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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstatsLOBD.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstatsLOBD_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsLOBD.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsLOBD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLOBD’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsLOBD.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MSstatsLOBD
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 OK 
test_MSstatsLOBD.R............    2 tests OK 
test_MSstatsLOBD.R............    3 tests OK 
test_MSstatsLOBD.R............    4 tests OK 
test_MSstatsLOBD.R............    5 tests OK 
test_MSstatsLOBD.R............    6 tests OK 
test_MSstatsLOBD.R............    7 tests OK 
test_MSstatsLOBD.R............    8 tests OK 
test_MSstatsLOBD.R............    9 tests OK 
test_MSstatsLOBD.R............   10 tests OK 
test_MSstatsLOBD.R............   11 tests OK %%%%
test_MSstatsLOBD.R............   11 tests OK 
test_MSstatsLOBD.R............   12 tests OK 
test_MSstatsLOBD.R............   13 tests OK 
test_MSstatsLOBD.R............   14 tests OK 
test_MSstatsLOBD.R............   15 tests OK 
test_MSstatsLOBD.R............   16 tests OK 
test_MSstatsLOBD.R............   17 tests OK 
test_MSstatsLOBD.R............   18 tests OK 
test_MSstatsLOBD.R............   19 tests OK 
test_MSstatsLOBD.R............   20 tests OK 
test_MSstatsLOBD.R............   21 tests OK 
test_MSstatsLOBD.R............   22 tests OK 
test_MSstatsLOBD.R............   22 tests OK 
test_MSstatsLOBD.R............   23 tests OK 
test_MSstatsLOBD.R............   24 tests OK 
test_MSstatsLOBD.R............   25 tests OK 
test_MSstatsLOBD.R............   26 tests OK 
test_MSstatsLOBD.R............   27 tests OK 
test_MSstatsLOBD.R............   27 tests OK 
test_MSstatsLOBD.R............   28 tests OK 
test_MSstatsLOBD.R............   29 tests OK 
test_MSstatsLOBD.R............   30 tests OK 
test_MSstatsLOBD.R............   31 tests OK 0.8s
All ok, 31 results (0.8s)
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 
  1.488   0.089   1.567