Back to Build/check report for BioC 3.17
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2023-01-02 09:00:40 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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

CHECK results for MSstatsLOBD on palomino5


To the developers/maintainers of the MSstatsLOBD package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1271/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLOBD 1.7.0  (landing page)
Devon Kohler
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/MSstatsLOBD
git_branch: master
git_last_commit: 58167c5
git_last_commit_date: 2022-11-01 11:25:06 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: MSstatsLOBD
Version: 1.7.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLOBD.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MSstatsLOBD_1.7.0.tar.gz
StartedAt: 2022-12-29 01:41:13 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:41:51 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 38.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsLOBD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLOBD.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MSstatsLOBD_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MSstatsLOBD.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsLOBD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsLOBD' version '1.7.0'
* 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 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MSstatsLOBD.Rcheck/00check.log'
for details.

Installation output

MSstatsLOBD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MSstatsLOBD
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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)

Tests output

MSstatsLOBD.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 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 1.1s
All ok, 31 results (1.1s)
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 
   1.81    0.29    2.09

Example timings

MSstatsLOBD.Rcheck/MSstatsLOBD-Ex.timings

nameusersystemelapsed
linear_quantlim0.090.000.09
nonlinear_quantlim0.110.020.13
plot_quantlim1.030.061.09
raw_data0.020.000.02
spikeindata0.010.000.01