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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstatsQC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstatsQC_2.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsQC.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 ‘MSstatsQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsQC’ version ‘2.23.0’
* 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 ‘MSstatsQC’ 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 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 ... NOTE
MissingDataMap: no visible binding for global variable ‘AcquiredTime’
MissingDataMap: no visible binding for global variable ‘Precursor’
Undefined global functions or variables:
  AcquiredTime Precursor
* 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 ... ERROR
Running examples in ‘MSstatsQC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ChangePointEstimator
> ### Title: A function to identify the time of a change in the mean or
> ###   variability of a metric
> ### Aliases: ChangePointEstimator
> ### Keywords: change chart control point,
> 
> ### ** Examples
> 
> # First process the data to make sure it's ready to use
> sampleData <- DataProcess(S9Site54)
[1] "Your data is ready to go!"
> head(sampleData)
   AcquiredTime Precursor   Annotations MinStartTime MaxEndTime
1 9/19/11 13:14 VLVLDTDYK Not Available        24.30      25.08
2 9/19/11 14:45 VLVLDTDYK Not Available        24.36      25.17
3 9/19/11 16:15 VLVLDTDYK Not Available        24.19      24.96
4 9/19/11 17:46 VLVLDTDYK Not Available        24.22      25.02
5 9/19/11 19:16 VLVLDTDYK Not Available        24.27      25.05
6 9/19/11 20:47 VLVLDTDYK Not Available        24.42      25.22
  BestRetentionTime TotalArea MaxFWHM missing
1             24.62 116034248    0.29       0
2             24.70 127339240    0.31       0
3             24.53 110745576    0.31       0
4             24.59 130619640    0.31       0
5             24.62 113469472    0.30       0
6             24.76 120836432    0.30       0
> # Find the name of the peptides
> levels(sampleData$Precursor)
 [1] "CAVVDVPFGGAK"   "DDGSWEVIEGYR"   "DGGIDPLVR"      "FFVAPFPEVFGK"  
 [5] "GFCGLSQPK"      "HLVDEPQNLIK"    "LVNELTEFAK"     "SLHTLFGDELCK"  
 [9] "TAAYVNAIEK"     "VGPLLACLLGR"    "VLDALDSIK"      "VLVLDTDYK"     
[13] "YNGVFQECCQAEDK" "YNLGLDLR"       "YSTDVSVDEVK"   
> # Calculate change point statistics
> ChangePointEstimator(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime")
> ChangePointEstimator(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime",
+                      ytitle = "Change Point Plot - variability", type = "variability")
> ChangePointEstimator(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime",
+                      selectMean = 27.78, selectSD = 8.19)
> ChangePointEstimator(data = sampleData, peptide = "DDGSWEVIEGYR", metric = "TotalArea")
> ChangePointEstimator(data = sampleData, peptide = "DDGSWEVIEGYR", metric = "TotalArea",
+                      selectMean = 35097129, selectSD = 34132861)
> ChangePointEstimator(data = sampleData, peptide = "TAAYVNAIEK", metric = "MaxFWHM")
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in base::file(file, open = "w+b") :
  cannot open file '/tmp/Rtmpm43rCI/viewhtml16ce22578477c0/index.html': No space left on device
Error in base::file(file, open = "w+b") : cannot open the connection
Calls: <Anonymous> ... html_print -> save_html -> save_html.default -> <Anonymous>
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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MSstatsQC
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MSstatsQC’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (MSstatsQC)

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.

> library(testthat)
> library(MSstatsQC)
> 
> test_check("MSstatsQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 10.398   0.520  10.907