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MotifPeeker
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/neurogenomics/MotifPeeker
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Hi @HDash
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:
Type: Package
Package: MotifPeeker
Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Version: 0.99.0
Authors@R: c(
person(given = "Hiranyamaya",
family = "Dash",
role = c("cre", "aut"),
email = "[email protected]",
comment = c(ORCID = "0009-0005-5514-505X")),
person(given = "Thomas",
family = "Roberts",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0009-0006-6244-8670")),
person(given = "Nathan",
family = "Skene",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-6807-3180"))
)
Description: MotifPeeker is used to compare and analyse datasets from
epigenomic profiling methods with motif enrichment as the key
benchmark. The package outputs an HTML report consisting of three
sections: (1. General Metrics) Overview of peaks-related general
metrics for the datasets (FRiP scores, peak widths and motif-summit
distances). (2. Known Motif Enrichment Analysis) Statistics for the
frequency of user-provided motifs enriched in the datasets. (3.
De-Novo Motif Enrichment Analysis) Statistics for the frequency of
de-novo discovered motifs enriched in the datasets and compared with
known motifs.
License: GPL (>= 3)
URL: https://github.com/neurogenomics/MotifPeeker
BugReports: https://github.com/neurogenomics/MotifPeeker/issues
Depends:
R (>= 4.4.0)
Imports:
BiocFileCache,
BiocParallel,
DT,
ggplot2,
plotly,
universalmotif,
GenomicRanges,
IRanges,
rtracklayer,
tools,
htmltools,
rmarkdown,
viridis,
SummarizedExperiment,
htmlwidgets,
Rsamtools,
GenomicAlignments,
GenomeInfoDb,
Biostrings,
BSgenome,
memes,
S4Vectors,
magrittr,
dplyr,
purrr,
tidyr,
heatmaply,
stats,
utils
Suggests:
BiocStyle,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38,
downloadthis,
knitr,
markdown,
methods,
remotes,
rworkflows,
testthat (>= 3.0.0),
withr,
emoji,
curl,
jsonlite
VignetteBuilder:
knitr
biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
MultipleComparison, FunctionalGenomics, MotifDiscovery,
SequenceMatching, Software, Alignment
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 7.3.2
SystemRequirements: MEME Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html>
Can you please update the vignette to have the code chunks that should not be executed directly be in backticks, brackets, with an eval=FALSE to be sure there is no mistakes or in case there is ever a change in how markdown code chunks are executed.
Hi @lshep, I have updated the README and vignettes to follow the {lang, eval = FALSE} convention for code chunks that should not be executed directly. Please let me know if there are any further adjustments needed.
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.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
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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.
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.
The following are build products from R CMD build on the Single Package Builder: 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
[email protected]:packages/MotifPeeker to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @HDash,
Can you write an INSTALL file for MEME suite? I will use this to perform the install on our build machines.
Hi @jwokaty, I have pushed an INSTALL file with the installation instructions for the system dependency.
Hi @HDash I'll take a look. Remember you should increment the version and also push to Bioconductor, which is generally part of the workflow whenever you update your package.
I will keep in mind the version bump point next time I make any changes. As for the INSTALL file, I can confirm pushing it to Bioconductor. Thank you for your time accommodating the system dependency.
Hi @HDash we had some discussion about WSL as we don't currently have it enabled on the windows builders and have decided not to enable for the time being as it's not clear what the impact will be. You may want to consider allowing your package to fail gracefully if Meme suite isn't installed or for Windows, adding a .BBSoptions at the top level with UnsupportedPlatforms: win to skip the windows builders. I'll work on installing MEME suite by tomorrow so we may not see the results until next week. I'll kick off a build for MotifPeeker when it's installed.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: 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
[email protected]:packages/MotifPeeker 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: 834b0917e082ce2e15f50fa0d4233d7344547a2b
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: 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
[email protected]:packages/MotifPeeker to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I have pushed .BBSoptions with a version bump. Thank you for your time setting up the MEME suite; I will keep an eye out for the manual build.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: 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
[email protected]:packages/MotifPeeker to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
We installed the meme suite and it is found when we test manually but it seems to not be picked up when we build through the single package builder. It will involve some more investigation on our part
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): MotifPeeker_0.99.1.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
[email protected]:packages/MotifPeeker to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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 Single Package Builder: macOS 12.7.1 Monterey: MotifPeeker_0.99.1.tar.gz Linux (Ubuntu 22.04.3 LTS): MotifPeeker_0.99.1.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
[email protected]:packages/MotifPeeker to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@HDash I figured out the issue. The most recent report above builds the package on Linux and Mac but has some other errors you can now address since it's finding MEME suite.
Hello @lshep / @jwokaty, thank you for getting the MEME suite to work. Unfortunately, I spot many erroneous errors or warnings popping up in the build log, where the traceback is not helpful. For instance-
- Packages listed under
Importsbut missing-S4Vectors,universalmotif,GenomicRangesandIRanges - Packages not referenced in code but throw an error because they are missing-
BiocGenerics,Biobase,XVectorandzlibbioc utils::sessionInfo()(best guess) fails for no apparent reason (Mac runner only)
Apparently, different packages are missing depending on the builder platform; not sure why. Other errors and warnings also seem to be platform-specific.
The package passes builds and checks without any errors or warnings when run on my local machine and a Linux Docker container-
FROM --platform=linux/amd64 bioconductor/bioconductor_docker:devel
ENV MEME_VERSION=5.5.5
RUN wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz && \
tar zxf meme-$MEME_VERSION.tar.gz && \
cd meme-$MEME_VERSION && \
./configure --prefix=/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt && \
make && \
make install && \
cd .. && \
rm -rf meme-$MEME_VERSION meme-$MEME_VERSION.tar.gz
RUN yes | sudo cpan install XML::Parser
ENV MEME_BIN=/meme/bin
ENV PATH="$PATH:/meme/bin:/meme/libexec/meme-$MEME_VERSION"
The build product from macOS 12.7.1 Monterey Single Package Builder also passes checks with no errors or warnings when run with devtools::check_built().
I am unsure why 10s of errors and warnings like these are popping up on Bioconductor builders. I wonder if the MEME suite setup has to do anything with this?
This might just be bad timing as the daily builds just started during that reports run. I've kicked another build, which is looking better. The report should appear in a bit.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "TIMEOUT, 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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): MotifPeeker_0.99.1.tar.gz macOS 12.7.1 Monterey: MotifPeeker_0.99.1.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
[email protected]:packages/MotifPeeker 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: 40040b004f7c03b6675831bae9ca0f98b94e4606
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "WARNINGS, TIMEOUT". 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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): MotifPeeker_0.99.2.tar.gz macOS 12.7.1 Monterey: MotifPeeker_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
[email protected]:packages/MotifPeeker 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: ee2e9d21bb3b8d60254058f10e4eee33e294e15c
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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 Single Package Builder: macOS 12.7.1 Monterey: MotifPeeker_0.99.3.tar.gz Linux (Ubuntu 22.04.3 LTS): MotifPeeker_0.99.3.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
[email protected]:packages/MotifPeeker 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: 9a1eb4aab140a9686d3964d1a9f8d70fe9521ae2
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: macOS 12.7.1 Monterey: MotifPeeker_0.99.4.tar.gz Linux (Ubuntu 22.04.3 LTS): MotifPeeker_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
[email protected]:packages/MotifPeeker to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hello @jwokaty / @lshep, I can confirm that the MEME suite has been installed and is functioning as expected. I successfully managed to get my package to build and check without errors or warnings. Thank you for your time again!
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.