##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rawrr.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rawrr_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/rawrr.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rawrr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rawrr' version '1.14.0'
* 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 'rawrr' 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 whether 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 'rawrr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readSpectrum
> ### Title: Reads spectral data from a raw file.
> ### Aliases: readSpectrum rawrr
> 
> ### ** Examples
> 
> 
> # Example 1
> S <- rawrr::sampleFilePath() |> rawrr::readSpectrum(scan = 1:9)
> 
> S[[1]]
Total Ion Current:	 78725448
Scan Low Mass:	 350
Scan High Mass:	 1800
Scan Start Time (min):	 0.001619751
Scan Number:	 1
Base Peak Intensity:	 5979308
Base Peak Mass:	 445.1181
Scan Mode:	 FTMS + c NSI Full ms [350.0000-1800.0000]
======= Instrument data =====   :	NULL
Multiple Injection:	ii
Multi Inject Info:	IT=28;28 
AGC:	On
Micro Scan Count:	1
Scan Segment:	1
Scan Event:	1
Master Index:	0
Charge State:	0
Monoisotopic M/Z:	0.0000
Ion Injection Time (ms):	55.000
Max. Ion Time (ms):	55.00
FT Resolution:	120000
MS2 Isolation Width:	1450.00
MS2 Isolation Offset:	0.00
AGC Target:	3000000
HCD Energy:	
Analyzer Temperature:	27.06
=== Mass Calibration:	NULL
Conversion Parameter B:	211820589.2896
Conversion Parameter C:	-41163067.8349
Temperature Comp. (ppm):	-2.35
RF Comp. (ppm):	-0.09
Space Charge Comp. (ppm):	-2.30
Resolution Comp. (ppm):	0.57
Number of Lock Masses:	0
Lock Mass #1 (m/z):	0.0000
Lock Mass #2 (m/z):	0.0000
Lock Mass #3 (m/z):	0.0000
LM Search Window (ppm):	0.0
LM Search Window (mmu):	0.0
Number of LM Found:	0
Last Locking (sec):	0.0
LM m/z-Correction (ppm):	0.00
=== Ion Optics Settings:	NULL
S-Lens RF Level:	40.00
S-Lens Voltage (V):	21.00
Skimmer Voltage (V):	15.00
Inject Flatapole Offset (V):	5.00
Bent Flatapole DC (V):	2.00
MP2 and MP3 RF (V):	900.00
Gate Lens Voltage (V):	2.25
C-Trap RF (V):	2400.0
====  Diagnostic Data:	NULL
Dynamic RT Shift (min):	0.00
Intens Comp Factor:	1.4281
Res. Dep. Intens:	0.981
CTCD NumF:	0
CTCD Comp:	1.009
CTCD ScScr:	0.844
RawOvFtT:	2378645.5
LC FWHM parameter:	15.0
Rod:	0
PS Inj. Time (ms):	0.640
AGC PS Mode:	1
AGC PS Diag:	3501800
HCD Energy eV:	0.000
AGC Fill:	0.76
Injection t0:	-0.071
t0 FLP:	355.07
Access Id:	0
Analog Input 1 (V):	0.000
Analog Input 2 (V):	0.000
> 
> names(S[[1]])
 [1] "scan"                          "basePeak"                     
 [3] "TIC"                           "massRange"                    
 [5] "scanType"                      "StartTime"                    
 [7] "rtinseconds"                   "pepmass"                      
 [9] "centroidStream"                "HasCentroidStream"            
[11] "centroid.mZ"                   "centroid.intensity"           
[13] "title"                         "monoisotopicMz"               
[15] "charge"                        "mZ"                           
[17] "intensity"                     "noises"                       
[19] "resolutions"                   "charges"                      
[21] "baselines"                     "Multiple Injection:"          
[23] "Multi Inject Info:"            "AGC:"                         
[25] "Micro Scan Count:"             "Scan Segment:"                
[27] "Scan Event:"                   "Master Index:"                
[29] "Charge State:"                 "Monoisotopic M/Z:"            
[31] "Ion Injection Time (ms):"      "Max. Ion Time (ms):"          
[33] "FT Resolution:"                "MS2 Isolation Width:"         
[35] "MS2 Isolation Offset:"         "AGC Target:"                  
[37] "HCD Energy:"                   "Analyzer Temperature:"        
[39] "=== Mass Calibration: ===:"    "Conversion Parameter B:"      
[41] "Conversion Parameter C:"       "Temperature Comp. (ppm):"     
[43] "RF Comp. (ppm):"               "Space Charge Comp. (ppm):"    
[45] "Resolution Comp. (ppm):"       "Number of Lock Masses:"       
[47] "Lock Mass #1 (m/z):"           "Lock Mass #2 (m/z):"          
[49] "Lock Mass #3 (m/z):"           "LM Search Window (ppm):"      
[51] "LM Search Window (mmu):"       "Number of LM Found:"          
[53] "Last Locking (sec):"           "LM m/z-Correction (ppm):"     
[55] "=== Ion Optics Settings: ===:" "S-Lens RF Level:"             
[57] "S-Lens Voltage (V):"           "Skimmer Voltage (V):"         
[59] "Inject Flatapole Offset (V):"  "Bent Flatapole DC (V):"       
[61] "MP2 and MP3 RF (V):"           "Gate Lens Voltage (V):"       
[63] "C-Trap RF (V):"                "====  Diagnostic Data:  ====:"
[65] "Dynamic RT Shift (min):"       "Intens Comp Factor:"          
[67] "Res. Dep. Intens:"             "CTCD NumF:"                   
[69] "CTCD Comp:"                    "CTCD ScScr:"                  
[71] "RawOvFtT:"                     "LC FWHM parameter:"           
[73] "Rod:"                          "PS Inj. Time (ms):"           
[75] "AGC PS Mode:"                  "AGC PS Diag:"                 
[77] "HCD Energy eV:"                "AGC Fill:"                    
[79] "Injection t0:"                 "t0 FLP:"                      
[81] "Access Id:"                    "Analog Input 1 (V):"          
[83] "Analog Input 2 (V):"          
> 
> plot(S[[1]])
> 
> 
> 
> # Example 2 - find best peptide spectrum match using the |> pipe operator
> # fetch via ExperimentHub
> 
> if (require(ExperimentHub) & require(protViz)){
+ eh <- ExperimentHub::ExperimentHub()
+ EH4547 <- normalizePath(eh[["EH4547"]])
+ 
+ (rawfile <- paste0(EH4547, ".raw"))
+ if (!file.exists(rawfile)){
+     file.link(EH4547, rawfile)
+ }
+ 
+ GAG <- "GAGSSEPVTGLDAK"
+ 
+ .bestPeptideSpectrumMatch <- function(rawfile,
+     sequence="GAGSSEPVTGLDAK"){
+     readIndex(rawfile) |>
+         subset(abs((1.008 + (protViz::parentIonMass(sequence) - 1.008) / 2) -
+             precursorMass) < 0.001, select = scan) |>
+         unlist() |>
+         readSpectrum(rawfile = rawfile) |>
+         lapply(function(x) {
+           y <- protViz::psm(sequence = GAG, spec=x, plot=FALSE);
+           y$scan <- x$scan; y
+         }) |>
+         lapply(FUN= function(x){
+           score <- sum(abs(x$mZ.Da.error) < 0.01);
+           cbind(scan=x$scan, score=score)
+         }) |>
+         (function(x) as.data.frame(Reduce(rbind, x)))() |>
+         subset(score > 0) |>
+         (function(x) x[order(x$score, decreasing = TRUE),
+             'scan'])() |>
+         head(1)
+ }
+ 
+ start_time <- Sys.time()
+ bestMatch <- .bestPeptideSpectrumMatch(rawfile, GAG) |>
+     rawrr::readSpectrum(rawfile=rawfile) |>
+     lapply(function(x) protViz::peakplot(peptideSequence = GAG, x))
+ 
+ end_time <- Sys.time()
+ end_time - start_time
+ 
+ # Example 3
+ # using proteomicsdb \doi{10.1101/2020.09.08.287557}
+ # through https://www.proteomicsdb.org/use/
+ 
+ .UniversalSpectrumExplorer <- function(x, sequence){
+     m <- protViz::psm( sequence, x)
+     cat(paste(x$mZ[m$idx], "\t", x$intensity[m$idx]), sep = "\n")
+ }
+ 
+ rawrr::readSpectrum(rawfile=rawfile, 11091) |>
+    lapply(function(x).UniversalSpectrumExplorer(x, sequence = GAG))
+  }  
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: protViz
see ?tartare and browseVignettes('tartare') for documentation
loading from cache

Unhandled Exception: System.IO.FileLoadException: Could not load file or assembly 'ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies. The process cannot access the file because it is being used by another process. (Exception from HRESULT: 0x80070020)
   at FGCZ_Raw.Program.Main(String[] args)
Warning in system2(exe, stdout = TRUE) :
  running command '"C:\Users\biocbuild\AppData\Local/R/cache/R/rawrr/rawrrassembly/rawrr.exe"' had status 17234
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'X' in selecting a method for function 'lapply': argument is of length zero
Calls: lapply ... <Anonymous> -> .isAssemblyWorking -> .handleSimpleError -> h
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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.20-bioc/meat/rawrr.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rawrr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'rawrr' ...
** using staged installation
** R
** 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 (rawrr)

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> #R
> 
> library(testthat)
> 
> suppressPackageStartupMessages(library(rawrr))
> 
> test_check("rawrr")
Total Ion Current:	 78725448
Scan Low Mass:	 350
Scan High Mass:	 1800
Scan Start Time (min):	 0.001619751
Scan Number:	 1
Base Peak Intensity:	 5979308
Base Peak Mass:	 445.1181
Scan Mode:	 FTMS + c NSI Full ms [350.0000-1800.0000]
======= Instrument data =====   :	NULL
Multiple Injection:	ii
Multi Inject Info:	IT=28;28 
AGC:	On
Micro Scan Count:	1
Scan Segment:	1
Scan Event:	1
Master Index:	0
Charge State:	0
Monoisotopic M/Z:	0.0000
Ion Injection Time (ms):	55.000
Max. Ion Time (ms):	55.00
FT Resolution:	120000
MS2 Isolation Width:	1450.00
MS2 Isolation Offset:	0.00
AGC Target:	3000000
HCD Energy:	
Analyzer Temperature:	27.06
=== Mass Calibration:	NULL
Conversion Parameter B:	211820589.2896
Conversion Parameter C:	-41163067.8349
Temperature Comp. (ppm):	-2.35
RF Comp. (ppm):	-0.09
Space Charge Comp. (ppm):	-2.30
Resolution Comp. (ppm):	0.57
Number of Lock Masses:	0
Lock Mass #1 (m/z):	0.0000
Lock Mass #2 (m/z):	0.0000
Lock Mass #3 (m/z):	0.0000
LM Search Window (ppm):	0.0
LM Search Window (mmu):	0.0
Number of LM Found:	0
Last Locking (sec):	0.0
LM m/z-Correction (ppm):	0.00
=== Ion Optics Settings:	NULL
S-Lens RF Level:	40.00
S-Lens Voltage (V):	21.00
Skimmer Voltage (V):	15.00
Inject Flatapole Offset (V):	5.00
Bent Flatapole DC (V):	2.00
MP2 and MP3 RF (V):	900.00
Gate Lens Voltage (V):	2.25
C-Trap RF (V):	2400.0
====  Diagnostic Data:	NULL
Dynamic RT Shift (min):	0.00
Intens Comp Factor:	1.4281
Res. Dep. Intens:	0.981
CTCD NumF:	0
CTCD Comp:	1.009
CTCD ScScr:	0.844
RawOvFtT:	2378645.5
LC FWHM parameter:	15.0
Rod:	0
PS Inj. Time (ms):	0.640
AGC PS Mode:	1
AGC PS Diag:	3501800
HCD Energy eV:	0.000
AGC Fill:	0.76
Injection t0:	-0.071
t0 FLP:	355.07
Access Id:	0
Analog Input 1 (V):	0.000
Analog Input 2 (V):	0.000
Total Ion Current:	 78725448
Scan Low Mass:	 350
Scan High Mass:	 1800
Scan Start Time (min):	 0.001619751
Scan Number:	 1
Base Peak Intensity:	 5979308
Base Peak Mass:	 445.1181
Scan Mode:	 FTMS + c NSI Full ms [350.0000-1800.0000]
XIC generated from sample.raw consisting of 27 data points.
   Filter : ms
   m/z : 445.1181
   Tolerance : 10 ppm
   RT : 0.001619751 - 0.7801059 min
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 179 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 179 ]
> 
> proc.time()
   user  system elapsed 
  11.04    3.71   30.29