PFILE=/srv/www/htdocs/Data2San/sync_LOGS/pfiles.txt ; 
cat ${PFILE} \
  | cut -f4 -d";" \
  | cut -d"/" -f3 \
  | sort \
  | uniq \
  |while read i ; 
  do 
        grep -E "/${i}/.*autoQC01.*raw$" ${PFILE} \
          | tail -n 2; 
  done \
  | cut -d";" -f4 \
  | while read raw ; 
    do 
        [[ -f /srv/www/htdocs/${raw} ]] && echo ${raw} ; 
  done

    if (Sys.which("msbuild") == "" && Sys.which("xbuild") == "")
    {
        warning ("could not find msbuild or xbuild in path; will not be able to use rDotNet unless corrected and rebuilt")
        return()
    }

The Journal of Proteome Research is preparing to publish its Second Biennial Special Issue on Software Tools and Resources in February 2021.

Software tools and data resources are essential to research in all omics domains, including proteomics and metabolomics. The goal of this recurring special issue is to highlight the latest novel and significantly updated software tools, web applications, and databases scientists can use for data analysis and visualization in proteomics and related research.

For readers, this provides an easily identifiable source of tools specifically reviewed for their applicability and ease of adoption. For authors, this provides visibility for and wider adoption of their tools in the proteomics community through dissemination and documentation.

The same team that led the first Special Issue on Software Tools and Resources will also lead this one:

Journal of Proteome Research Associate Editor Susan Weintraub, The University of Texas Health Science Center at San Antonio
Michael Hoopmann, Institute for Systems Biology
Magnus Palmblad, Leids Universitair Medisch Centrum
They invite you to submit a manuscript by October 31, 2020.

What to Submit—Deadline: October 31, 2020
For inclusion in this special issue, authors must present either a complete description of a relevant novel tool, library, web application, or database (article) or a substantial and meaningful update of a previously published tool or resource (technical note). The full working tool or database must be available free-of-charge to editors and reviewers for evaluation at the time of manuscript submission.

Tools with a graphical or web browser interface are preferred, but the editors will also consider well-documented web service APIs or libraries of functional building blocks for custom data analysis pipelines.

Manuscript Requirements
Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system by October 31, 2020, and conform to the Journal of Proteome Research Author Guidelines.

Authors, please:

 Indicate in your cover letter that the manuscript is for the Special Issue on Software Tools and Resources.
Remember, the full working tool or database must be available free-of-charge to editors and reviewers for evaluation at the time of manuscript submission.
Be concise and focus the manuscript on the unique or novel functionality of the tool. It should be clear to any reader what problem the system addresses and how it is used.
 For tools and libraries, use the table form to describe the input, operations, and output of each tool or function. A screenshot of the interface may be included if this has novel or unusual features.
LEARN MORE: Read the first Special Issue on Software Tools and Resources, including the Editorial by Susan Weintraub, Michael Hoopmann, and Magnus Palmblad.

checking for executable files ...
   Found the following executable files:
     exec/ThermoFisher.CommonCore.BackgroundSubtraction.dll
     exec/ThermoFisher.CommonCore.Data.dll
     exec/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
     exec/ThermoFisher.CommonCore.RawFileReader.dll
     exec/rawR.exe
   Source packages should not contain undeclared executable files.
   See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

1.1.7 Non-R scripts in packages

Code which needs to be compiled (C, C++, Fortran …) is included in the src subdirectory and discussed elsewhere in this document.

Subdirectory exec could be used for scripts for interpreters such as the shell, BUGS, JavaScript, Matlab, Perl, php (amap), Python or Tcl (Simile), or even R. However, it seems more common to use the inst directory, for example WriteXLS/inst/Perl, NMF/inst/m-files, RnavGraph/inst/tcl, RProtoBuf/inst/python and emdbook/inst/BUGS and gridSVG/inst/js.

Sample Name	autoQC01	
Comment		
Seq Row	10	
Sample Type	Unknown	
Path	D:\Data2San\p2469\Proteomics\QEXACTIVEHF_2\bpfister_20200714	
Cal Level		
Cal File		
Inj Volume	2	
Sample Weight	0	
Sample Volume	0	
Sample Id	NA	
Istd Amount	0	
CD Factor	0	
Bar Code		
Bar Code Status	0	
Inst Method	C:\Xcalibur\methods\__autoQC\trap\autoQC01.meth	
Proc Method		
User Text1	2469	
User Text2		
User Text3	FGCZ	
User Text4		
User Text5		
Tray Index	80	
Tray Name	ANSI-48Vial2mLHolder/ANSI-48Vial2mLHolder	
Tray Shape	Rectangular	
Vial Index	48	
Vials Per Tray	48	
Vials Per TrayX	8	
Vials Per TrayY	6	
Instrument Name	Q Exactive HF Orbitrap	
Instrument Model	Q Exactive HF Orbitrap	
Instrument Number	Exactive Series slot #2496	
Instrument SoftWare	2.9-290204/2.9.3.2948	
Instrument Hardware	rev. 1	
Flags		
Mass Tolerance	0.5 amu	
Created by	Administrator	

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved

> citation(package = "rawrr")

To cite package ‘rawrr’ in publications use:

  Christian Panse and Tobias Kockmann (NA). rawrr: Access to Thermo Fisher Scientific raw
  files from R. R package version 0.1.7. https://github.com/fgcz/rawR/

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {rawrr: Access to Thermo Fisher Scientific raw files from R},
    author = {Christian Panse and Tobias Kockmann},
    note = {R package version 0.1.7},
    url = {https://github.com/fgcz/rawR/},
  }

Warning messages:
1: In citation(package = "rawrr") :
  no date field in DESCRIPTION file of package ‘rawrr’
2: In citation(package = "rawrr") :
  could not determine year for ‘rawrr’ from package DESCRIPTION file

R CMD check rawR_0.1.1.tar.gz

* package encoding: UTF-8
* checking CRAN incoming feasibility ... ERROR
Maintainer: 'Christian Panse <[email protected]>'
New submission
Conflicting package names (submitted: rawR, existing: rawr [https://CRAN.R-project.org])
Conflicting package names (submitted: rawR, existing: rawr [CRAN archive])
The Title field should be in title case. Current version is:
'Access to Thermo Fisher Scientific raw files from R'
In title case that is:

R> BiocCheck("rawR_0.1.1.tar.gz")
This is BiocCheck version 1.26.0. BiocCheck is a work in
progress. Output and severity of issues may change. Installing
package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
    Package version 0.1.1; pre-release
* Checking R Version dependency...
* Checking package size...
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'rawRcolor.tif'
* Checking biocViews...
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball
  name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import grDevices, graphics, utils in
      DESCRIPTION as well as NAMESPACE.
* Checking vignette directory...
    This is an unknown type of package
    * ERROR: No 'vignettes' directory.
* Checking library calls...
* Checking for library/require of rawR...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        rawR.R (line 1011, column 29)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        rawR.R (line 600, column 36)
        rawR.R (line 745, column 70)
Warning in readLines(infile) :
  incomplete final line found on '/tmp/RtmpLJg2l6/filedebd713f5408/rawR/tests/testthat/test-header.R'
    * WARNING: Avoid class() == or class() != ; use is() or
      !is()
      Found in files:
        R/rawR.R (line 68)
* Checking parsed R code in R directory, examples,
  vignettes...
* Checking function lengths..........
    * NOTE: Recommended function length <= 50 lines.
      There are 5 functions > 50 lines.
      The longest 5 functions are:
        plot.rawRspectrum() (R/rawR.R, line 711): 108 lines
        readChromatogram() (R/rawR.R, line 429): 105 lines
        print.rawRspectrum() (R/rawR.R, line 839): 84 lines
        readFileHeader() (R/rawR.R, line 106): 61 lines
        validate_rawRspectrum() (R/rawR.R, line 635): 52 lines
* Checking man page documentation...
    * WARNING: Add non-empty \value sections to the following
      man pages: man/plot.rawRchromatogram.Rd,
      man/plot.rawRchromatogramSet.Rd,
      man/plot.rawRspectrum.Rd, man/print.rawRspectrum.Rd,
      man/summary.rawRspectrum.Rd
      man/plot.rawRspectrum.Rd, man/print.rawRspectrum.Rd,
      man/summary.rawRspectrum.Rd
    * ERROR: At least 80% of man pages documenting exported
      objects must have runnable examples. The following pages
      do not:
      new_rawRspectrum.Rd, plot.rawRchromatogramSet.Rd,
  validate_rawRspectrum.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page
      examples.
      14% of man pages use one of these cases.
      Found in the following files:
        readChromatogram.Rd
        readSpectrum.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        readChromatogram.Rd
        readSpectrum.Rd
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news
      will be included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R
  source, and vignette source...
    * NOTE: Consider shorter lines; 32 lines (2%) are > 80
      characters long.
    First 6 lines:
      R/rawR.R:7 .writeRData <- function(rawfile, outputfile=paste0...
      R/rawR.R:14         list(scanType=rv$scanType, mZ=rv$mZ, inte...
      R/rawR.R:28                 warning("Can not find Mono JIT co...
      R/rawR.R:41             rvs <- system2(Sys.which('mono'), arg...
      R/rawR.R:64 #' pathToRawFile <- file.path(path.package(packag...
      R/rawR.R:154                 e$info$`Instrument method` <- ba...
    * NOTE: Consider 4 spaces instead of tabs; 5 lines (0%)
      contain tabs.
    First 5 lines:
      R/zzz.R:5 	if(interactive()){
      R/zzz.R:6 		version <- packageVersion('rawR')
      R/zzz.R:7 		packageStartupMessage("Package 'rawR' version ", ...
      R/zzz.R:8 	  invisible()
      R/zzz.R:9 	}
    * NOTE: Consider multiples of 4 spaces for line indents,
      233 lines(14%) are not.
    First 6 lines:
      R/rawR.R:107    mono = if(Sys.info()['sysname'] %in% c("Darwi...
      R/rawR.R:108    exe = system.file('exec/rawR.exe',package = '...
      R/rawR.R:109    mono_path = "",
      R/rawR.R:110    argv = "infoR",
      R/rawR.R:111    system2_call = TRUE,
      R/rawR.R:112                            method = "thermo"){
    See
      http://bioconductor.org/developers/how-to/coding-style/
    See styler package:
      https://cran.r-project.org/package=styler as described
      in the BiocCheck vignette.
* Checking if package already exists in CRAN...
    * ERROR: Package must be removed from CRAN.
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed
      to the bioc-devel mailing list (requires admin
      credentials). Subscribe here:
      https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
Summary:
ERROR count: 4
WARNING count: 4
NOTE count: 10
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.12/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "No biocViews terms found."                                                                                      
[2] "No 'vignettes' directory."                                                                                      
[3] "At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not:"
[4] "Package must be removed from CRAN."                                                                             
$warning
[1] "The following files are over 5MB in size: 'rawRcolor.tif'"                                                                                                                                                 
[2] "Import grDevices, graphics, utils in DESCRIPTION as well as NAMESPACE."                                                                                                                                    
[3] " Avoid class() == or class() != ; use is() or !is()"                                                                                                                                                       
[4] "Add non-empty \\value sections to the following man pages: man/plot.rawRchromatogram.Rd, man/plot.rawRchromatogramSet.Rd, man/plot.rawRspectrum.Rd, man/print.rawRspectrum.Rd, man/summary.rawRspectrum.Rd"
$note
 [1] " Avoid sapply(); use vapply()"                                                                                                                                                     
 [2] " Avoid 1:...; use seq_len() or seq_along()"                                                                                                                                        
 [3] "Recommended function length <= 50 lines."                                                                                                                                          
 [4] "Usage of dontrun{} / donttest{} found in man page examples."                                                                                                                       
 [5] "Use donttest{} instead of dontrun{}."                                                                                                                                              
 [6] "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."                                                                         
 [7] "Consider shorter lines; 32 lines (2%) are > 80 characters long."                                                                                                                   
 [8] "Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs."                                                                                                                     
 [9] "Consider multiples of 4 spaces for line indents, 233 lines(14%) are not."                                                                                                          
R> 

> plot(S[[1]], centroid=TRUE)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  Length of 'x' and 'y' do not match

library(rawrr)
library(tidyverse)

#reading Index and selecting scans with ms_order = "Ms"
ms_order <- "Ms"
IDX <- as_tibble(readIndex(path))
scans <- IDX %>% filter(MSOrder == ms_order) %>% pull(scan)

SPC <- readSpectrum(path, scan = scans)

print(names(header(msfile)))

 [1] "seqNum"                     "acquisitionNum"            
 [3] "msLevel"                    "polarity"                  
 [5] "peaksCount"                 "totIonCurrent"             
 [7] "retentionTime"              "basePeakMZ"                
 [9] "basePeakIntensity"          "collisionEnergy"           
[11] "ionisationEnergy"           "lowMZ"                     
[13] "highMZ"                     "precursorScanNum"          
[15] "precursorMZ"                "precursorCharge"           
[17] "precursorIntensity"         "mergedScan"                
[19] "mergedResultScanNum"        "mergedResultStartScanNum"  
[21] "mergedResultEndScanNum"     "injectionTime"             
[23] "filterString"               "spectrumId"                
[25] "centroided"                 "ionMobilityDriftTime"      
[27] "isolationWindowTargetMZ"    "isolationWindowLowerOffset"
[29] "isolationWindowUpperOffset" "scanWindowLowerLimit"      
[31] "scanWindowUpperLimit"      

L 
   | - (xi, yi)
   | - (xi, yi)
   | - (xi, yi)

XICs <- lapply(Raws, function(raw) { readChromatogram(raw, masses, tols) })
Error in .rawrrSystem2Source(rawfile, input = mass, rawrrArgs = sprintf("xic %f %s",  : 
  **Rcode file to parse does not exist. 'C:\Users\MyUserName\AppData\Local/R/cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
	C:\Users\MyUserName\AppData\Local\Temp\2\RtmpeQSRv0\file62986016698d.stderr
	C:\Users\MyUserName\AppData\Local\Temp\2\RtmpeQSRv0\file629849cf6634.stdout
and the System Requirements
Called from: .rawrrSystem2Source(rawfile, input = mass, rawrrArgs = sprintf("xic %f %s", 
    tol, shQuote(filter)))**

RawRspectrum:

> Total Ion Current:	 4870947
> Scan Low Mass:	 50
> Scan High Mass:	 250
> Scan Start Time (Min):	 0
> Scan Number:	 1
> Base Peak Intensity:	 -1
> Base Peak Mass:	 -1
> Scan Mode:	 FTMS + p NSI Full ms [50.00-250.00]
> ======= Instrument data =====   : 	
> 
> Multiple Injection: 	
> 
> Multi Inject Info: 	
> 
> AGC:	On
> Micro Scan Count:	1
> Scan Segment:	0
> Scan Event:	0
> Master Index:	0
> Charge State:	1
> Monoisotopic M/Z:	78.0468
> Ion Injection Time (ms):	100.000
> Max. Ion Time (ms): 	
> 
> FT Resolution:	30000
> MS2 Isolation Width:	0.0
> MS2 Isolation Offset: 	
> 
> AGC Target: 	
> 
> HCD Energy: 	
> 
> Analyzer Temperature: 	
> 
> === Mass Calibration: 	
> 
> Conversion Parameter B:	47557789.235
> Conversion Parameter C:	-2547049.695
> Temperature Comp. (ppm): 	
> 
> RF Comp. (ppm): 	
> 
> Space Charge Comp. (ppm): 	
> 
> Resolution Comp. (ppm): 	
> 
> Number of Lock Masses: 	
> 
> Lock Mass #1 (m/z): 	
> 
> Lock Mass #2 (m/z): 	
> 
> Lock Mass #3 (m/z): 	
> 
> LM Search Window (ppm): 	
> 
> LM Search Window (mmu): 	
> 
> Number of LM Found: 	
> 
> Last Locking (sec): 	
> 
> LM m/z-Correction (ppm): 	
> 
> === Ion Optics Settings: 	
> 
> S-Lens RF Level: 	
> 
> S-Lens Voltage (V): 	
> 
> Skimmer Voltage (V): 	
> 
> Inject Flatapole Offset (V): 	
> 
> Bent Flatapole DC (V): 	
> 
> MP2 and MP3 RF (V): 	
> 
> Gate Lens Voltage (V): 	
> 
> C-Trap RF (V): 	
> 
> ====  Diagnostic Data: 	
> 
> Dynamic RT Shift (min): 	
> 
> Intens Comp Factor: 	
> 
> Res. Dep. Intens: 	
> 
> CTCD NumF: 	
> 
> CTCD Comp: 	
> 
> CTCD ScScr: 	
> 
> RawOvFtT: 	
> 
> LC FWHM parameter: 	
> 
> Rod: 	
> 
> PS Inj. Time (ms): 	
> 
> AGC PS Mode: 	
> 
> AGC PS Diag: 	
> 
> HCD Energy eV: 	
> 
> AGC Fill: 	
> 
> Injection t0: 	
> 
> t0 FLP: 	
> 
> Access Id: 	
> 
> Analog Input 1 (V): 	
> 
> Analog Input 2 (V): 	

docker run -a stdin -a stdout -i -t rocker/verse:4.0.5 R

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.99.13_19.tar.gz', repo=NULL)


rawfile <- rawrr::sampleFilePath()

h <- rawrr::readFileHeader(rawfile)
i <- rawrr::readIndex(rawfile)
x <- rawrr::readChromatogram(rawfile=rawfile, type="tic")
s <- rawrr::readSpectrum(rawfile, 1:9)

docker run -a stdin -a stdout -i -t c95c10872a5d

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.99.13_19.tar.gz', repo=NULL)

rawfile <- rawrr::sampleFilePath()

h <- rawrr::readFileHeader(rawfile)
i <- rawrr::readIndex(rawfile)
x <- rawrr::readChromatogram(rawfile=rawfile, type="tic")
s <- rawrr::readSpectrum(rawfile, 1:9)

FROM rocker/verse:4.0.5
 
RUN apt-get update \
&& sudo apt-get install mono-runtime -y

CMD ["R"]

docker run -a stdin -a stdout -i -t f53000645fca

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.99.13_19.tar.gz', repo=NULL)

rawfile <- rawrr::sampleFilePath()


h <- rawrr::readFileHeader(rawfile)
i <- rawrr::readIndex(rawfile)
x <- rawrr::readChromatogram(rawfile=rawfile, type="tic")
s <- rawrr::readSpectrum(rawfile, 1:9)

FROM rocker/verse:4.0.5
 
RUN apt-get update \
&& sudo apt-get install mono-mcs mono-xbuild -y

CMD ["R"]

docker run -a stdin -a stdout -i -t -v /usr/local/lib/RawFileReader/:/usr/local/lib/RawFileReader/ d6cec6026a70

docker run -i -v /usr/local/lib/RawFileReader/:/usr/local/lib/RawFileReader/ d6cec6026a70 R --no-save << EOF

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.99.13_19.tar.gz', repo=NULL)
Sys.getenv("MONO_PATH")


rawfile <- rawrr::sampleFilePath()

h <- rawrr::readFileHeader(rawfile)
i <- rawrr::readIndex(rawfile)
x <- rawrr::readChromatogram(rawfile=rawfile, type="tic")
s <- rawrr::readSpectrum(rawfile, 1:9)

EOF

FROM rocker/verse:4.0.5
 
RUN apt-get update \
&& sudo apt-get install mono-mcs mono-xbuild -y

CMD ["R"]

int GetInstrumentCountOfType (Device type)

Device GetInstrumentType(int index);

int InstrumentCount { get; }

[[22]]
$mass
[1] 554.2606

$times
[1] 0.1216408 0.1516450 0.4810452 0.5409557 0.7801059

$intensities
[1] 3005.061 4328.104 3658.515 3862.011 4992.357

$filename
[1] "sample.raw"

attr(,"class")
[1] "list" "XIC" 

attr(,"class")
[1] "list" "XICs"
> X[[20]]
$mass
[1] 653.3617

$times
 [1] 0.001619751 0.031642766 0.061663615 0.091651065 0.121640750 0.151644970
 [7] 0.181667770 0.211526280 0.241284530 0.271307600 0.301222200 0.331145000
[13] 0.361147270 0.391168050 0.421057700 0.450970250 0.481045180 0.510989030
[19] 0.540955750 0.570893130 0.600724580 0.630620300 0.660428770 0.690318400
[25] 0.720320350 0.750197620 0.780105920

$intensities
 [1] 374171.6 405717.2 350914.7 373948.4 328768.2 425965.4 360327.9 453483.1
 [9] 445894.1 430538.9 422901.3 545305.5 433117.8 357588.1 435593.4 351018.2
[17] 407768.5 406468.8 446027.8 385148.5 579871.8 461409.0 390769.3 458988.6
[25] 378339.6 480078.4 467780.0

$filename
[1] "sample.raw"

attr(,"class")

#' Plot \code{rawrrChromatogramSet} objects
#'
#' @param x A \code{rawrrChromatogramSet} object to be plotted.
#' @param ... Passes additional arguments.
#' @param diagnostic Show diagnostic legend?
#' @author Tobias Kockmann, 2020.
#' @export
#' @importFrom grDevices hcl.colors
#' @importFrom graphics lines text