Closed jorainer closed 1 month ago
Hi @jorainer
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: SpectraQL
Title: MassQL support for Spectra
Version: 0.99.0
Description: The Mass Spec Query Language (MassQL) is a domain-specific
language enabling to express a query and retrieve mass spectrometry (MS)
data in a more natural and understandable way for MS users. It is inspired
by SQL and is by design programming language agnostic. The SpectraQL
package adds support for the MassQL query language to R, in particular
to MS data represented by Spectra objects. Users can thus apply MassQL
expressions to analyze and retrieve specific data from Spectra objects.
Authors@R: c(person(given = "Johannes", family = "Rainer",
email = "Johannes.Rainer@eurac.edu",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-6977-7147")),
person(given = "Andrea", family = "Vicini",
email = "andrea.vicini@eurac.edu",
role = "aut"),
person(given = "Sebastian", family = "Gibb",
email = "mail@sebastiangibb.de",
role = "ctb",
comment = c(ORCID = "0000-0001-7406-4443"))
)
Depends:
R (>= 4.4.0),
ProtGenerics (>= 1.25.1)
Imports:
Spectra (>= 1.5.6),
MsCoreUtils,
methods
Suggests:
testthat,
msdata (>= 0.19.3),
roxygen2,
rmarkdown,
knitr,
BiocStyle,
mzR
License: Artistic-2.0
LazyData: false
VignetteBuilder: knitr
BugReports: https://github.com/RforMassSpectrometry/SpectraQL/issues
URL: https://github.com/RforMassSpectrometry/SpectraQL
biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.3.2
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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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): SpectraQL_0.99.0.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: 9eb4fc63017ce73555df13b2050f887e4fa9fb5b
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Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): SpectraQL_0.99.1.tar.gz
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Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8240f07b562e9b26a452d8b34078c63f4230f069
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): SpectraQL_0.99.2.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
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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.
Thank you for submitting your package to Bioconductor. The package passed check and build. It is in pretty good shape. I am looking for a bone in an egg now. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.
for
loops present, try to replace them by *apply
funcitons.
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
in BioCheck,
could you please change the word error
to other word in
.filter
, .what
, and .where
.translate_condition_ms2nl
, .translate_condition_ms2prec
, .translate_condition_peak_mz
, and .translate_filter_mz_value
Thanks for your review @jianhong ! Below I address your points - I will add each point as a separate comment to avoid having a single very long comment.
[ ] NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.
I had a look at the mentioned for
loop at line 171, but could not come up with a (safe) and more efficient way using *apply
. I'm accessing two different variables mini
and maxi
within that loop, so I would anyway to loop over an index - and doing that using e.g. lapply
(lapply(seq_len(l), function ...
would IMHO not be more efficient - and also less readable. So, if you agree, I would like to keep the for
loop in that particular case. Note that I usually use vapply
whenever possible.
[ ] To avoid the NOTE: Avoid redundant 'stop' and 'warn' in signal conditions in BioCheck,
Thanks for the comment. It indeed would look ugly. I changed the wording from Syntax error to Wrong syntax.
code repetition:
repetition in .filter, .what, and .where
Thanks, that's a great suggestion! I've moved the respective code into a new .parse_query
function (that is called by .what
, .where
etc.
The changes are in this commit: https://github.com/rformassspectrometry/SpectraQL/commit/cf1dd9a7b843e34c7797af0cf76278e4cd86d550
code repetition:
repetition in .translate_condition_ms2nl, .translate_condition_ms2prec, .translate_condition_peak_mz, and .translate_filter_mz_value
Thanks for spotting this! I've created two new helper functions to reduce the repeated code.
The changes are in this commit: https://github.com/rformassspectrometry/SpectraQL/commit/49f4b1e72fc8816db42600696bdfab6c5d3e3a5e
Note: Vignette installation section should be formatted as source code.
Also done.
Changes are in this commit: https://github.com/rformassspectrometry/SpectraQL/commit/f4bbe03f7eeb3db99545542940496c9cc53e1f5a
Received a valid push on git.bioconductor.org; starting a build for commit id: f4bbe03f7eeb3db99545542940496c9cc53e1f5a
Changes have now all been pushed to BioC too. Thanks again for the review @jianhong ! Looking forward to the second round of review.
Dear Package contributor,
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Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): SpectraQL_0.99.3.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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