| Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:13 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1168/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Congcong Gong
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the mbOmic 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: mbOmic |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mbOmic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mbOmic_1.6.0.tar.gz |
| StartedAt: 2024-04-17 18:25:39 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 18:28:44 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 184.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: mbOmic.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mbOmic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mbOmic_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/mbOmic.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 ‘mbOmic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbOmic’ version ‘1.6.0’
* 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 ‘mbOmic’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'mbOmic' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/mbOmic.Rcheck/00install.out’ for details.
* 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 ... ERROR
Running examples in ‘mbOmic-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enterotyping
> ### Title: enterotyping
> ### Aliases: enterotyping
>
> ### ** Examples
>
> dat <- read.delim('http://enterotypes.org/ref_samples_abundance_MetaHIT.txt')
Warning in file(file, "rt") :
cannot open URL 'http://enterotypes.org/ref_samples_abundance_MetaHIT.txt': HTTP status was '404 Not Found'
Error in file(file, "rt") :
cannot open the connection to 'http://enterotypes.org/ref_samples_abundance_MetaHIT.txt'
Calls: read.delim -> read.table -> file
Execution halted
* 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 ERROR, 1 WARNING
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/mbOmic.Rcheck/00check.log’
for details.
mbOmic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mbOmic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘mbOmic’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘nrow’ from package ‘base’ in package ‘mbOmic’ Creating a generic function for ‘ncol’ from package ‘base’ in package ‘mbOmic’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: Package 'mbOmic' is deprecated and will be removed from Bioconductor version 3.19 ** testing if installed package can be loaded from final location Warning: Package 'mbOmic' is deprecated and will be removed from Bioconductor version 3.19 ** testing if installed package keeps a record of temporary installation path * DONE (mbOmic)
mbOmic.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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(mbOmic)
Warning message:
Package 'mbOmic' is deprecated and will be removed from Bioconductor
version 3.19
>
> test_check("mbOmic")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
7.443 0.393 7.869
mbOmic.Rcheck/mbOmic-Ex.timings
| name | user | system | elapsed | |
| Set-class | 0 | 0 | 0 | |
| bSet-class | 0.021 | 0.002 | 0.024 | |
| bSet | 0.004 | 0.001 | 0.004 | |
| clean_analytes | 0.023 | 0.002 | 0.025 | |
| cluster_jsd | 0.012 | 0.002 | 0.015 | |
| coExpress | 12.450 | 0.420 | 12.884 | |
| corr | 2.832 | 0.374 | 3.207 | |
| dist_jsd | 0.004 | 0.002 | 0.006 | |