| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 683/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fastreeR 1.4.0 (landing page) Anestis Gkanogiannis
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
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. |
| 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 |
##############################################################################
##############################################################################
###
### 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
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)
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
fastreeR.Rcheck/fastreeR-Ex.timings
| name | user | system | elapsed | |
| dist2clusters | 0.880 | 0.091 | 1.223 | |
| dist2tree | 0.195 | 0.014 | 0.225 | |
| fasta2dist | 2.452 | 0.172 | 2.451 | |
| tree2clusters | 0.216 | 0.015 | 0.217 | |
| vcf2clusters | 1.496 | 0.110 | 0.942 | |
| vcf2dist | 0.426 | 0.070 | 0.334 | |
| vcf2istats | 0.796 | 0.033 | 0.688 | |
| vcf2tree | 0.392 | 0.018 | 0.296 | |