Closed seriph78 closed 2 years ago
Hi @seriph78
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: COTAN
Type: Package
Title: COexpression Tables ANalysis
Version: 0.99.0
Authors@R: c(
person("Galfrè", "Silvia Giulia",email = "silvia.galfre@uniroma1.it", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
person("Morandin","Francesco", email = "francesco.morandin@unipr.it", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
Description: Statistical and computational method to analyze the co-expression of
gene pairs at single cell level. It provides the foundation for single-cell gene
interactome analysis. The basic idea is studying the zero UMI counts’ distribution
instead of focusing on positive counts; this is done with a generalized contingency
tables framework. COTAN can effectively assess the correlated or anti-correlated
expression of gene pairs. It provides a numerical index related to the correlation and an
approximate p-value for the associated independence test. COTAN can also evaluate whether
single genes are differentially expressed, scoring them with a newly defined global
differentiation index. Moreover, this approach provides ways to plot and cluster genes
according to their co-expression pattern with other genes, effectively helping the study
of gene interactions and becoming a new tool to identify cell-identity marker genes.
URL: https://github.com/seriph78/COTAN
BugReports: https://github.com/seriph78/COTAN/issues
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Imports:
dplyr,
methods,
grDevices,
Matrix,
ggplot2,
ggrepel,
stats,
parallel,
tibble,
tidyr,
basilisk,
reticulate,
ComplexHeatmap,
circlize,
grid,
scales,
utils,
rlang
Suggests:
testthat (>= 3.0.0),
spelling,
knitr,
data.table,
rmarkdown,
R.utils,
tidyverse,
htmlwidgets,
MASS,
factoextra,
Rtsne,
plotly,
dendextend,
cowplot
Config/testthat/edition: 3
SystemRequirements:
python
Language: en-US
biocViews:
SystemsBiology,
Transcriptomics,
GeneExpression,
SingleCell
VignetteBuilder: knitr
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
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: 70c9b2244bb581b761749467b8b1575e921b09f5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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. This link will be 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/COTAN
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: dabf4893cc6c9f521e5d1dcddc64e207701bc45e
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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. This link will be 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/COTAN
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: 51f98b71b76c7e5dd70fefc699127deac467eb21
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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. This link will be 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/COTAN
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: 4dc2955fb171fb37fe7d922abed6708a5ba839f4
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS, 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. This link will be 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/COTAN
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi, I'm trying to fix my release on the Windows server. Last push gives me this error
Windows Server 2019 Standard/x64 WARNINGS ERROR OK OK
but when I check the details I found:
Error: Your current architecture is 32bit; however, this version of Python was compiled for 64bit. Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
I'm missing something or the problem is not my package but the installation of windows server? Because, from what I understood from the first line the machine is a x64 architecture but python is compiled for a x32... am I wrong?
The warning was one Warning: file 'COTAN/configure' did not have execute permissions: corrected
So I think that I just need to wait...
Thanks in advance for the help
Received a valid push on git.bioconductor.org; starting a build for commit id: cd6bda73f7991fb8b7886e8747b10c7248cde328
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
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: 769d1d39ba25e804d6b19c69f1eac9b6d23f8c6a
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @nturaga ,
I modified the permissions on my server and it looks fine... -rwxrwxr-x 1 seriph seriph 70 lug 4 17:15 configure -rwxrwxr-x 1 seriph seriph 87 lug 4 17:15 configure.win
Where do you think still the problem?
Best regards
Hi,
Please take a closer look at the build reports you have. There are several NOTE issues that need to be addressed
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
COTAN_main.R (line 70, column 31)
COTAN_main.R (line 71, column 31)
COTAN_main.R (line 74, column 31)
COTAN_main.R (line 213, column 25)
COTAN_main.R (line 930, column 38)
COTAN_main.R (line 997, column 37)
COTAN_main.R (line 1222, column 60)
internal_functions.R (line 201, column 50)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/Rtmplxkda9/file52edf720a03ff/COTAN/R/COTAN_main.R (line
1384, column 24)
/tmp/Rtmplxkda9/file52edf720a03ff/COTAN/R/internal_functions.R
(line 343, column 24)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/tmp/Rtmplxkda9/file52edf720a03ff/COTAN/R/COTAN_main.R (line
433, column 28)
/tmp/Rtmplxkda9/file52edf720a03ff/COTAN/R/COTAN_main.R (line
1360, column 24)
/tmp/Rtmplxkda9/file52edf720a03ff/COTAN/R/COTAN_main.R (line
1384, column 30)
/tmp/Rtmplxkda9/file52edf720a03ff/COTAN/R/internal_functions.R
(line 343, column 30)
and
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/get.expected.ct.Rd
Found @ in man/get.gene.coexpression.space.Rd
Found @ in man/get.observed.ct.Rd
Found @ in vignettes/Guided_tutorial.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
Although these are NOTE messages and not WARNING or ERROR, they are still important.
Please fix and issue a new build report. We are looking into the Windows issue you have encountered, it is most likely identified already. Please try again.
Received a valid push on git.bioconductor.org; starting a build for commit id: b6fba2a38c603d04609edcd90f91fc51aadb5207
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
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: 3d050ffd6560283ec635f0a311294f26b502b04e
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
All notes are fixed. Now only the warning regarding the execute permissions for the configure file remains .
Dear @nturaga do I have to built another version to consider the last warning? As already mention, it does not seems to be a package problem but a problem regarding the windows compiler.... I think...
Yes. Please.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7ea9d488addf651e5641052771ced4125009c151
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @nturaga I fixed everything except the warning: "file 'COTAN/configure' did not have execute permissions" that I don't think depend on my code... Is it now ok?
Best regards
Hi @seriph78 Yes, this is much better. I will review your package now.
Best
General comments: Please note the release schedule that is posted here -\ http://bioconductor.org/developers/release-schedule/.
We'll try to get your package in before that.
ok
ok
ok
NOTE: Use donttest{} instead of dontrun{}.
Remove commented out code.
Use <-
for assignment and not =
.
@seriph78 may we expect to see updates soon? We like to see progress and response to review within 3-4 weeks.
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.
Sorry. Now I will have time to work on it again... Posting here automatically reopen the issue or I should create a new issue?
Dear @seriph78 ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
Perfect. Thanks!
Received a valid push on git.bioconductor.org; starting a build for commit id: 27234e7a79944604aaa843ccb62bb66e5124d963
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". 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. This link will be 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/COTAN
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi, as usual there is "Warning: file 'COTAN/configure' did not have execute permissions: corrected" also if the file already has the right permissions,
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
Sorry, may be I missed something I don't see COTAN anywhere in Bioconductor website. Do I need to do something?
I will be running the processing script for accepted packages this afternoon. Once that occurs, it should appear in devel within 24-48 hours.
The master branch of your GitHub repository has been added to Bioconductor's git repository.
To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/seriph78.keys is not empty), then no further steps are required. Otherwise, do the following:
See further instructions at
https://bioconductor.org/developers/how-to/git/
for working with this repository. See especially
https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
to keep your GitHub and Bioconductor repositories in sync.
Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at
https://bioconductor.org/checkResults/
(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("COTAN")
. The package 'landing page' will be created at
https://bioconductor.org/packages/COTAN
If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.
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