| Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-01-04 17:32:24 -0500 (Thu, 04 Jan 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.2 (2023-10-31) -- "Eye Holes" | 4394 |
| 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 1014/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ImmuneSpaceR 1.30.0 (landing page) ImmuneSpace Package Maintainer
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the ImmuneSpaceR 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: ImmuneSpaceR |
| Version: 1.30.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ImmuneSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ImmuneSpaceR_1.30.0.tar.gz |
| StartedAt: 2024-01-03 16:40:06 -0500 (Wed, 03 Jan 2024) |
| EndedAt: 2024-01-03 16:41:51 -0500 (Wed, 03 Jan 2024) |
| EllapsedTime: 105.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ImmuneSpaceR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ImmuneSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ImmuneSpaceR_1.30.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ImmuneSpaceR.Rcheck’
* using R version 4.3.2 (2023-10-31)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ImmuneSpaceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ImmuneSpaceR’ version ‘1.30.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/src/contrib:
Line starting '<!DOCTYPE html> ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/src/contrib:
Line starting '<!DOCTYPE html> ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/src/contrib:
Line starting '<!DOCTYPE html> ...' is malformed!
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 ‘ImmuneSpaceR’ 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 ... NOTE
':::' call which should be '::': ‘Rlabkey:::labkey.getRequestOptions’
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘Rlabkey:::.lkdefaults’
See the note in ?`:::` about the use of this operator.
* 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 ‘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-3.18-bioc-mac-arm64/meat/ImmuneSpaceR.Rcheck/00check.log’
for details.
ImmuneSpaceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ImmuneSpaceR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘ImmuneSpaceR’ ... ** 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 (ImmuneSpaceR)
ImmuneSpaceR.Rcheck/tests/testthat.Rout
R version 4.3.2 (2023-10-31) -- "Eye Holes"
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(ImmuneSpaceR)
>
> if (Sys.info()["user"] != "biocbuild") test_check("ImmuneSpaceR")
>
> proc.time()
user system elapsed
4.279 0.295 4.571
ImmuneSpaceR.Rcheck/ImmuneSpaceR-Ex.timings
| name | user | system | elapsed | |
| CreateConnection | 0.051 | 0.010 | 0.539 | |
| ISpalette | 0.005 | 0.001 | 0.006 | |
| ImmuneSpaceConnection | 0.010 | 0.003 | 0.158 | |
| check_netrc | 0.000 | 0.000 | 0.001 | |
| interactive_netrc | 0 | 0 | 0 | |
| loadConnection | 0.078 | 0.003 | 0.082 | |
| template_IS | 0.024 | 0.038 | 0.150 | |
| theme_IS | 0.493 | 0.028 | 0.521 | |
| write_netrc | 0.001 | 0.001 | 0.001 | |