| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 674/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fastreeR 1.5.1 (landing page) Anestis Gkanogiannis
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: fastreeR |
| Version: 1.5.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings fastreeR_1.5.1.tar.gz |
| StartedAt: 2023-06-05 22:20:56 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 22:22:11 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 75.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fastreeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings fastreeR_1.5.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/fastreeR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘fastreeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastreeR’ version ‘1.5.1’
* 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 ... 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 loading without being on the library search path ... 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 ...
‘fastreeR_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
fastreeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL fastreeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
0.201 0.009 0.197
fastreeR.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:25 VCFManager: START READ
16777216
2023/06/05 22:21:25 VCFManager: END READ
Processed variants : 4
VCF2TREE : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:25 VCFManager: START READ
2023/06/05 22:21:25 VCFManager: END READ
Processed variants : 4
2023/06/05 22:21:25 Distances=3x3
hierarchical method=Complete
3 4
2023/06/05 22:21:25 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:25 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2023/06/05 22:21:25 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:25 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2023/06/05 22:21:25 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:25 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2023/06/05 22:21:25 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:25 Clusters=2
S2 0 1
S1 1 2
S3 1 2
100 1000
2023/06/05 22:21:26 Distances=100x100
hierarchical method=Complete
..cutHeight not given, setting it to 0.0794 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:26 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 : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:26 VCFManager: START READ
2023/06/05 22:21:26 VCFManager: END READ
Processed variants : 4
3 0
2023/06/05 22:21:26 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:26 Clusters=2
S2 0 1
S1 1 2
S3 1 2
3 4
2023/06/05 22:21:26 Distances=3x3
hierarchical method=Complete
100 1000
2023/06/05 22:21:26 Distances=100x100
hierarchical method=Complete
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:26 VCFManager: START READ
2023/06/05 22:21:26 VCFManager: END READ
Processed variants : 4
3 0
2023/06/05 22:21:26 Distances=3x3
hierarchical method=Complete
FASTA2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:26 FastaManager: START READ
CHUNK_SIZE=16777216
2023/06/05 22:21:26 FastaManager: Chunk with 7 lines.
2023/06/05 22:21:26 FastaManager: END READ
2023/06/05 22:21:26 FastaManager: FASTA
2 S1
2 S2
3 S3
FASTA2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:26 FastaManager: START READ
2023/06/05 22:21:26 FastaManager: Chunk with 7 lines.
2 S1
2 S2
2023/06/05 22:21:26 FastaManager: END READ
3 S3
2023/06/05 22:21:26 FastaManager: FASTA
FASTA2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:26 FastaManager: START READ
2023/06/05 22:21:26 FastaManager: Chunk with 7 lines.
2023/06/05 22:21:26 FastaManager: END READ
2 S1
2023/06/05 22:21:26 FastaManager: FASTA
2 S2
3 S3
FASTA2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:27 FastaManager: START READ
2023/06/05 22:21:27 FastaManager: Chunk with 7 lines.
1 S1
2023/06/05 22:21:27 FastaManager: END READ
2 S2
2023/06/05 22:21:27 FastaManager: FASTA
3 S3
FASTA2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:27 FastaManager: START READ
2023/06/05 22:21:27 FastaManager: Chunk with 96 lines.
2023/06/05 22:21:27 FastaManager: END READ
2023/06/05 22:21:27 FastaManager: FASTA
2 contig-202000258
3 contig-73001792
4 contig-198000031
5 contig-13001800
6 contig-366001068
7 contig-295001825
8 contig-237001826
9 contig-100000567
10 contig-15000592
11 contig-168000048
12 contig-620000331
13 contig-573001861
14 contig-30001369
15 contig-12001376
16 contig-201001879
17 contig-11000629
18 contig-25000365
18 contig-364
20 contig-127000661
21 contig-136001638
22 contig-16001175
23 contig-20000917
24 contig-448001924
25 contig-171000141
26 contig-5001683
27 contig-7001201
28 contig-5000427
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-19001776
48 contig-186000247
2023/06/05 22:21:27 CalculateD2ChildTask(51): 50
..done.
2023/06/05 22:21:28 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.
2023/06/05 22:21:28 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.
2023/06/05 22:21:28 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:28 VCFManager: START READ
2023/06/05 22:21:28 VCFManager: END READ
Processed variants : 4
3 0
2023/06/05 22:21:28 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:28 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:28 VCFManager: START READ
2023/06/05 22:21:28 VCFManager: END READ
Processed variants : 4
3 0
2023/06/05 22:21:28 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:28 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:28 VCFManager: START READ
2023/06/05 22:21:28 VCFManager: END READ
Processed variants : 4
3 0
2023/06/05 22:21:28 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:28 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:28 VCFManager: START READ
2023/06/05 22:21:28 VCFManager: END READ
Processed variants : 4
3 0
2023/06/05 22:21:28 Distances=3x3
hierarchical method=Complete
..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:28 Clusters=2
S2 0 1
S1 1 2
S3 1 2
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:28 VCFManager: START READ
2023/06/05 22:21:28 VCFManager: END READ
Processed variants : 1000
2023/06/05 22:21:28 CalculateDistancesChildTask(38): 50
2023/06/05 22:21:28 CalculateDistancesChildTask(68): 100
100 0
2023/06/05 22:21:28 Distances=100x100
hierarchical method=Complete
..cutHeight not given, setting it to 0.0794 ===> 99% of the (truncated) height range in dendro.
..done.
2023/06/05 22:21:28 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 Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 4
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 4
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 4
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 4
VCF2DIST : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 1000
2023/06/05 22:21:29 CalculateDistancesChildTask(38): 50
2023/06/05 22:21:29 CalculateDistancesChildTask(67): 100
VCF2ISTATS : Mon Jun 05 08:22:47 UTC 2023
Num of Ind = 3
VCF2ISTATS : Mon Jun 05 08:22:47 UTC 2023
Num of Ind = 3
VCF2ISTATS : Mon Jun 05 08:22:47 UTC 2023
Num of Ind = 3
VCF2TREE : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 4
2023/06/05 22:21:29 Distances=3x3
hierarchical method=Complete
VCF2TREE : Mon Jun 05 08:22:47 UTC 2023
cpus=32
using=2
2023/06/05 22:21:29 VCFManager: START READ
2023/06/05 22:21:29 VCFManager: END READ
Processed variants : 1000
2023/06/05 22:21:29 CalculateDistancesChildTask(91): 50
2023/06/05 22:21:29 CalculateDistancesChildTask(70): 100
2023/06/05 22:21:29 Distances=100x100
hierarchical method=Complete
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 100 ]
>
> proc.time()
user system elapsed
10.845 0.545 6.267
fastreeR.Rcheck/fastreeR-Ex.timings
| name | user | system | elapsed | |
| dist2clusters | 0.949 | 0.075 | 0.749 | |
| dist2tree | 0.180 | 0.008 | 0.092 | |
| fasta2dist | 3.321 | 0.188 | 1.502 | |
| tree2clusters | 0.196 | 0.031 | 0.151 | |
| vcf2clusters | 2.091 | 0.064 | 0.498 | |
| vcf2dist | 0.965 | 0.016 | 0.275 | |
| vcf2istats | 0.829 | 0.043 | 0.274 | |
| vcf2tree | 0.746 | 0.009 | 0.166 | |