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rawrr #1886

Closed cpanse closed 3 years ago

cpanse commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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bioc-issue-bot commented 3 years ago

Hi @cpanse

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: rawrr
Type: Package
Title: Direct Access to Orbitrap Data and Beyond
Version: 0.99.0
Authors@R: c(person("Christian", "Panse",
        email = "cp@fgcz.ethz.ch",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0003-1975-3064")),
        person("Tobias", "Kockmann",
    email = "tobias.kockmann@fgcz.ethz.ch",
    role = "aut",
    comment = c(ORCID = "0000-0002-1847-885X")))
Depends: R (>= 4.1)
Imports: 
        grDevices, graphics, stats, utils
Suggests:
    protViz (>= 0.6),
    knitr,
    lattice,
    parallel,
    rmarkdown,
    testthat
Description: Provides an interface for Thermo Fisher Scientifc raw files
        branched from rawDiag <doi:10.1021/acs.jproteome.8b00173>.
    This package wraps the functionality
    of the RawFileReader .NET assembly. Within the R environment
    spectra and chromatograms are represented by S3 objects.
    All objects are currently kept in memory.
    (Kockmann T. et al (2020) <doi:10.1101/2020.10.30.362533>)
        The package is developed, tested, and used at the Functional
        Genomics Center Zurich, Switzerland <https://fgcz.ch>.
License: GPL-3
SystemRequirements: mono 4.x or higher on OSX / Linux, .NET 4.x or
        higher on Windows, 'msbuild' and 'nuget' available in the path
    and New RawFileReader .Net Assembly from Thermo Fisher Scientific
URL: https://github.com/fgcz/rawrr/
BugReports: https://github.com/fgcz/rawrr/issues
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
RoxygenNote: 7.1.1
biocViews: MassSpectrometry, Proteomics, Metabolomics
VignetteBuilder: knitr
bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

cpanse commented 3 years ago

@hpages

The error is caused because the system requirements are not fulfilled:

SystemRequirements: mono on OSX / Linux, .NET 4.x  on Windows, 'msbuild'
and New RawFileReader .Net Assembly from Thermo Fisher Scientific.

https://planetorbitrap.com/rawfilereader

C

tobiasko commented 3 years ago

Dear @hpages,

can we do something to assist?

Best, Tobi

hpages commented 3 years ago

Yes you can. Please provide an INSTALL file that explains how to install the system requirements in the most straightforward manner on Linux (Debian-based and RPM-based distros), Windows, and Mac. Ideally one should be able to just copy/paste a few commands like apt-get install <some-deb-pkg> or brew install <something>.

Note that it's unusual for a Bioconductor package to depend on external software that is complicated to install. The project has a strong preference for packages that are easy to install and a long history of wrapping external software in R packages (e.g. Rgraphiz, zlibbioc, Rhdf5lib, Rhtslib, gmapR, Rbowtie, etc...). This makes life easier for the end user and ensures that everybody uses the same version of the external software, which helps reproducibility.

Thanks!

tobiasko commented 3 years ago

ok! Should we push the INSTALL file to the main directory of the package repo (same location as DESCRIPTION)?

cpanse commented 3 years ago

Install system requirements

Debian 8,9,10

taken from the rawrr continuous integration workflow.

apt-get install mono-mcs mono-xbuild

Apple

brew install mono

or install from

https://www.mono-project.com/

Microsoft

if the native C# compiler is not available install mono:

or install from

https://www.mono-project.com/

Install the .NET assemblies

the following files should be placed in the following folder:

inst/rawrrassembly/bin/ThermoFisher.CommonCore.BackgroundSubtraction.dll
inst/rawrrassembly/bin/ThermoFisher.CommonCore.Data.dll
inst/rawrrassembly/bin/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
inst/rawrrassembly/bin/ThermoFisher.CommonCore.RawFileReader.dll
inst/rawrrassembly/bin/rawrr.exe

In general, ThermoFisher.CommonCore dlls can be obtained through:

https://planetorbitrap.com/rawfilereader

by contacting Jim Shofstahl using

jim.Shofstahl@thermofisher.com

Once the dlls have been copied to this folder, you should be able to install rawrr from source by using:

R CMD build rawrr && R CMD INSTALL rawrr_*.gz

We recommend installing rawrr by using GitHub releases published at:

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

These contain the dlls and the rawrr.exe already!

as alternative you can set the MONO_PATH enviroment, e.g.,

export MONO_PATH="/path/to/ThermoFisher/CommonCore/DLL/files"

on Apple and Linux

RAWRR_RELEASE='http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.2.2.tar.gz'

MONO_PATH='/usr/local/lib/RawFileReader/'

curl --silent $RAWRR_RELEASE | (cd /tmp/ && tar xfvz - --wildcards '*.dll') \
  && sudo mkdir -p $MONO_PATH \
  && sudo find /tmp/rawrr -type f -exec mv -v {} $MONO_PATH \;

export MONO_PATH

on Microsoft

dll files should be placed anywhere in the PATH or in %systemroot%\system32

hpages commented 3 years ago

Wait, we need to contact a guy to get his DLLs and copy them to the inst/rawrrassembly/ folder of the package source tree before building the source package on Windows?

As you probably know we use an automated system that runs every day to produce source and binary packages for Linux, Windows, and Mac, for about 2000 software packages. The automated system is just going to clone your package repo and run the standard R CMD build on it to produce the source tarball, like it does on every other package, every day. That's all. We're not adding extra things to the source tree before running R CMD build. How could we do that?

What kind of licence these DLLs have that you can't include them in your package source tree? Note that your package is GPL-3 so if there's licence incompatibility I don't think we can distribute a Windows binary of rawrr that includes the DLLs, even if they are added at the last minute (i.e. just before running R CMD build). If you can't find a way to include these DLLs in your package then I'm afraid we'll have to mark the package as unsupported on Windows.

Yes please, put the INSTALL file in the top-level directory of the source tree.

Thanks

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 96a5bf69cd4c358bf4c2ca944fb221db5f31f703

cpanse commented 3 years ago

Dear @hpages, I pushed the rawrr package source, including the INSTALL files and the .Net assemblies, to git@git.bioconductor.org:packages/rawrr.

You can find the license of the assemblies in inst/rawrrassembly/RawFileReaderLicense.doc.

Of note, as an alternative to including the .Net assemblies in the package, you can also place the dlls on the package build/test system on Apple|Linux|Windows by setting the MONO_PATH.

Sorry for the delay. I was offline while skiing in the Swiss Alps.

Christian

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 55bfec74413eb6b104eb9061b36c4f6b99ae5086

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f4b5e1215a26fafcfaf1c39bfd9382dd37993781

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 20cca2fc1fca8d215c6db4c2aa3728f6a1192a3a

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

cpanse commented 3 years ago

@hpages the build errors for Linux and macOS will remain until mono is available on the test systems.

on Linux (Debian/Ubuntu) apt-get install mono-mcs mono-xbuild and for macOS brew install mono.

Of note, the dlls and the exe BLOBs will work on all major R platforms (including Linux arm, not checked Apple M1 yet). Also, if a mono compiler is available on the build system rawrr.exe is derived from rawrr.cs.

for the build mechanism, we have copied the https://CRAN.R-project.org/package=rDotNet package build concept.

Also, please note that the entire work/concept of this submission has been developed in the last five years, and it has been presented multiple times at European Bioconductor meetings:

  1. EuroBioc2018
  2. EuroBioc2019

I am convinced that the rawrr package can be a fundamental first step towards efficient and effective access of proprietary mass spec data into R via MsBackendRawFileReader or issue 1930 to the Spectra Biocpkg and finally to the R user.

And yes, we are aware that this is not just another Bioconductor package submission and it will take some extra effort and discussions.

hpages commented 3 years ago

Please include a plain text version of the RawFileReader license in the package.

I have some serious concerns about this license. In particular with the following items:

2.1. You may not decompile, disassemble, reverse engineer, use reflection or modify this Software.

...

If you distribute this Software to others, you agree to:

3.1. Indemnify, defend and hold harmless the Licensor from any claims, including attorneys’ fees, related to the distribution or use of this Software;

...

3.3. Require your end users to agree to a license agreement that prohibits them from redistributing this Software to others.

...

4.2. You may not commercially exploit this Software or products that incorporate this Software without the prior written consent of Licensor. Commercial exploitation includes, but is not limited to, charging a purchase price, license fee, maintenance fee, or subscription fee; or licensing, transferring or redistributing the Software in exchange for consideration of any kind.

2.1 strongly suggests that RawFileReader is closed source which means that RawFileReader is basically a black box that users are expected to trust. Is this compatible with an open source project like Bioconductor?

I don't even understand the rationale for 3.3. If you are allowed to distribute RawFileReader, why your users wouldn't be allowed too?

And finally:

4.3. Your rights to this Software do not include any license, right, power or authority to subject this Software in whole or in part to any of the terms of an Excluded License. "Excluded License" means any license that requires as a condition of use, modification and/or distribution of software subject to the Excluded License, that such software or other software combined and/or distributed with such software be (a) disclosed or distributed in source code form; or (b) licensed for the purpose of making derivative works. Without limiting the foregoing obligation, you are specifically prohibited from distributing this Software with any software that is subject to the General Public License (GPL) or similar license in a manner that would create a combined work.

Someone is going to have to decipher exactly what they mean but the very last sentence is worrisome. Isn't that a deal breaker? Maybe someone needs to contact the RawFileReader authors for clarifications.

In the meantime I installed mono-mcs and mono-xbuild on malbec2. Please bump the version of the package in order to trigger a new build and we'll start from there. We'll ignore BiocCheckGitClone's false positive on Linux and Windows for now, as well as the build error on macOS.

Note that you'll need to add a BinaryFiles file to list the binary executables included in the package in order to avoid an R CMD check warning. See "Writing R Extensions" manual for more information.

In your INSTALL file:

Looks like on Ubuntu if I only install mono-runtime (instead of mono-mcs and mono-xbuild) then the package installs and loads without any complain but then rawrr::readChromatogram() silently returns a broken rawrrChromatogram object:

library(ExperimentHub)
eh <- ExperimentHub::ExperimentHub()
EH4547 <- normalizePath(eh[["EH4547"]])
rawfile <- paste0(EH4547, ".raw")
if (!file.exists(rawfile)){ file.link(EH4547, rawfile) }

library(rawrr)
x <- rawrr::readChromatogram(rawfile = rawfile, type = "tic")
x$times
# NULL
x$intensities
# NULL

You'll need to make your code a lot more robust to missing system requirements.

Found in .onAttach():

packagedir <- system.file(package = 'rawrr')
rawrrAssembly <- sprintf("%s/rawrrassembly/bin/rawrr.exe", packagedir)

and in rawrr:::.rawrrAssembly():

f <- system.file("rawrrassembly/bin/rawrr.exe", package = "rawrr")

Don't make explicit use of / when you're assembling a path. Always use system.file() or file.path() instead. Also, you've defined internal helper .rawrrAssembly() to do the job so you should use it every time you need to perform that job.

tobiasko commented 3 years ago

Dear @hpages,

I will contact Jim and ask for a clarification.

Best, Tobi

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d4ba9534ce1984debf4712d36e282999fda70183

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 40a566ecdab933b7ee26e84b7a5edecf9e76eae7

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ab8746c62f859db5bc0a871f1f1666478deeb27a

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 908af476c945446bdf2758b516cb6c52e43fa21b

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

hpages commented 3 years ago

Hi @cpanse , @tobiasko ,

There's been some internal discussion about this. Bioconductor is open source and has never distributed proprietary DLLs before so this would create a precedent. We think it would be better to have the RawFileReader DLLs automatically retrieved by the rawrr package the first time the user needs them (they could get installed in a place like tools::R_user_dir("rawrr", which="cache"), in particular it's important to not install them in rawrr's installation folder because on many systems this is a read-only place). This would also provide a natural stop for asking the user to agree on the terms of the RawFileReader licence.

The package would also need to interact meaningfully with the Bioconductor ecosystem e.g. by making use of Bioc existing classes for data representation. This is a generic requirement that applies to all submissions. For example, in the single cell experiment world, submission that deal with single cell data are strongly encouraged to use the SingleCellExperiment class, or at least to be able to operate on SingleCellExperiment objects.

We suggest that you join the community-bioc Slack if you've not done so already, in particular the #metabolomics or #proteomics channels. This is a great place to meet other Bioconductor developers and discuss the interoperability topic with them.

Best, H.

tobiasko commented 3 years ago

Dear @hpages,

thanks for your reply and for triggering the internal discussion. In order to get a clearer picture what you mean by the bioc ecosystem and interoperability: I am not aware of any official bioc classes or containers that deal with raw mass spectromerty data. The most recent efforts to work towards this goal are spearheaded by https://www.rformassspectrometry.org/, which is exactly the idea behind our submission. We need rawrr to become part of bioc in order to generate an alternative backend (dependencies need to be available on CRAN or bioc) for packages like https://bioconductor.org/packages/release/bioc/html/Spectra.html We even joined a workshop to discuss these topics in person during the EuroBioc2019 meeting in Brussels and showed our prototype implementation (MsBackendRawFileReader) as a poster. Is there anything that we missed in this respect? Any efforts taken by the bioc core team or other developers?

I also had a brief look at the bioc slack at https://bioc-community.herokuapp.com/, but could not find any proteomics channel.

Best, Tobi

tobiasko commented 3 years ago

ok. sorry about the channel, I found it. It was hidden.

jorainer commented 3 years ago

Regarding the interoperability - would it make sense to eventually include the the MsBackendRawFileReader backend for the Spectra package directly in the rawrr package?

tobiasko commented 3 years ago

Hi @jorainer ! That was actually our idea.

tobiasko commented 3 years ago

Or the backend would become a package on it's own that depend on rawrr. Not sure...what is better.

jorainer commented 3 years ago

the advantage of having the backend within rawrr would be that you would then re-use classes and functionality already present in BioC. Without that rawrr could also happily live within CRAN or similar as there are no dependencies on othe BioC packages (unless there are some). Also, AFAIK, the MsBackendRawFileReader depends anyway on the rawrr package - so why not fuse them?

cpanse commented 3 years ago

@jorainer at the moment where I have no idea where we are heading I would keep things separated. so we would have the following layers:

  1. rawrr for fast extracting information of the Thermo Fisher BLOBs. (similar to hd5, mzR, XML, see your drawing)
  2. Backend for whatsoever containers/classes, e.g., MsBackendRawFileReader but using rawrr instead of the current rdotnet package (which is missing in your drawing).
  3. Spectra
  4. rawDiag diagnostic plots (we remove the entire reading functionality)

Screenshot 2021-03-16 at 14 31 00

merging layers 0. and 1. is for sure possible in a later stage.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ae27c4b2b16d803ec4f9b833fd58b5decf9fa4c0

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

cpanse commented 3 years ago

Dear @hpages,

I have implemented your proposed method. Thank you! I wonder if at least one test platform (Linux) could call the mono compiler deriving the rawrr.exe from the rawrr.cs source code.

Best,

Christian

hpages commented 3 years ago

Hi Christian,

mono-mcs and mono-xbuild are already on the Linux builder as discussed one month ago. If there's anything else that needs to be installed, please let me know and update your SystemRequirements field and INSTALL files accordingly.

BTW right now the SystemRequirements field is:

SystemRequirements: mono-runtime 4.x or higher on Linux/macOS,
            .NET 4.x or higher on Microsoft Windows,
            and New RawFileReader .Net Assembly from Thermo Fisher Scientific
            in the path.

2 things:

Thanks, H.

bioc-issue-bot commented 3 years ago

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cpanse commented 3 years ago

Dear Hervé,

1. On my docker example, the mono-runtime package is sufficient to execute the .Net assembly.

FROM ubuntu:20.04
MAINTAINER Christian Panse <Christian.Panse@gmail.com>

#RUN apt-get install mono-mcs mono-xbuild -y
#COPY rawrrassembly /tmp/rawrrassembly

RUN apt-get update --fix-missing && apt-get install wget mono-runtime -y

RUN cd /tmp \
  && wget https://github.com/compomics/ThermoRawFileParser/raw/master/packages/mzLib.1.0.450/lib/netstandard2.0//ThermoFisher.CommonCore.Data.dll \
  && wget https://github.com/compomics/ThermoRawFileParser/raw/master/packages/mzLib.1.0.450/lib/netstandard2.0//ThermoFisher.CommonCore.MassPrecisionEstimator.dll \
  && wget https://github.com/compomics/ThermoRawFileParser/raw/master/packages/mzLib.1.0.450/lib/netstandard2.0//ThermoFisher.CommonCore.RawFileReader.dll \
  && wget http://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr.exe \
  && wget ftp://massive.ucsd.edu/MSV000086542/raw/20181113_010_autoQC01.raw
docker build . && docker run  -ti DOCKERBUILT  mono /tmp/rawrr.exe /tmp/20181113_010_autoQC01.raw infoR

2. To my understanding, mono always considers the MONO_PATH. Therefore, we have more flexibility in handling the ThermoFisher.CommonCore*dll files before the package installation. If the MONO_PATH is not set, someone has to trigger r rawrr::installRawfileReaderDLLs() r rawrr::installRawrrExe() (I fixed the description n INSTALL) otherwise, the test case will fail, and the vignette file cannot be rendered.

Is that procedure working for Bioconductor?

Thank you and best wishes,

Christian

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 91b449d359532bc6572669994e3329d61258abda

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b3526de4e142052dc37faee2574ed7d1c9b8b190

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/rawrr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.