Back to Mac ARM64 build report for BioC 3.19
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This page was generated on 2024-05-07 11:32:33 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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 705/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fastreeR 1.8.0  (landing page)
Anestis Gkanogiannis
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/fastreeR
git_branch: RELEASE_3_19
git_last_commit: 6d4fbfb
git_last_commit_date: 2024-04-30 11:41:06 -0400 (Tue, 30 Apr 2024)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for fastreeR on kjohnson3


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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-05-06 21:30:07 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 21:30:25 -0400 (Mon, 06 May 2024)
EllapsedTime: 18.2 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/fastreeR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fastreeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastreeR’ version ‘1.8.0’
* 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 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 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: 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/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  0.071   0.019   0.085 

fastreeR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:20 VCFManager: START READ
16777216
2024/05/06 21:30:20 VCFManager: END READ

Processed variants : 	       4
VCF2TREE : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:20 VCFManager: START READ
2024/05/06 21:30:20 VCFManager: END READ

Processed variants : 	       4
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
3 4
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:20 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:20 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:20 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:20 Clusters=2

S2	0	1
S1	1	2
S3	1	2



100 1000
2024/05/06 21:30:20 Distances=100x100
hierarchical method=Complete
 ..cutHeight not given, setting it to 0.0794  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:20 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 : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:20 VCFManager: START READ
2024/05/06 21:30:20 VCFManager: END READ

Processed variants : 	       4
3 0
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:20 Clusters=2

S2	0	1
S1	1	2
S3	1	2



3 4
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
100 1000
2024/05/06 21:30:20 Distances=100x100
hierarchical method=Complete
VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:20 VCFManager: START READ
2024/05/06 21:30:20 VCFManager: END READ

Processed variants : 	       4
3 0
2024/05/06 21:30:20 Distances=3x3
hierarchical method=Complete
FASTA2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:20 FastaManager: START READ
CHUNK_SIZE=16777216
2024/05/06 21:30:20 FastaManager: Chunk with 7 lines.
2024/05/06 21:30:20 FastaManager: END READ
2024/05/06 21:30:20 FastaManager: FASTA
2	S2
2	S1
3	S3
FASTA2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 FastaManager: START READ
2024/05/06 21:30:21 FastaManager: Chunk with 7 lines.
2024/05/06 21:30:21 FastaManager: END READ
2	S2
2	S1
2024/05/06 21:30:21 FastaManager: FASTA
3	S3
FASTA2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 FastaManager: START READ
2024/05/06 21:30:21 FastaManager: Chunk with 7 lines.
2024/05/06 21:30:21 FastaManager: END READ
2024/05/06 21:30:21 FastaManager: FASTA
2	S1
2	S2
3	S3
FASTA2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 FastaManager: START READ
2024/05/06 21:30:21 FastaManager: Chunk with 7 lines.
1	S1
2024/05/06 21:30:21 FastaManager: END READ
2	S2
2024/05/06 21:30:21 FastaManager: FASTA
3	S3
FASTA2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 FastaManager: START READ
2024/05/06 21:30:21 FastaManager: Chunk with 96 lines.
2024/05/06 21:30:21 FastaManager: END READ
2024/05/06 21:30:21 FastaManager: FASTA
2	contig-202000258
3	contig-73001792
4	contig-13001800
5	contig-198000031
6	contig-366001068
7	contig-295001825
8	contig-100000567
9	contig-237001826
10	contig-15000592
11	contig-168000048
12	contig-620000331
13	contig-573001861
14	contig-12001376
15	contig-30001369
16	contig-201001879
17	contig-11000629
18	contig-364
18	contig-25000365
20	contig-127000661
21	contig-136001638
21	contig-16001175
23	contig-20000917
24	contig-448001924
25	contig-171000141
26	contig-5001683
27	contig-5000427
28	contig-7001201
29	contig-19001684
30	contig-218001938
31	contig-6001939
32	contig-60001206
33	contig-65000152
34	contig-263001217
35	contig-600000955
36	contig-261001227
37	contig-47000966
38	contig-16001959
39	contig-623000970
40	contig-98000731
41	contig-52000465
42	contig-118001491
43	contig-48000188
44	contig-53001003
45	contig-230000764
46	contig-40000768
47	contig-105000229
48	contig-186000247
48	contig-19001776
2024/05/06 21:30:21 CalculateD2ChildTask(40): 	50
 ..done.
2024/05/06 21:30:21 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.
2024/05/06 21:30:21 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.
2024/05/06 21:30:21 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 VCFManager: START READ
2024/05/06 21:30:21 VCFManager: END READ

Processed variants : 	       4
3 0
2024/05/06 21:30:21 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:21 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 VCFManager: START READ
2024/05/06 21:30:21 VCFManager: END READ

Processed variants : 	       4
3 0
2024/05/06 21:30:21 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:21 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 VCFManager: START READ
2024/05/06 21:30:21 VCFManager: END READ

Processed variants : 	       4
3 0
2024/05/06 21:30:21 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:21 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 VCFManager: START READ
2024/05/06 21:30:21 VCFManager: END READ

Processed variants : 	       4
3 0
2024/05/06 21:30:21 Distances=3x3
hierarchical method=Complete
 ..cutHeight not given, setting it to 1.74  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:21 Clusters=2

S2	0	1
S1	1	2
S3	1	2



VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:21 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	    1000
2024/05/06 21:30:22 CalculateDistancesChildTask(36): 	50
2024/05/06 21:30:22 CalculateDistancesChildTask(68): 	100
100 0
2024/05/06 21:30:22 Distances=100x100
hierarchical method=Complete
 ..cutHeight not given, setting it to 0.0794  ===>  99% of the (truncated) height range in dendro.
 ..done.
2024/05/06 21:30:22 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 : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	       4
VCF2DIST : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	    1000
2024/05/06 21:30:22 CalculateDistancesChildTask(79): 	50
2024/05/06 21:30:22 CalculateDistancesChildTask(54): 	100
VCF2ISTATS : Mon May 06 15:31:54 EDT 2024
Num of Ind = 3
VCF2ISTATS : Mon May 06 15:31:54 EDT 2024
Num of Ind = 3
VCF2ISTATS : Mon May 06 15:31:54 EDT 2024
Num of Ind = 3
VCF2TREE : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	       4
2024/05/06 21:30:22 Distances=3x3
hierarchical method=Complete
VCF2TREE : Mon May 06 15:31:54 EDT 2024
cpus=24
using=2
2024/05/06 21:30:22 VCFManager: START READ
2024/05/06 21:30:22 VCFManager: END READ

Processed variants : 	    1000
2024/05/06 21:30:22 CalculateDistancesChildTask(40): 	50
2024/05/06 21:30:22 CalculateDistancesChildTask(69): 	100
2024/05/06 21:30:22 Distances=100x100
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 100 ]
> 
> proc.time()
   user  system elapsed 
  3.524   0.416   2.441 

Example timings

fastreeR.Rcheck/fastreeR-Ex.timings

nameusersystemelapsed
dist2clusters0.3720.0500.271
dist2tree0.0750.0060.036
fasta2dist1.2010.1630.560
tree2clusters0.0450.0070.032
vcf2clusters0.8170.0580.223
vcf2dist0.2580.0360.104
vcf2istats0.2640.0300.089
vcf2tree0.2440.0150.064