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Issue with readChromatogram when type = "xic" #47

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Arthfael opened this issue Feb 1, 2022 · 14 comments
Closed

Issue with readChromatogram when type = "xic" #47

Arthfael opened this issue Feb 1, 2022 · 14 comments

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@Arthfael
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Arthfael commented Feb 1, 2022

I have been using this package for ~1 year now, specifically the readChromatogram function for extracting "tic" and "base peak". It works nicely and has been very useful. However, I have just for the first time tried to extract an "xic" for some masses of interest, and here is what I get:

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)))**

This is on a Windows 2019 Server machine, using R version 4.1.0 (2021-05-18) in RStudio 1.4.1717.
File "C:/Users/MyUserName/AppData/Local/R/cache/R/rawrr/rawrrassembly/rawrr.exe" does exist, but maybe this is an issue with slashes in Windows, since the error uses inconsistently backwards (Windows) and forward (Linux) slashes? In which case, including normalizePath(..., winslash = "/") would probably be enough to fix it?
@tobiasko
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Hi @Arthfael

That is indeed a bit strange! Could you please upload your sessionInfo? Do you get the same error when reading from a single file (outside of the lapply function)? Are other reading functions of the package also affected (readIndex)?

Best,
Tobi

@Arthfael
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Arthfael commented Feb 16, 2022 via email

@Arthfael
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Arthfael commented Feb 16, 2022 via email

@tobiasko
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Hi @Arthfael

since release 3.13 rawrr is a Bioconductor package, see

https://bioconductor.org/packages/release/bioc/html/rawrr.html

I would recommend to use the latest BioC release 3.14 to install rawrr with the help of the BiocManager:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rawrr")

I am honestly not sure what you get when installing from GitHub directly using devtools::. Version 0.2.1 is stone age. Please don't use it.

@Arthfael
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Arthfael commented Feb 16, 2022 via email

@Arthfael
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Arthfael commented Feb 16, 2022 via email

@tobiasko
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Did you follow this

https://bioconductor.org/packages/release/bioc/install/rawrr/INSTALL

or specifically did you install the RawFileReader DLLs and rawrr exe on your system:

> installRawFileReaderDLLs()
Do you accept the Thermo License agreement 'X:/Rlibs/rawrr/rawrrassembly/RawFileReaderLicense.txt'? [Y/n]: Y
trying URL 'https://github.com/thermofisherlsms/ThermoRawFileParser/raw/master/packages/ThermoFisher.CommonCore.RawFileReader.4.0.26/lib//ThermoFisher.CommonCore.Data.dll'
Content type 'application/octet-stream' length 360448 bytes (352 KB)
downloaded 352 KB

trying URL 'https://github.com/thermofisherlsms/ThermoRawFileParser/raw/master/packages/ThermoFisher.CommonCore.RawFileReader.4.0.26/lib//ThermoFisher.CommonCore.MassPrecisionEstimator.dll'
Content type 'application/octet-stream' length 11264 bytes (11 KB)
downloaded 11 KB

trying URL 'https://github.com/thermofisherlsms/ThermoRawFileParser/raw/master/packages/ThermoFisher.CommonCore.RawFileReader.4.0.26/lib//ThermoFisher.CommonCore.RawFileReader.dll'
Content type 'application/octet-stream' length 620544 bytes (606 KB)
downloaded 606 KB

                  ThermoFisher.CommonCore.Data.dll ThermoFisher.CommonCore.MassPrecisionEstimator.dll 
                                                 0                                                  0 
         ThermoFisher.CommonCore.RawFileReader.dll 
                                                 0 
> installRawrrExe()
trying URL 'http://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr.1.1.12.exe'
Content type 'application/x-msdos-program' length 26624 bytes (26 KB)
downloaded 26 KB

MD5 6d5f6d19512eaba73e92d2bfb474e6f2 C:\Users\tobiasko.FGCZ-NET\AppData\Local/R/cache/R/rawrr/rawrrassembly/rawrr.exe
[1] 0
>

@tobiasko
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The problem is:

Bioc was not willing to host the binary rawrr.x.exe as part of the package. So it is downloaded on demand after the package installation through BiocManager. Same-same for the RawFileReader dlls. They are fetched from a Thermo GitHub Repo. I know this is kind of annoying, but it was the only option.

@Arthfael
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Arthfael commented Feb 16, 2022 via email

@Arthfael
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Arthfael commented Feb 16, 2022 via email

@tobiasko
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That is all pretty wired. I meanwhile installed rawrr 1.2.0 using BiocManager on a very similar system (Windows Server 2021):

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rawrr_1.2.0         BiocManager_1.30.16

loaded via a namespace (and not attached):
 [1] magrittr_2.0.2    tidyselect_1.1.1  R6_2.5.1          rlang_1.0.1       fastmap_1.1.0     fansi_1.0.2      
 [7] dplyr_1.0.8       tools_4.1.0       DT_0.20           utf8_1.2.2        cli_3.2.0         DBI_1.1.2        
[13] htmltools_0.5.2   ellipsis_0.3.2    yaml_2.2.2        assertthat_0.2.1  digest_0.6.29     tibble_3.1.6     
[19] lifecycle_1.0.1   crayon_1.5.0      purrr_0.3.4       htmlwidgets_1.5.4 vctrs_0.3.8       glue_1.6.1       
[25] compiler_4.1.0    pillar_1.7.0      generics_0.1.2    pkgconfig_2.0.3

What do you get when reading from the sample data that comes with the package?

> rawfile <- sampleFilePath()
> Idx <- readIndex(rawfile)
> str(Idx)
'data.frame':	573 obs. of  8 variables:
 $ scan          : int  1 2 3 4 5 6 7 8 9 10 ...
 $ scanType      : chr  "FTMS + c NSI Full ms [350.0000-1800.0000]" "FTMS + c NSI Full ms2 487.2567@hcd28.00 [140.0000-1015.0000]" "FTMS + c NSI Full ms2 644.8226@hcd28.00 [140.0000-1335.0000]" "FTMS + c NSI Full ms2 683.8279@hcd28.00 [140.0000-1415.0000]" ...
 $ rtinseconds   : num  0.097 0.35 0.419 0.489 0.558 0.627 0.696 0.766 0.835 0.904 ...
 $ precursorMass : num  1075 487 645 684 547 ...
 $ MSOrder       : chr  "Ms" "Ms2" "Ms2" "Ms2" ...
 $ charge        : int  0 2 2 2 2 2 2 2 2 2 ...
 $ masterScan    : int  NA NA NA NA NA NA NA NA NA NA ...
 $ dependencyType: logi  NA NA NA NA NA NA ...

My path to the sample data is:

> rawfile
[1] "X:/Rlibs/rawrr/extdata/sample.raw"

The rawrr assembly path (the path were the dll are placed) is

> rawrrAssemblyPath()
[1] "C:\\Users\\tobiasko.FGCZ-NET\\AppData\\Local/R/cache/R/rawrr/rawrrassembly"

as you can see, also here I am getting this strange mixture of \\ and / in a single path. But that is obviously not a problem, since readIndex works.

The exe and the dlls should be at the assembly path location together with the EULA text:

> list.files(rawrrAssemblyPath())
[1] "eula.txt"                                           "rawrr.exe"                                         
[3] "ThermoFisher.CommonCore.Data.dll"                   "ThermoFisher.CommonCore.MassPrecisionEstimator.dll"
[5] "ThermoFisher.CommonCore.RawFileReader.dll"         
>

Could you just execute the same commands and upload the returns?

@Arthfael
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Arthfael commented Feb 17, 2022 via email •
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@tobiasko
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Puh! Yip, we need to check more carefully if the parameters are valid (length = 1) and raise an error right away. That could be avoided very easily by a stopifnot() statement at the start of readChromatogram.

@tobiasko
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@cpanse

We need to check this here:

readChromatogram <- function(rawfile,
                             mass = NULL,
                             tol = 10,
                             filter = "ms",
                             type = 'xic'){
    
    .isAssemblyWorking()
    .checkRawFile(rawfile)
    
    stopifnot(type %in% c('xic', 'bpc', 'tic'))

@Heriette Heriette mentioned this issue Aug 30, 2024
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@Arthfael @tobiasko