installation of NewRawFileReader on MacOS

[tobiasko]

I tried to follow

"Register the .Net assembly in your system similar to a Linux installation", but it is unclear to me what this implies. The following things are done:

• downloaded the NewRawFileReader archive from Thermo
• installed mono

What are the next steps? How do I install the NuGet packe? Do I need VisualStudio? If not, what are the alternatives? We need to document this in a way that people without any prior experience in this area will to able to complete installation.

[tobiasko]

tobiasko@public-docking-hpx-1240:~/Downloads/OneDrive_1_14-06-2018/Windows_MacOS > gacutil -i lib/monomac/ThermoFisher.CommonCore.BackgroundSubtraction.dll Failure adding assembly lib/monomac/ThermoFisher.CommonCore.BackgroundSubtraction.dll to the cache: Strong name cannot be verified for delay-signed assembly

[tobiasko]

I used strategy 2 as given in the README (copied dlls to exec folder of package). Calling read.raw() gives an error using sample file provided with the package: `

(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw')) [1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rawDiag/extdata/sample.raw" system.time(RAW <- read.raw(file = rawfile)) executing mono /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rawDiag/exec/fgcz_raw.exe /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rawDiag/extdata/sample.raw qc ...

Unhandled Exception: System.IO.FileNotFoundException: Could not load file or assembly 'ThermoFisher.CommonCore.Data, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies. File name: 'ThermoFisher.CommonCore.Data, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953' [ERROR] FATAL UNHANDLED EXCEPTION: System.IO.FileNotFoundException: Could not load file or assembly 'ThermoFisher.CommonCore.Data, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies. File name: 'ThermoFisher.CommonCore.Data, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953' Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Timing stopped at: 0.016 0.018 0.116

sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.6

locale: [1] C

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

other attached packages: [1] rawDiag_0.0.2

loaded via a namespace (and not attached): [1] Rcpp_0.12.16 bindr_0.1.1 magrittr_1.5 bit_1.1-12 munsell_0.4.3
[6] lattice_0.20-35 colorspace_1.3-2 R6_2.2.2 rlang_0.2.0 blob_1.1.1
[11] plyr_1.8.4 dplyr_0.7.4 tools_3.3.2 parallel_3.3.2 grid_3.3.2
[16] gtable_0.2.0 DBI_0.8 lazyeval_0.2.1 bit64_0.9-7 assertthat_0.2.0 [21] digest_0.6.15 tibble_1.4.2 bindrcpp_0.2.2 purrr_0.2.4 tidyr_0.8.0
[26] ggplot2_2.2.1 memoise_1.1.0 glue_1.2.0 RSQLite_2.1.0 pillar_1.2.1
[31] scales_0.5.0 hexbin_1.27.1 pkgconfig_2.0.1 `

[cpanse]

On how to install the New ThermoRawFileReader follow the guidelines by Thermo.

[tobiasko]

@cpanse Your childish behaviour is not helpful! I have read the docs provided by Thermo and I still was not able to complete the installation. Do you believe that the reviewers will be smarter more talented than me?

[tobiasko]

btw: I meanwhile found out what happens. The dlls get eliminated, each time the R package gets updated/reinstalled. Now it works: `

system.time(RAW <- read.raw(file = rawfile)) executing mono /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rawDiag/exec/fgcz_raw.exe /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rawDiag/extdata/sample.raw qc ... MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode user system elapsed 0.396 0.103 4.829 Warning message: In is.rawDiag(object) : missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode (rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw')) [1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rawDiag/extdata/sample.raw" `

[cpanse]

@tobiasko
if the user agrees on the license we provide a ready to run R package tarball for download.