/10/17 19:17:00 VCFManager: END READ

Processed variants : 	    1000
2023/10/17 19:17:00 CalculateDistancesChildTask(40): 	50
2023/10/17 19:17:00 CalculateDistancesChildTask(71): 	100
VCF2ISTATS : Sun Oct 15 16:48:51 EDT 2023
Num of Ind = 3
VCF2ISTATS : Sun Oct 15 16:48:51 EDT 2023
Num of Ind = 3
VCF2ISTATS : Sun Oct 15 16:48:51 EDT 2023
Num of Ind = 3
VCF2TREE : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:17:00 VCFManager: START READ
2023/10/17 19:17:00 VCFManager: END READ

Processed variants : 	       4
2023/10/17 19:17:01 Distances=3x3
hierarchical method=Complete
VCF2TREE : Sun Oct 15 16:48:51 EDT 2023
cpus=8
using=2
2023/10/17 19:17:01 VCFManager: START READ
2023/10/17 19:17:01 VCFManager: END READ

Processed variants : 	    1000
2023/10/17 19:17:01 CalculateDistancesChildTask(87): 	50
2023/10/17 19:17:01 CalculateDistancesChildTask(65): 	100
2023/10/17 19:17:01 Distances=100x100
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 100 ]
> 
> proc.time()
   user  system elapsed 
  9.142   0.741  11.442 

Example timings

fastreeR.Rcheck/fastreeR-Ex.timings

nameusersystemelapsed
dist2clusters0.8800.0911.223
dist2tree0.1950.0140.225
fasta2dist2.4520.1722.451
tree2clusters0.2160.0150.217
vcf2clusters1.4960.1100.942
vcf2dist0.4260.0700.334
vcf2istats0.7960.0330.688
vcf2tree0.3920.0180.296