Devon Kohler
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MSstatsLOBD |
| git_branch: RELEASE_3_17 |
| git_last_commit: a17e7ab |
| git_last_commit_date: 2023-04-25 11:30:21 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -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 1317/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsLOBD 1.8.0 (landing page) Devon Kohler
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the MSstatsLOBD 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: MSstatsLOBD |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsLOBD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsLOBD_1.8.0.tar.gz |
| StartedAt: 2023-10-18 10:06:35 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 10:07:42 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 66.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsLOBD.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsLOBD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsLOBD_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsLOBD.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 ‘MSstatsLOBD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLOBD’ version ‘1.8.0’
* 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 ‘MSstatsLOBD’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
'LinkingTo' field is unused: package has no 'src' directory
* 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.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/MSstatsLOBD.Rcheck/00check.log’
for details.
MSstatsLOBD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsLOBD ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘MSstatsLOBD’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (MSstatsLOBD)
MSstatsLOBD.Rcheck/tests/tinytest.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.
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("MSstatsLOBD")
+ }
test_MSstatsLOBD.R............ 0 tests %%%%
test_MSstatsLOBD.R............ 0 tests
test_MSstatsLOBD.R............ 1 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 2 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 3 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 4 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 5 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 6 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 7 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 8 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 9 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 10 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 11 tests [0;32mOK[0m %%%%
test_MSstatsLOBD.R............ 11 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 12 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 13 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 14 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 15 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 16 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 17 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 18 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 19 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 20 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 21 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 22 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 22 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 23 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 24 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 25 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 26 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 27 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 27 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 28 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 29 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 30 tests [0;32mOK[0m
test_MSstatsLOBD.R............ 31 tests [0;32mOK[0m [0;34m1.7s[0m
All ok, 31 results (1.7s)
Warning messages:
1: The `panel.margin` argument of `theme()` is deprecated as of ggplot2 2.2.0.
ℹ Please use the `panel.spacing` argument instead.
ℹ The deprecated feature was likely used in the MSstatsLOBD package.
Please report the issue at <https://github.com/Vitek-Lab/MSstatsLODQ/issues>.
2: In geom_point(data = data.frame(x = LOD_pred, y = y_LOD_pred, shape = "LOD"), :
Ignoring unknown aesthetics: guide
3: In geom_point(data = data.frame(x = LOQ_pred, y = y_LOQ_pred, shape = "LOQ"), :
Ignoring unknown aesthetics: guide
4: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
of ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the MSstatsLOBD package.
Please report the issue at <https://github.com/Vitek-Lab/MSstatsLODQ/issues>.
5: In geom_point(data = data.frame(x = LOD_pred, y = y_LOD_pred, shape = "LOD"), :
Ignoring unknown aesthetics: guide
6: In geom_point(data = data.frame(x = LOQ_pred, y = y_LOQ_pred, shape = "LOQ"), :
Ignoring unknown aesthetics: guide
7: In geom_point(data = data.frame(x = LOD_pred, y = y_LOD_pred, shape = "LOD"), :
Ignoring unknown aesthetics: guide
8: In geom_point(data = data.frame(x = LOQ_pred, y = y_LOQ_pred, shape = "LOQ"), :
Ignoring unknown aesthetics: guide
9: In geom_point(data = data.frame(x = LOD_pred, y = y_LOD_pred, shape = "LOD"), :
Ignoring unknown aesthetics: guide
10: In geom_point(data = data.frame(x = LOQ_pred, y = y_LOQ_pred, shape = "LOQ"), :
Ignoring unknown aesthetics: guide
>
>
> proc.time()
user system elapsed
2.149 0.179 3.315
MSstatsLOBD.Rcheck/MSstatsLOBD-Ex.timings
| name | user | system | elapsed | |
| linear_quantlim | 0.110 | 0.010 | 0.166 | |
| nonlinear_quantlim | 0.196 | 0.011 | 0.292 | |
| plot_quantlim | 1.545 | 0.035 | 2.314 | |
| raw_data | 0.011 | 0.001 | 0.018 | |
| spikeindata | 0.031 | 0.000 | 0.049 | |