Kevin Rue-Albrecht
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/TVTB |
| git_branch: RELEASE_3_17 |
| git_last_commit: f28d805 |
| git_last_commit_date: 2023-04-25 10:50:43 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:14 -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 2157/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TVTB 1.26.0 (landing page) Kevin Rue-Albrecht
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the TVTB 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: TVTB |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TVTB_1.26.0.tar.gz |
| StartedAt: 2023-10-19 08:44:13 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 08:57:27 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 794.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TVTB.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TVTB_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TVTB.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 ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.26.0’
* 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 ‘TVTB’ 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 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 ... WARNING
checkRd: (5) VcfBasicRules-class.Rd:133-136: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:141-146: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:147-151: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:161-164: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:165-168: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:179-192: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:193-201: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:85-92: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:93-96: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:97-103: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:104-108: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:124-127: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:134-140: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:141-149: \item in \describe must have non-empty label
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotInfo-methods 8.150 0.389 17.195
VcfBasicRules-class 2.897 0.152 5.328
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 1 WARNING
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TVTB.Rcheck/00check.log’
for details.
TVTB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TVTB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘TVTB’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (TVTB)
TVTB.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(TVTB)
>
> test_check("TVTB")
Class: Genotypes
@ref (hom. ref.): "REF" {0/0}
@het (heter.) : "HET" {0/1, 1/0}
@alt (hom. alt.): "ALT" {1/1}class: TVTBparam
@genos: class: Genotypes
@ref (hom. ref.): "REF" {0|0}
@het (heter.): "HET" {0|1, 1|0}
@alt (hom. alt.): "ALT" {1|1}
@ranges: 0 GRanges on 0 sequence(s)
@aaf (alt. allele freq.): "AAF"
@maf (minor allele freq.): "MAF"
@vep (Ensembl VEP key): "CSQ"
@svp: <ScanVcfParam object>
@bp: <SerialParam object>
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366
TRUE FALSE FALSE FALSE FALSE FALSE
rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672
TRUE TRUE FALSE FALSE TRUE FALSE
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382
TRUE FALSE TRUE TRUE FALSE FALSE
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600
FALSE FALSE FALSE FALSE FALSE FALSE
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548
FALSE FALSE FALSE FALSE TRUE
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366
FALSE FALSE FALSE FALSE FALSE FALSE
rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672
FALSE FALSE FALSE FALSE FALSE FALSE
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382
FALSE FALSE FALSE FALSE FALSE FALSE
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600
FALSE FALSE FALSE FALSE FALSE FALSE
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548
FALSE FALSE FALSE FALSE FALSE
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366
TRUE FALSE FALSE FALSE FALSE FALSE
rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672
TRUE TRUE FALSE FALSE TRUE FALSE
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382
TRUE FALSE TRUE TRUE FALSE FALSE
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600
FALSE FALSE FALSE FALSE FALSE FALSE
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548
FALSE FALSE FALSE FALSE TRUE
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_VcfFilterRules-class.R:438:1',
'test_VcfFilterRules-class.R:468:1'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
>
> proc.time()
user system elapsed
48.009 4.681 116.072
TVTB.Rcheck/TVTB-Ex.timings
| name | user | system | elapsed | |
| Genotypes-class | 0.003 | 0.001 | 0.013 | |
| TVTBParam-class | 0.201 | 0.006 | 0.357 | |
| VcfBasicRules-class | 2.897 | 0.152 | 5.328 | |
| VcfFilterRules-class | 1.857 | 0.060 | 3.390 | |
| addCountGenos-methods | 0.914 | 0.037 | 1.709 | |
| addFrequencies-methods | 0.871 | 0.038 | 1.622 | |
| addOverallFrequencies-methods | 0.866 | 0.037 | 1.598 | |
| addPhenoLevelFrequencies-methods | 0.838 | 0.034 | 1.705 | |
| autodetectGenotypes | 0.723 | 0.036 | 1.347 | |
| countGenos-methods | 0.726 | 0.038 | 1.352 | |
| dropInfo-methods | 0.933 | 0.043 | 1.730 | |
| pairsInfo-methods | 1.870 | 0.063 | 3.451 | |
| plotInfo-methods | 8.150 | 0.389 | 17.195 | |
| readVcf-methods | 0.506 | 0.009 | 1.348 | |
| tSVE | 0 | 0 | 0 | |
| variantsInSamples-methods | 0.723 | 0.060 | 2.118 | |
| vepInPhenoLevel-methods | 0.926 | 0.129 | 2.730 | |