Closed cpanse closed 7 months 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: rawDiag
Type: Package
Title: Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Version: 0.99.0
Authors@R: c(person(given = "Christian", family = "Panse", email = "cp@fgcz.ethz.ch", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-1975-3064")),
person(given = "Christian", family = "Trachsel", email = "Christian.Trachsel@fgcz.ethz.ch", role = "aut"),
person(given = "Tobias", family = "Kockmann", email = "Tobias.Kockmann@fgcz.ethz.ch", role = "aut"))
Depends:
R (>= 4.3)
Imports:
dplyr,
ggplot2 (>= 3.4),
grDevices,
rawrr (>= 1.10),
rlang,
reshape2,
scales,
shiny,
stats
Suggests:
BiocStyle (>= 2.28),
ExperimentHub,
tartare,
knitr,
testthat
Description: Optimizing methods for liquid chromatography coupled to mass
spectrometry (LC–MS) poses a nontrivial challenge. The rawDiag package
facilitates rational method optimization by generating MS operator-tailored
diagnostic plots of scan-level metadata. The package is designed for use on
the R shell or as a Shiny application on the Orbitrap instrument PC.
License: GPL-3
URL: https://github.com/cpanse/rawDiag/
BugReports: https://github.com/cpanse/rawDiag/issues
Encoding: UTF-8
NeedsCompilation: no
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Metabolomics
It looks like the set up for the rawrr package needs to be run in order to use your package. I highly suggest referencing the https://github.com/fgcz/rawrr/blob/devel/INSTALL
in an INSTALL file of your own and making note of it perhaps in the package level man page?
I ran
rawrr::installRawFileReaderDLLs()
rawrr::installRawrrExe()
and when I still try to build your package locally I am getting an ERROR
lorikern@jbcj433:~/PkgReview$ R CMD build rawDiag
* checking for file 'rawDiag/DESCRIPTION' ... OK
* preparing 'rawDiag':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘rawDiag.Rmd’ using rmarkdown
trying URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/tartare_1.17.0.tar.gz'
Content type 'application/x-gzip' length 314914 bytes (307 KB)
==================================================
downloaded 307 KB
* installing *source* package ‘tartare’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tartare)
The downloaded source packages are in
'/tmp/RtmpzC3q1y/downloaded_packages'
Quitting from lines 65-68 [readOrbitrap] (rawDiag.Rmd)
Error: processing vignette 'rawDiag.Rmd' failed with diagnostics:
no lines available in input
--- failed re-building ‘rawDiag.Rmd’
SUMMARY: processing the following file failed:
‘rawDiag.Rmd’
Error: Vignette re-building failed.
Execution halted
Dear @lshep,
I added an INSTALL file; SystemRequirements @DESCRIPTION and a note in the ?rawDiag man page. https://github.com/cpanse/rawDiag/commit/7db172841ef420168ced14f48578bfdca8825ebd C
I still get an ERROR when I try to build locally but I'll pass it into the build system for now and see if it reproduces there.
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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@lshep OK; I copied the part from the MsBackendRawFileReader vignette. Thanks, Christian
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Please fix all ERROR, Warning, Notes before a reviewer is assigned for an in depth review. thank you
@lshep; I don’t know how to fix the error. One way is that rawrr is working (meaning having all the libraries installed) or I need to fetch the proprietary vendor libraries when rendering the vignette. Thanks and best wishes, C
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ERROR: Subscribe to the Bioc-devel mailing list by going to
I get emails sent to bioc-devel@r-project.org
We can ignore this error for now as there seems to be an issue with the BiocCheck for the bioc-devel mailing list. I did confirm you are registered. Is there a way to reduce the package size as there is still a warning concerning package size?
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Dear @lshep; I could reduce the output of the vignette. Thanks, Christian
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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.2 LTS): rawDiag_0.99.17.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.17.tar.gz
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A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Hi @cpanse
Thanks for submitting rawDiag :tada:! Below is my review of your package. Please reply here if anything is unclear or needs any further explanation.
What next?
Please address the comments as best as you can. When you are ready for me to check the package again please reply to let me know with a summary of changes you have made or any other responses. You can use the "Quote reply" option in the ...
menu on this comment to reply directly to my points below.
Luke
Key: :rotating_light: Required :warning: Recommended :green_circle: Optional :question: Question
R CMD build
BiocCheck::BiocCheck()
WARNING
about using .Deprecated
R CMD check
read.raw
to be consistent with the other functionsecho = TRUE
is preferred in vignettes to show the code that is being run[ ] :green_circle: I got an error when I tried to run the plotting chunk:
Error in `ggplot()`:
! `mapping` should be created with `aes()`.
✖ You've supplied a <character> object
context()
function is superseded in recent {testthat} versionsR/
directorypaste
in message()
, warning()
, stop()
is not neededmatch.arg
BiocParallel
packageshiny()
function is very generation, I would recommend changing it to something more specific to the packageappDir
argument in the shiny()
function, I don't think a user would ever need to set thisrawDir
argument in the shiny()
function. The default value is unlikely to work for most users and making it required would be clearer..f()
function a more descriptive nameReceived a valid push on git.bioconductor.org; starting a build for commit id: edbda4b1e92f009b79239ed4f0e323d8d648c689
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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): rawDiag_0.99.18.tar.gz
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