Closed MarkusMuck closed 10 months ago
Hi @MarkusMuck
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: peakCombiner
Title: The R package to curate and merge enriched genomic regions into consensus peak sets
Version: 0.99.0
Description: peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.
Authors@R: c(person("Markus", "Muckenhuber",
email = "markusmuckenhuber@gmx.at",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-1897-2329")),
person("Kathleen", "Sprouffske",
email = "",
role = c("aut"),
comment = c(ORCID = "0000-0001-7081-2598")),
person("Michael", "Stadler",
email = "",
role = c("aut"),
comment = c(ORCID = "0000-0002-2269-4934")))
Depends: R (>= 4.2)
License: MIT + file LICENSE
LazyData: FALSE
biocViews:
WorkflowStep,
Preprocessing,
ChipOnChip
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests:
testthat (>= 3.0.0),
rmarkdown,
styler,
cli,
lintr,
rtracklayer,
knitr,
devtools,
qpdf
DEPENDS:
dplyr (>= 1.1.2),
GenomicRanges
Imports:
stringr,
tidyr,
purrr (>= 1.0.1),
readr (>= 2.1.2),
tibble (>= 3.2.1),
stats,
IRanges,
rlang
URL:
BugReports:
Config/testthat/edition: 3
VignetteBuilder: knitr
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 Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: ERROR before build products produced.
Links above 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/peakCombiner
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I am seeing
> ## ----eval=TRUE----------------------------------------------------------------
> prepare_input_regions(
+ data = sample_sheet,
+ show_messages .... [TRUNCATED]
Error in `load_input_regions()` at peakCombiner/R/prepare_input_regions.R:249:4:
→ `data` contains column with name 'file_path'.
✖ At least one file does not exist.
Run `rlang::last_trace()` to see where the error occurred.
Enter a frame number, or 0 to exit
1: source("peakCombiner.R", echo = TRUE)
2: withVisible(eval(ei, envir))
3: eval(ei, envir)
4: eval(ei, envir)
5: peakCombiner.R#120: prepare_input_regions(data = sample_sheet, show_message
6: prepare_input_regions.R#249: load_input_regions(data = data)
7: prepare_input_regions_helper.R#142: cli::cli_abort(c(`>` = "`data` contains
8
please repair and note here.
Also I saw
Warning message:
In .merge_two_Seqinfo_objects(x, y) :
Each of the 2 combined objects has sequence levels not in the other:
- in 'x': chr42, chr4 2, chr4-2, chr4?2, chr4|2, Chr2
- in 'y': chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY
Make sure to always combine/compare objects based on the same reference
genome (use suppressWarnings() to suppress this warning).
on ending the session in which I try to source vignette code.
I am seeing
> ## ----eval=TRUE---------------------------------------------------------------- > prepare_input_regions( + data = sample_sheet, + show_messages .... [TRUNCATED] Error in `load_input_regions()` at peakCombiner/R/prepare_input_regions.R:249:4: → `data` contains column with name 'file_path'. ✖ At least one file does not exist. Run `rlang::last_trace()` to see where the error occurred. Enter a frame number, or 0 to exit 1: source("peakCombiner.R", echo = TRUE) 2: withVisible(eval(ei, envir)) 3: eval(ei, envir) 4: eval(ei, envir) 5: peakCombiner.R#120: prepare_input_regions(data = sample_sheet, show_message 6: prepare_input_regions.R#249: load_input_regions(data = data) 7: prepare_input_regions_helper.R#142: cli::cli_abort(c(`>` = "`data` contains 8
please repair and note here.
Hi, I fixed that error in the github repo and updated it there. I am currently working to push the bioconductor repo to trigger a new build.
Also I saw
Warning message: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other: - in 'x': chr42, chr4 2, chr4-2, chr4?2, chr4|2, Chr2 - in 'y': chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY Make sure to always combine/compare objects based on the same reference genome (use suppressWarnings() to suppress this warning).
on ending the session in which I try to source vignette code.
We described this message in the documentation and the vignette. It is an expected message to occur and does not impact the results.
Cause: We use blacklisted genomic regions from ENCODE to remove in a filtering operation any overlaps between blacklisted regions and the users input files. Therefore we use the IRanges::subsetByOverlaps function, which creates this message. The ENCODE lists do have pre-defined sequence levels (chromosome names) with which we do not want to interfere. It is expected to find entries NOT occurring in both, the blacklist and the user-defined input data files. For example, non-classical chromosome names like "chr11_KI270721v1_random" might be still in the input data.
Solutions: We decided of the release, not to use the suggested function (suppressWarnings()) to hide the message. Our aim is to keep the package as transparent as possible. We explain that this message can occur and it is not unexpected but has no impact on your downstream processing.
I hope that is helpful. We are open to implement feedback to this point. Thanks
Received a valid push on git.bioconductor.org; starting a build for commit id: d241c8421d98c691de04aa8d73d469bc6402bdc8
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: ERROR before build products produced.
Links above 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/peakCombiner
to trigger a new build.
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: cfe7cc3ca5a673af855843968cca09ad9b14d096
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): peakCombiner_0.99.4.tar.gz macOS 12.6.5 Monterey: peakCombiner_0.99.4.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
git@git.bioconductor.org:packages/peakCombiner
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
combpeaksr does not appear to be a package in CRAN or Bioconductor. All package dependencies must be on CRAN or Bioconductor or cannot be used. Please update the package to not use combpeaksr.
@MarkusMuck do you plan on updating the package?
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
Thank you for your interest in Bioconductor.
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