Closed xiaowenchenjax closed 5 years ago
Hi @xiaowenchenjax
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: epihet
Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Date: 2018-04-10
Version: 0.99.0
Authors@R: c(person("Xiaowen", "Chen", email = "Xiaowen.Chen@jax.org",
role = c("aut", "cre")),person("Haitham", "Ashoor",
role = c("aut")),person("Ryan", "Musich",
email = "rjmusich@gmail.com",role = c("aut")),
person("Jiahui","Wang",role = "aut"),person("Sheng", "Li", role = "aut"))
Description: epihet is an R-package that calculates the epigenetic
heterogeneity between cancer cells and/or normal cells. The functions
establish a pipeline that take in bisulfite sequencing data from multiple
samples and use the data to track similarities and differences in
epipolymorphism,proportion of discordantly methylated sequencing reads
(PDR),and Shannon entropy values at epialleles that are shared between
the samples.epihet can be used to perform analysis on the data by creating
pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be
created by calculating the differential heterogeneity of the samples.
And we construct co-epihet network and perform network analysis.
Depends:
R(>= 3.3),GenomicRanges, IRanges, S4Vectors,ggplot2,foreach,Rtsne,
igraph
License: Artistic-2.0
biocViews:
DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Imports:
data.table, doMC, EntropyExplorer, graphics, stats,
grDevices, pheatmap,Rcpp, utils, qvalue,
WGCNA, ReactomePA
LinkingTo: Rcpp
Maintainer: Xiaowen Chen <Xiaowen.Chen@jax.org>
Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut, cre],
Ryan Musich [aut, cre], Jiahui Wang [aut], Sheng Li [aut]
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr,clusterProfiler,doParallel,ggfortify,
rmarkdown
VignetteBuilder: knitr
BuildVignettes: TRUE
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IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.
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.
HI @xiaowenchenjax ,
Please try to fix all the ERRORs in the build report, and a technical review will be given shortly after the building is successfully. Let us know for any questions by commenting here. Thanks for your contribution to Bioconductor.
cheers, Qian
Hi @xiaowenchenjax ,
Please fix any error and warnings that shows in the build report. You can comment back here with any questions. Be sure to make efforts in fixing them by making commits and version bumps, which will trigger new build and shows here. Because the Bioconductor core team usually have a rule of 2 weeks for any new issue here, if no fixes, responses, or any efforts showing that you are working on it, the issue would be closed. But if you feel like you would not be available recently for the new package, you can let us know also, we'll close the issue, and you can always open it once have time.
Regards, Qian
Hi @xiaowenchenjax ,
I am closing this issue since no response within 2 weeks and the last notice. Please feel free to reopen it when you are more available. Thanks for your contribution to Bioconductor.
Best, Qian
There has been no progress on this issue for an extended period of time and therefore will be closed due to inactivity. You may reopen the issue when you feel you have the time to actively participate in the review/submission process. Please also keep in mind when a package is accepted to Bioconductor a level of active maintenance is expected.
Thank you for interest in Bioconductor.
I fixed the error in epihet package, please reopen it and check it. Thanks.
Hi @mtmorgan, I fixed the error in epihet package, please reopen it and check it. Thanks.
Hi @mtmorgan , I fixed the error in epihet package, please reopen it and check it. Thanks.
Hi @bioc-issue-bot , I fixed the error in epihet package, please reopen it and check it. Thanks.
Please ensure that the web hook is active and then increment the version number of your package in the DESCRIPTION file to 0.99.1, and push the commit to github.
Received a valid push; starting a build. Commits are:
a27955c Update DESCRIPTION
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: "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.
HI @bioc-issue-bot , I change the R dependency from 3.4 to 3.5, git ignore '.gitattributes', and delete set.seed function in diffHet() and epiTSNE() funtion.
did you remember to increment the version of your package, to 0.99.2? That is what the 'VERSION BUMP REQUIRED' tag means.
Received a valid push; starting a build. Commits are:
8400c1e Update DESCRIPTION
Hi @bioc-issue-bot Sorry about it. all set now
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: "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.
Hi @bioc-issue-bot , i already add ".gitattributes" to the .gitignore file this time, why build report also complain it. Could you give me some clue? THANK YOU VERY MUCH.
You can see, in a new clone, that .gitattributes is present in the repository
c02xd1anjgh6:NewPackages ma38727$ git clone https://github.com/TheJacksonLaboratory/epihet
Cloning into 'epihet'...
remote: Enumerating objects: 18, done.
remote: Counting objects: 100% (18/18), done.
remote: Compressing objects: 100% (15/15), done.
remote: Total 385 (delta 5), reused 6 (delta 2), pack-reused 367
Receiving objects: 100% (385/385), 4.47 MiB | 1.73 MiB/s, done.
Resolving deltas: 100% (113/113), done.
c02xd1anjgh6:NewPackages ma38727$ cd epihet/
c02xd1anjgh6:epihet ma38727$ ls -a
. .git DESCRIPTION R inst
.. .gitattributes NAMESPACE README.md man
.Rbuildignore .gitignore NEWS data vignettes
By adding it to .gitignore you've told git to ignore any revisions to it, but not to remove it. So
git rm .gitattributes
and then version bump & push.
Received a valid push; starting a build. Commits are:
1ea2099 Update DESCRIPTION
Hi @bioc-issue-bot , All set . Please build and check it. Thank you!
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.
@bioc-issue-bot , Thank you!
Hi @bioc-issue-bot , I have a question: after the package built without errors or warnings on all platforms, when i can find my package in Bioconductor? and what else i should do? Thank you.
please review the material in the link 'what to expect' appearing in an earlier comment.
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.
Hi @xiaowenchenjax ,
I will start looking at your package and give a technical review. You are expected to fix all issues from the building report (errors / warnings / notes to your best effort) and issues raised in the technical review. Please respond within 2 weeks for every comment I make here to keep this issue open. The last day for the new package acceptance is Wednesday Oct 24th to make the new Bioconductor release which happens on Oct 31st..
Let's try to have everything ready by that time to make the new release. But if we can not, the package will still go to the new Bioconductor devel which is Bioc 3.9.
Cheers, Qian
Hi @Liubuntu , It is great, thanks.
Hi @xiaowenchenjax ,
I have posted this review last Friday, but didn't know why it disappeared. So I am posting again. Sorry for the delay in my end. Please seek to address the below issues ASAP so that we can make the release. I'm glad to work together with you on that! Thank you!
Best, Qian
Refer here
Date
field.LazyData = true
. This rarely proves to be a good
thing. In our experience it only slows down the loading of packages
with large data.URL:
field for the relevant links to the GitHub
repository.BugReport:
. It is encouraged to include this field for
the relevant links to Github for reporting Issues.BiocManager
instead of
BiocInstaller
for downing the package. You should include
something like this:1. Download the package from Bioconductor.
{r getPackage, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pkgName")
Or install the development version of the package from Github.
{r, eval = FALSE}
BiocManager::install(“githubUserName/pkgname”)
2. Load the package into R session.
{r Load, message=FALSE}
library(pkgName)
Please add a table of contents for better organization. This could be easily specified in the header. check here: https://rmarkdown.rstudio.com/html_document_format.html.
Please add in the end of the vignette a section of SessionInfo
for your
vignette running environment. e.g.,
{r}
sessionInfo()
Function naming: Use camelCaps: initial lowercase, then alternate case between words.. Refer here. for "moduleanno", "modulesim", "modulevisual"...
Add some basic checks for the function arguments, since some are required to be specific class or having specific information as explained in "@param", e.g., "compMatrix(epi.gr, ...)", add something like:
stopifnot( is(epi.gr, "GRanges") )
Also check other scripts for similar issue. e.g., "diffHet(subtype, ...)", "epiBox(type, ...)", "epiMa(pval.matrix, )", "epiMap(annotate, )", "epiPCA(type, )", "epiTSNE(type, )", "modulevisual(value.matrix, )", "summarize(gr1, gr2, )", "userobj(data)", ...
vectorize your code. The following could be rewritten (diffHet.R:L53):
mean1.v = apply(val1.r, 1, mean)
mean2.v = apply(val2.r, 1, mean)
as:
mean1.v = rowMeans(val1.r)
mean2.v = rowMeans(val2.r)
Do not need to test twice for logical values (diffHet.R:L58): if (length(loci.filter)>0)
could be only: if (length(loci.filter))
. Also in "epinetwork.R":L166.
Avoid using of 1:...
, use seq_len()
or seq_along
instead.
Avoid sapply()
, use vapply()
instead.
Please use " <- " for assignment instead of "=".
typo: summarize.R: L4-5, should be "GenomicRanges".
#' background
#'
#' A data frame containing 31995 elements as background used for pathway
#' enrichment analysis:
#' @docType data
#' @keywords datasets
#' @name background
#' @rdname data
"background"
"datTraits"
## NEWS
- Looks good!
Hi @xiaowenchenjax ,
The final date to include new packages would be 10/24/2018, which is today. Since we are having some delay in the review, we can extend the date to be 10/26/2018, Friday. Please let me know if you have any questions about the review issues. Thanks!
Best, Qian
Hi @Liubuntu, I am sorry. i did not check it on time. i am working on it today. So I think i miss this release.
Hi @Liubuntu Could you tell me what time the next release?
The next release (Bioc 3.9) would be end of April, 2019. But anyway, when this package is accepted, it will be in the Bioc devel (https://www.bioconductor.org/developers/how-to/useDevel/), which is meant to have your package go through users' tests and easy to make updates during this period. This is usually encouraged for the new packages. After 6 months, the stable version of package will be included in the new release.
Hi @Liubuntu Ok, Thanks. i am working on it now.
HI @xiaowenchenjax ,
Please make sure to respond with any updates or fixes or questions within 2 weeks since your last comment, so that this issue will remain active. Thanks!
Best, Qian
Hi @Liubuntu , The updates already done. I want to build and check the modified package. But some dependencies fail to install in my R/3.5.1. It almost close. I will finish it as soon as possible. Thanks. Best, Xiaowen
Hi @Liubuntu I have updated my package, but i could check it using R/3.5.1 on our helix. it complain ">library(ggplot2) Error: package or namespace load failed for ‘ggplot2’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/gpfs/ctgs0/software/helix/R/3.5.1/lib64/R/library/Rcpp/libs/Rcpp.so': /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /gpfs/ctgs0/software/helix/R/3.5.1/lib64/R/library/Rcpp/libs/Rcpp.so)" because our package use ggplot2 package a lot. So could you help me check this package? Thanks a lot! Best, Xiaowen
Hi @xiaowenchenjax ,
I'll see if I can reproduce this error on my linux system and let you updated. Thanks!
Best, Qian
Hi @Liubuntu , Thanks. i can library ggplot2 on other versions of R. Best, Xiaowen
Hi @xiaowenchenjax ,
I have tried to build your package (before I do the check) but there are several issues you need to fix first:
GenomicRanges
instead of GenomicRaes
. Source code is in R/summarize.R
.
importFrom(GenomicRaes,findOverlaps)
importFrom(GenomicRaes,values)
BiocManager
instead of BioManager
.
BioManager::install("EpiHet")
Depends: R(>= 3.5.1)
For your question, could you try to first update.packages()
in your R session, and redo the library(ggplot2)
? And you can also check your package using devtools::check()
inside R, or R CMD build epihet
=> R CMD CHECK epihet_0.99.3.tar.gz
in terminal command line.
Let me know if this could be of any help and we can further discuss it. Thanks!
Best, Qian
Hi @Liubuntu , thank you for your suggestion. i will try it. Best, Xiaowen
Hi @Liubuntu , i had updated my package. Best, Xiaowen
HI @xiaowenchenjax ,
You need to bump version in DESCRIPTION
so that the changes could be caught and trigger a new build.
Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.
Best, Qian
Received a valid push; starting a build. Commits are:
e72cc95 Update DESCRIPTION
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: "ABNORMAL". 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.
Hi @Liubuntu Sorry about that. I am done
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.
Hi @Liubuntu , I would like to change my package name "epihet" to "EpiHet", to keep same with the manuscript which i want to submit some journal. Is it easy to change it? Thanks. Best, Xiaowen
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