| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:01 -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 616/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EDIRquery 1.0.0 (landing page) Laura D.T. Vo Ngoc
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the EDIRquery 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: EDIRquery |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EDIRquery.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EDIRquery_1.0.0.tar.gz |
| StartedAt: 2023-10-17 17:20:21 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 17:24:51 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 270.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EDIRquery.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EDIRquery.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EDIRquery_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/EDIRquery.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 ‘EDIRquery/DESCRIPTION’ ... OK
* this is package ‘EDIRquery’ version ‘1.0.0’
* 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 ‘EDIRquery’ 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 ... NOTE
gene_lookup : gen_filter : <anonymous>: no visible binding for global
variable ‘hgnc_symbol’
gene_lookup : gen_filter : <anonymous>: no visible binding for global
variable ‘ensembl_gene_id’
Undefined global functions or variables:
ensembl_gene_id hgnc_symbol
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/EDIRquery.Rcheck/00check.log’
for details.
EDIRquery.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EDIRquery ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘EDIRquery’ ... ** using staged installation ** R ** data ** 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 (EDIRquery)
EDIRquery.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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(EDIRquery)
>
> test_check("EDIRquery")
Parameters
Repeat length: 10 bp
Gene: ENSG00000171298 / GAA
Gene length: 18325 bp
Transcript ID: ENST00000302262
Distance: 0-1000 bp
Mismatch: TRUE
repeat_length unique_seqs tot_instances tot_structures avg_dist
1 10 1172 1227 690 500.2217
norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb
1 0.06695771 66957.71 0.03765348 37653.48
Runtime: 0.781 sec elapsed
Parameters
Gene: ENSG00000171298 / GAA
Gene length: 18325 bp
Transcript ID: ENST00000302262
Distance: 0-1000 bp
Mismatch: TRUE
repeat_length unique_seqs tot_instances tot_structures avg_dist
1 7 5172 10460 14562 486.2603
2 8 5677 7592 7062 516.1827
3 9 3160 3461 2226 508.7588
4 10 1172 1227 690 500.2217
5 11 389 399 209 492.5263
6 12 122 124 63 454.6190
7 13 42 42 21 346.2857
8 14 14 14 7 271.1429
9 15 4 4 2 43.0000
10 16 2 2 1 42.0000
norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb
1 0.5708049113 570804.9113 7.946521e-01 794652.11460
2 0.4142974079 414297.4079 3.853752e-01 385375.17053
3 0.1888676671 188867.6671 1.214734e-01 121473.39700
4 0.0669577080 66957.7080 3.765348e-02 37653.47885
5 0.0217735334 21773.5334 1.140518e-02 11405.18417
6 0.0067667121 6766.7121 3.437926e-03 3437.92633
7 0.0022919509 2291.9509 1.145975e-03 1145.97544
8 0.0007639836 763.9836 3.819918e-04 381.99181
9 0.0002182810 218.2810 1.091405e-04 109.14052
10 0.0001091405 109.1405 5.457026e-05 54.57026
Runtime: 1.497 sec elapsed
Parameters
Repeat length: 10 bp
Gene: ENSG00000171298 / GAA
Gene length: 18325 bp
Transcript ID: ENST00000302262
Distance: 0-1000 bp
Mismatch: FALSE
repeat_length unique_seqs tot_instances tot_structures avg_dist
1 10 34 68 34 473.0588
norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb
1 0.003710778 3710.778 0.001855389 1855.389
Runtime: 0.768 sec elapsed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
>
> proc.time()
user system elapsed
10.921 0.447 16.387
EDIRquery.Rcheck/EDIRquery-Ex.timings
| name | user | system | elapsed | |
| gene_lookup | 3.482 | 0.066 | 4.619 | |