Newbie: can't even get the first command to run properly

fgcz / rawrr

Access Orbitrap data in R lang using C# mono assembly - bioconductor package

https://bioconductor.org/packages/rawrr/

53 stars 8 forks source link

Newbie: can't even get the first command to run properly #76

Open buzuddha opened 3 days ago

buzuddha commented 3 days ago

Sorry to be completely inept with this...

I've installed Rawrr according to the instructions:

> BiocManager::install("rawrr")
$ sudo apt-get install mono-runtime libmono-system-data4.0-cil -y
> rawrr::installRawFileReaderDLLs()
> rawrr::installRawrrExe()

When I try to run the first command in the docs on a .raw file I run into problems. I don't really understand the Rcode file to parse does not exist message, but I'm new to rawrr.

> library(rawrr)
Package 'rawrr' version 1.10.2 using
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
> rawfile <- "~/Downloads/ftp_local/1284_01.raw"
> H <- rawrr::readFileHeader(rawfile = rawfile)
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") :
  Rcode file to parse does not exist. '/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
        /tmp/RtmpI8hKLq/file772e2ea5b01d.stderr
        /tmp/RtmpI8hKLq/file772e4799b292.stdout
and the System Requirements

The .dll files appear to be in place and so is the rawrr.exe.

> list.files("/home/user/.cache/R/rawrr/rawrrassembly/")
[1] "eula.txt"
[2] "rawrr.exe"
[3] "ThermoFisher.CommonCore.BackgroundSubtraction.dll"
[4] "ThermoFisher.CommonCore.Data.dll"
[5] "ThermoFisher.CommonCore.MassPrecisionEstimator.dll"
[6] "ThermoFisher.CommonCore.RawFileReader.dll"

The logs don't seem to tell me much:

> system("cat /tmp/RtmpI8hKLq/file772e2ea5b01d.stderr")
> system("cat /tmp/RtmpI8hKLq/file772e4799b292.stdout")
Unable to access the RAW file using the RawFileReader class!

Any help here would be greatly appreciated.

$ uname -r
5.15.153.1-microsoft-standard-WSL2
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 24.04.1 LTS
Release:        24.04
Codename:       noble
$ R --version
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"

Similar issues trying this on macOS. No I can't install this on the windows system. The .raw file is from PXD028532 which appears to have been acquired on the correct Orbitrap Fusion instrument.

tobiasko commented 2 days ago

Hi @buzuddha,

could you try to use the package sample data?

> sampleFilePath()
[1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rawrr/extdata/sample.raw"
> readFileHeader(rawfile = sampleFilePath())
$`RAW file`
[1] "sample.raw"

$`RAW file version`
[1] "66"

$`Creation date`
[1] "2/13/2018 11:09:03 AM"

$Operator
[1] "ExactiveUser"

$`Number of instruments`
[1] 1

$Description
[1] ""

$`Instrument model`
[1] "Q Exactive HF-X Orbitrap"

$`Instrument name`
[1] "Q Exactive HF-X Orbitrap"

$`Instrument method`
[1] "C:/Xcalibur/methods/__General_methods/STM/autoQC01_GT20min_RT35min.meth"

$`Serial number`
[1] "Exactive Series slot #6114"

$`Software version`
[1] "2.9-290033/2.9.0.2926"

$`Firmware version`
[1] "rev. 1"

$Units
[1] "None"

$`Mass resolution`
[1] "0.500"

$`Number of scans`
[1] 574

$`Number of ms2 scans`
[1] 546

$`Scan range`
[1]   1 574

$`Time range`
[1] 0.00 0.78

$`Mass range`
[1]  140 1805

$`Scan filter (first scan)`
[1] "FTMS + c NSI Full ms [350.0000-1800.0000]"

$`Scan filter (last scan)`
[1] "FTMS + c NSI Full ms2 487.2567@hcd28.00 [140.0000-1015.0000]"

$`Total number of filters`
[1] "21"

$`Sample name`
[1] ""

$`Sample id`
[1] ""

$`Sample type`
[1] "Unknown"

$`Sample comment`
[1] ""

$`Sample vial`
[1] ""

$`Sample volume`
[1] "0"

$`Sample injection volume`
[1] "0"

$`Sample row number`
[1] "1"

$`Sample dilution factor`
[1] "0"

$`Sample barcode`
[1] ""

$`User text 0`
[1] ""

$`User text 1`
[1] ""

$`User text 2`
[1] ""

$`User text 3`
[1] ""

$`User text 4`
[1] ""

tobiasko commented 2 days ago

My feeling is that your rawrr.exe is not functional. Based on your R commands and the content of .../rawrrassembly/ you downloaded rawer.exe, see ?installRawrrExe. Maybe try to delete the downloaded rawrr.exe file and compile from the included C# code in the rawrr package. On my Mac this happens auto. on package startup, in case rawrr.exe is not found.

> BiocManager::install("rawrr")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Installing package(s) 'rawrr'
trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/macosx/big-sur-arm64/contrib/4.4/rawrr_1.12.0.tgz'
Content type 'application/x-gzip' length 2085113 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

The downloaded binary packages are in
    /var/folders/_l/psxm9vkj6m11z1vws9plwj6h0000gn/T//RtmptdCbm8/downloaded_packages
> library("rawrr")
'ThermoFisher.CommonCore.BackgroundSubtraction.dll' is missing.
'ThermoFisher.CommonCore.Data.dll' is missing.
'ThermoFisher.CommonCore.MassPrecisionEstimator.dll' is missing.
'ThermoFisher.CommonCore.RawFileReader.dll' is missing.
'ThermoFisher.CommonCore.*.dll' files are not available on the system.
Run 'rawrr::installRawFileReaderDLLs()' or setenv MONO_PATH to the location where the assemblies are located.
For more information, type '?ThermoFisher'.
Package 'rawrr' version 1.12.0 using
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
> rawrr::installRawFileReaderDLLs()
Do you accept the Thermo License agreement '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rawrr/rawrrassembly/RawFileReaderLicense.txt'? [Y/n]: Y
trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.BackgroundSubtraction.dll'
Content type 'application/octet-stream' length 44544 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.Data.dll'
Content type 'application/octet-stream' length 406016 bytes (396 KB)
==================================================
downloaded 396 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.MassPrecisionEstimator.dll'
Content type 'application/octet-stream' length 11264 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.RawFileReader.dll'
Content type 'application/octet-stream' length 654336 bytes (639 KB)
==================================================
downloaded 639 KB

 ThermoFisher.CommonCore.BackgroundSubtraction.dll                   ThermoFisher.CommonCore.Data.dll ThermoFisher.CommonCore.MassPrecisionEstimator.dll 
                                                 0                                                  0                                                  0 
         ThermoFisher.CommonCore.RawFileReader.dll 
                                                 0 

Restarting R session...

> library("rawrr")
Attempting to build 'rawrr.exe', one time setup ...
'rawrr.exe' successfully built in 
'/Users/tobiaskockmann/Library/Caches/org.R-project.R/R/rawrr/rawrrassembly/rawrr.exe'.
The build report should have been saved in
'/Users/tobiaskockmann/Library/Caches/org.R-project.R/R/rawrr/rawrrassembly/rawrr_build.log.28cb22339cb1'.
Package 'rawrr' version 1.12.0 using
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

You can also manually trigger the build using buildRawrrExe(). In each case you should see something like:

> list.files(rawrrAssemblyPath())
[1] "eula.txt"                                          
[2] "rawrr_build.log.28cb22339cb1"                      
[3] "rawrr.exe"                                         
[4] "ThermoFisher.CommonCore.BackgroundSubtraction.dll" 
[5] "ThermoFisher.CommonCore.Data.dll"                  
[6] "ThermoFisher.CommonCore.MassPrecisionEstimator.dll"
[7] "ThermoFisher.CommonCore.RawFileReader.dll"

tobiasko commented 2 days ago

... and better use

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich
tzcode source: internal

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

other attached packages:
[1] rawrr_1.12.0

loaded via a namespace (and not attached):
[1] compiler_4.4.1 tools_4.4.1

for environment infos.

tobiasko commented 2 days ago

You could also check the integrity/which rawrr.exe you currently have by comparing the md5 sum to

https://github.com/fgcz/rawrr/releases

buzuddha commented 2 days ago

Hi @tobiasko,

Many thanks for the detail response! In fact I am able to read the sample file headers using the test sample.raw.

> library(rawrr)
Package 'rawrr' version 1.10.2 using
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
> sampleFilePath()
[1] "/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/extdata/sample.raw"
> readFileHeader(rawfile = sampleFilePath())
$`RAW file`
[1] "sample.raw"

$`RAW file version`
[1] "66"

$`Creation date`
[1] "02/13/2018 11:09:03"

$Operator
[1] "ExactiveUser"

$`Number of instruments`
[1] 1

...

$`User text 4`
[1] ""

I don't believe it's an issue with the specific files I've attempted to load, as I've pulled a few different ones from the proteomExchange and they all have the same error.

PXD042189 PXD042189 PXD045263

> readFileHeader(rawfile = "~/Downloads/ftp_local/1284_01.raw")
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") :
  Rcode file to parse does not exist. '/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
        /tmp/RtmpBUXYFG/file79bd1ab850d3.stderr
        /tmp/RtmpBUXYFG/file79bd690f7e50.stdout
and the System Requirements
> readFileHeader(rawfile = "~/Downloads/ftp_local/2192_Hg_ARP_10_.raw")
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") :
  Rcode file to parse does not exist. '/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
        /tmp/RtmpBUXYFG/file79bd2d9b0196.stderr
        /tmp/RtmpBUXYFG/file79bd6b74cdb9.stdout
and the System Requirements
> readFileHeader(rawfile = "~/Downloads/ftp_local/50kDato75kDa.raw")
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") :
  Rcode file to parse does not exist. '/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
        /tmp/RtmpBUXYFG/file79bdeccccc4.stderr
        /tmp/RtmpBUXYFG/file79bd455a2571.stdout
and the System Requirements
> readFileHeader(rawfile = "~/Downloads/ftp_local/NF2-2_75737.raw")
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") :
  Rcode file to parse does not exist. '/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
        /tmp/RtmpBUXYFG/file79bd1502c044.stderr
        /tmp/RtmpBUXYFG/file79bd14fdfa32.stdout
and the System Requirements

I'm unable to build Rawrr.exe. I don't have msbuild nor xbuild and these appear to be dependencies:

$ rm /home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe
> library(rawrr)
Could not find 'msbuild' or 'xbuild' in the path. Therefore, it is not possible to build the 'rawrr.exe' assembly from source code.
Try to run rawrr::installRawrrExe().
Package 'rawrr' version 1.10.2 using
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
[1] rawrr_1.10.2

loaded via a namespace (and not attached):
[1] compiler_4.3.3 tools_4.3.3

I do have mono in the $PATH1, which I understand is the xbuild compiler.

$ which mono
/usr/bin/mono

$ ls -l /usr/lib/mono/
total 12
drwxr-xr-x  2 root root 4096 Oct 17 15:46 4.5
drwxr-xr-x  3 root root 4096 Oct 17 15:44 aot-cache
drwxr-xr-x 15 root root 4096 Oct 17 15:46 gac

Perhaps xbuild has been removed from the mono package? The mono website lists the xbuild page as outdated. How do I get one/both of these?

A quick apt install for either msbuild or xbuild yields E: Unable to locate package.

As an aside, the downloader appears to pull the rawrr.exe correctly when comparing to the hash on github. So likely not an issue there.

> rawrr::installRawrrExe()
trying URL 'https://github.com/fgcz/rawrr/releases/download/1.9.2/rawrr.1.9.2.exe'
Content type 'application/octet-stream' length 28672 bytes (28 KB)
==================================================
downloaded 28 KB

MD5 96e3a4cc1b7caaf92890d85ed4c72f77 /home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe
> md5sum("~/.cache/R/rawrr/rawrrassembly/rawrr.exe") == "96e3a4cc1b7caaf92890d85ed4c72f77"
/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe
                                             TRUE

tobiasko commented 2 days ago

Could you try

sudo apt-get install mono-mcs mono-xbuild

that was at least working for Ubuntu Linux at some point according to

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

tobiasko commented 2 days ago

Which mono version is installed on your system?

The latest stable release should be 6.12.

https://www.mono-project.com/download/stable/#download-lin

Not sure if it matters, but maybe update. I am running

tobiaskockmann@Tobiass-MacBook-Pro ~ % mono --version
Mono JIT compiler version 6.12.0 ((no/0cbf0e290c3 Wed Apr 24 13:37:51 UTC 2024)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
    TLS:           
    SIGSEGV:       normal
    Notification:  kqueue
    Architecture:  arm64
    Disabled:      none
    Misc:          softdebug 
    Interpreter:   yes
    LLVM:          supported, not enabled.
    Suspend:       preemptive
    GC:            sgen

tobiasko commented 2 days ago

According to your very first comment you only installed the mono runtime:

$ sudo apt-get install mono-runtime libmono-system-data4.0-cil -y

That is not sufficient to compile the C# code.

tobiasko commented 2 days ago

But it is interesting that the package sample data works, while all other downloaded files fail. Have you inspected one of the debug files listed?

buzuddha commented 2 days ago

Ah, I see... I guess I had figured precompiled would be quicker.

So, step 1: install mono-mcs mono-xbuild.

xbuild --version

>>>> xbuild tool is deprecated and will be removed in future updates, use msbuild instead <<<<

XBuild Engine Version 14.0
Mono, Version 6.8.0.105
Copyright (C) 2005-2013 Various Mono authors
MSBUILD: error MSBUILD0000: Project file '--version' not found.

Step 2: Build rawrr.exe, which now works. Promising...

> buildRawrrExe()
Attempting to build 'rawrr.exe', one time setup ...
'rawrr.exe' successfully built in
'/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe'.
The build report should have been saved in
'/home/user/.cache/R/rawrr/rawrrassembly/rawrr_build.log.10a726f960c1'.
[1] TRUE

Step 3: Check that the rawrr.exe is in place. It is...so close...

> list.files('/home/user/.cache/R/rawrr/rawrrassembly/')
[1] "eula.txt"
[2] "rawrr_build.log.10a726f960c1"
[3] "rawrr.exe"
[4] "ThermoFisher.CommonCore.BackgroundSubtraction.dll"
[5] "ThermoFisher.CommonCore.Data.dll"
[6] "ThermoFisher.CommonCore.MassPrecisionEstimator.dll"
[7] "ThermoFisher.CommonCore.RawFileReader.dll"

Step 4: Attempt to read file headers. Maybeeee...

> readFileHeader(rawfile = "~/Downloads/ftp_local/1284_01.raw")
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") :
  Rcode file to parse does not exist. '/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
        /tmp/Rtmpq0trwd/file10a72790015ad.stderr
        /tmp/Rtmpq0trwd/file10a7231cc5f1d.stdout
and the System Requirements

Step 5: Agonize Step 6: Check the debug logs. Nada.

> system('cat /tmp/Rtmpq0trwd/file10a72790015ad.stderr')
> system('cat /tmp/Rtmpq0trwd/file10a7231cc5f1d.stdout')
Unable to access the RAW file using the RawFileReader class!

So I'm still not sure where to go from here. I'll try getting mono 6.12 just in case.

For reference, the available mono version in the apt repository is:

$ sudo apt-cache policy mono-runtime
mono-runtime:
  Installed: 6.8.0.105+dfsg-3.6ubuntu2
  Candidate: 6.8.0.105+dfsg-3.6ubuntu2
  Version table:
 *** 6.8.0.105+dfsg-3.6ubuntu2 500
        500 http://archive.ubuntu.com/ubuntu noble/universe amd64 Packages
        100 /var/lib/dpkg/status

I added the mono repository with the instructions from the mono website, and now

 apt-cache policy mono-runtime
mono-runtime:
  Installed: 6.8.0.105+dfsg-3.6ubuntu2
  Candidate: 6.12.0.200-0xamarin2+ubuntu2004b1
  Version table:
     6.12.0.200-0xamarin2+ubuntu2004b1 500
        500 https://download.mono-project.com/repo/ubuntu stable-focal/main amd64 Packages
 *** 6.8.0.105+dfsg-3.6ubuntu2 500
        500 http://archive.ubuntu.com/ubuntu noble/universe amd64 Packages
        100 /var/lib/dpkg/status

but it's being held back for some reason...

$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Calculating upgrade... Done
The following upgrades have been deferred due to phasing:
  python3-distupgrade ubuntu-release-upgrader-core
The following packages have been kept back:
  libmono-corlib4.5-cil libmono-i18n4.0-cil
  libmono-system-configuration4.0-cil
  libmono-system-core4.0-cil libmono-system4.0-cil
  mono-4.0-gac mono-gac mono-mcs mono-runtime
  mono-runtime-common mono-runtime-sgen
0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
N: Some packages may have been kept back due to phasing.

buzuddha commented 2 days ago

Ruh roh...

So I removed everything sudo apt remove libmono-corlib4.5-cil libmono-i18n4.0-cil libmono-system-configuration4.0-cil libmono-system-core4.0-cil libmono-system4.0-cil mono-4.0-gac mono-gac mono-mcs mono-runtime mono-runtime-common mono-runtime-sgen

Then reinstalled the relevant packages sudo apt install mono-mcs mono-xbuild mono-runtime libmono-system-data4.0-cil

Confirmed I have the latest version of mono

mono --version
Mono JIT compiler version 6.12.0.200 (tarball Tue Jul 11 21:37:50 UTC 2023)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
        TLS:           __thread
        SIGSEGV:       altstack
        Notifications: epoll
        Architecture:  amd64
        Disabled:      none
        Misc:          softdebug
        Interpreter:   yes
        LLVM:          yes(610)
        Suspend:       hybrid
        GC:            sgen (concurrent by default)

Buuuut

> library(rawrr)
Attempting to build 'rawrr.exe', one time setup ...
Error: package or namespace load failed for ‘rawrr’:
 .onLoad failed in loadNamespace() for 'rawrr', details:
  call: buildRawrrExe()
  error: Building 'rawrr.exe' failed. For details see the build report, supposed to be saved in:
'/home/user/.cache/R/rawrr/rawrrassembly/rawrr_build.log.12236c638fb2'
Call 'rawrr::installRawrrExe()' to download and install a precompiled version
from a remote location. Note this requires internet connection.
In addition: Warning message:
In system2(cmd, cmdArgs, wait = TRUE, stderr = TRUE, stdout = TRUE) :
  running command ''xbuild' /p:OutputPath='/home/user/.cache/R/rawrr/rawrrassembly'/ /p:AdditionalLibPaths='/home/user/.cache/R/rawrr/rawrrassembly' /v:diagnostic /flp:LogFile='/home/user/.cache/R/rawrr/rawrrassembly/rawrr_build.log.12236c638fb2' rawrr.csproj 2>&1' had status 1

> system('cat /home/user/.cache/R/rawrr/rawrrassembly/rawrr_build.log.12236c638fb2')
Loading default tasks for ToolsVersion: 14.0 from /usr/lib/mono/xbuild/14.0/bin/Microsoft.Common.tasks

Build started 10/18/2024 17:04:42.
__________________________________________________
Project "/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj" (default target(s)):
Building target "Build" in project "/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj" ("/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj").
        Target Build:
        Task "Csc"
                Using task Csc from Microsoft.Build.Tasks.Csc, Microsoft.Build.Tasks.Core, Version=14.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a
        Task "Csc" execution -- FAILED
        Done building target "Build" in project "/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj".-- FAILED
Done building target "Build" in project "/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj" ("/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj").
Done building project "/home/user/R/x86_64-pc-linux-gnu-library/4.3/rawrr/rawrrassembly/rawrr.csproj".-- FAILED

Build FAILED.
         0 Warning(s)
         0 Error(s)

Time Elapsed 00:00:00.1546190

Ack...maybe those packages were held back for a reason?

buzuddha commented 2 days ago

Ok phew... I was able to 1) remove the mono repository from /etc/apt/sources.list.d/mono-official-stable.list 2) run the apt update 3) apt remove all the mono packages 4) apt install mono-mcs mono-xbuild mono-runtime libmono-system-data4.0-cil 5) confirm that the rawrr.exe build works (with Mono JIT compiler version 6.8.0.105)

> library(rawrr)
Attempting to build 'rawrr.exe', one time setup ...
'rawrr.exe' successfully built in
'/home/user/.cache/R/rawrr/rawrrassembly/rawrr.exe'.
The build report should have been saved in
'/home/user/.cache/R/rawrr/rawrrassembly/rawrr_build.log.12c8e6fd0a48a'.
Package 'rawrr' version 1.10.2 using
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

So I'm back stuck where I was before upgrading to 6.12 - can build rawrr.exe but still no ability to read in .raw files.

Any ideas? (Thanks for all your help by the way. Sorry to be a pain here)

tobiasko commented 13 hours ago

It is absolutely embarassing!

> readFileHeader(rawfile = "~/Downloads/20240925_C36374_006_S777857_MS2_mutpep_Mutant.raw")
Error in .rawrrSystem2Source(rawfile, input = NULL, rawrrArgs = "headerR") : 
  Rcode file to parse does not exist. '/Users/tobiaskockmann/Library/Caches/org.R-project.R/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
    /var/folders/_l/psxm9vkj6m11z1vws9plwj6h0000gn/T//Rtmpd04CR2/file28cbee6948e.stderr
    /var/folders/_l/psxm9vkj6m11z1vws9plwj6h0000gn/T//Rtmpd04CR2/file28cb7ee779b1.stdout
and the System Requirements
> readFileHeader(rawfile = "/Users/tobiaskockmann/Downloads/20240925_C36374_006_S777857_MS2_mutpep_Mutant.raw")
$`RAW file`
[1] "20240925_C36374_006_S777857_MS2_mutpep_Mutant.raw"

$`RAW file version`
[1] "66"

$`Creation date`
[1] "9/25/2024 9:12:07 PM"

$Operator
[1] "Orbitrap Lumos"

$`Number of instruments`
[1] 2

$Description
[1] ""

$`Instrument model`
[1] "Orbitrap Fusion Lumos"

$`Instrument name`
[1] "Orbitrap Fusion Lumos"

$`Instrument method`
[1] "C:/Xcalibur/methods/__Service/ProteinInteraction/DIA_70x10Da_GT45min_RT65min.meth"

$`Serial number`
[1] "FSN20682"

$`Software version`
[1] "3.4.3072.18"

$`Firmware version`
[1] ""

$Units
[1] "None"

$`Mass resolution`
[1] "0.500"

$`Number of scans`
[1] 72846

$`Number of ms2 scans`
[1] 71819

$`Scan range`
[1]     1 72846

$`Time range`
[1]  0.00 65.04

$`Mass range`
[1]  145 1450

$`Scan filter (first scan)`
[1] "FTMS + c ESI Full ms [350.0000-1050.0000]"

$`Scan filter (last scan)`
[1] "FTMS + c ESI Full ms2 1045.0000@hcd30.00 [145.0000-1450.0000]"

$`Total number of filters`
[1] "71"

$`Sample name`
[1] "MS2_mutpep"

$`Sample id`
[1] "777857"

$`Sample type`
[1] "Unknown"

$`Sample comment`
[1] "on beads dig, inj 3/20ul"

$`Sample vial`
[1] "1:A,3"

$`Sample volume`
[1] "0"

$`Sample injection volume`
[1] "3"

$`Sample row number`
[1] "4"

$`Sample dilution factor`
[1] "0"

$`Sample barcode`
[1] ""

$`User text 0`
[1] ""

$`User text 1`
[1] ""

$`User text 2`
[1] "FGCZ"

$`User text 3`
[1] ""

$`User text 4`
[1] ""

tobiasko commented 13 hours ago

It looks like the function can't deal with the a simple relative path. OMG! Is this 2024 or the 90s... This is also the reason why the sample data worked, while all your downloaded files didn't.

sampleFilePath()
[1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rawrr/extdata/sample.raw"

I am really sorry for this!

buzuddha commented 7 hours ago

OMG! I'm so glad it was something so simple! I was beginning to worry I was going to have major issues getting this thing working! Can confirm readFileHeader() worked for me using a PDX dataset.

Merci vielmal!