Closed mcneilllucy closed 3 years ago
Hi @mcneilllucy
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The DESCRIPTION file for this package is:
Package: synapsis
Type: Package
Title: An R package to automate the analysis of double-strand break repair during meiosis
Version: 0.99.0
Authors@R:
c(person(given = "Lucy",
family = "McNeill",
role = c("aut", "cre", "cph"),
email = "luc.mcneill@gmail.com",
comment = c(ORCID = "0000-0003-1752-4882")),
person(given = "Wayne",
family = "Crismani",
role = c("rev", "ctb"),
comment = c(ORCID = "0000-0003-0143-8293")))
Description: Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.
biocViews: Software, SingleCell
Depends:
R (>= 4.1)
Imports: EBImage, stats, utils, graphics
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0),
ggplot2,
tidyverse
Config/testthat/edition: 3
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This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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The vignette is very interesting but formatted oddly. When using markdown outline format, the section titles do not need to include numbers "1.", "2.", letters "a.", "b." and so forth. If you are already cross-referencing using letters please read up on markdown to standardize the approach. This is optional but will make for a more attractive vignette.
The auto_crop_fast function is chatty:
> path = paste0(system.file("extdata",package = "synapsis"))
> path
[1] "/home/stvjc/R-4-1-dist/lib/R/library/synapsis/extdata"
> auto_crop_fast(path, annotation = "on", max_cell_area = 30000, min_cell_area = 7000, file_ext = "tif")
function (description = "", open = "", blocking = TRUE, encoding = getOption("encoding"),
raw = FALSE, method = getOption("url.method", "default"))
{
.Internal(file(description, open, blocking, encoding, method,
raw))
}
<bytecode: 0x55706f857dc0>
<environment: namespace:base>
displaying enhanced image of cell channel
here is the mask
displaying the retained cells in mask (correct size/ shape)[1] "couldn't crop it since cell is on the edge. Neglected the following mask of a cell candidate:"
[1] "from the file:"
[1] "MLH3rabbit488_SYCP3mouse594_fancm_fvb_x_fancm_bl6_724++_slide01_006"
[1] "I cropped this cell:"
[1] "using this mask"
[1] "whose cell number is"
[1] 2
[1] 1
out of 1 images, we got 1 viable cells
Warning messages:
1: In dir.create(paste0(path_out, "/crops")) :
'/home/stvjc/R-4-1-dist/lib/R/library/synapsis/extdata/crops' already exists
2: In dir.create(paste0(path_out, "/crops-RGB")) :
'/home/stvjc/R-4-1-dist/lib/R/library/synapsis/extdata/crops-RGB' already exists
You should be able to control the verbosity of the function operation.
I found it strange that the example does not seem to work:
> example(auto_crop_fast)
at_cr_> demo_path = paste0(system.file("extdata",package = "synapsis"))
at_cr_> auto_crop_fast(demo_path, annotation = "on", max_cell_area = 30000,
at_cr_+ min_cell_area = 7000)
[1] 0
out of 0 images, we got 0 viable cells
Warning messages:
1: In dir.create(paste0(path_out, "/crops")) :
'/Users/vincentcarey/R-4-1-dist/lib/R/library/synapsis/extdata/crops' already exists
2: In dir.create(paste0(path_out, "/crops-RGB")) :
'/Users/vincentcarey/R-4-1-dist/lib/R/library/synapsis/extdata/crops-RGB' already exists
Please comment on your ability to address these concerns by the deadline. I think it is a very nice package but a bit of work would make it much more user-friendly.
Hi Vince, thanks very much for your feedback. I can fix these three issues before the weekend. Just to check- is the deadline Monday Oct 11? Or is it a couple of days before to allow you some time to run it again etc.?
Monday (actually Tuesday as it is a US holiday) is the deadline for changes to packages in Bioc version 3.13. The main deadlines for you, a 3.14 contributor, are Wednesday 13 October (no more API changes) and 22 October (must pass R CMD check).
On Thu, Oct 7, 2021 at 12:55 AM Lucy McNeill @.***> wrote:
Hi Vince, thanks very much for your feedback. I can fix these three issues before the weekend. Just to check- is the deadline Monday Oct 11? Or is it a couple of days before to allow you some time to run it again etc.?
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Great, thanks. I've removed the manually labelled section titles and example(auto_crop_fast) works now. I triggered a new build but I might keep thinking about successfully muting
function (description = "", open = "", blocking = TRUE, encoding = getOption("encoding"), raw = FALSE, method = getOption("url.method", "default")) { .Internal(file(description, open, blocking, encoding, method, raw)) } <bytecode: 0x55706f857dc0>
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
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Received a valid push on git.bioconductor.org; starting a build for commit id: da9cbae9bfb9fa73ab09502d8d2523873e59dff5
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BiocManager should not be in Imports field. I am not going to delay acceptance on this.
I will accept the package. But please make some improvements. The vignette does not say anything about the scientific purpose of the package and the tasks discussed. Please add introductory material and a reference as appropriate. The conclusion of the vignette is very terse.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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