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SAFEclustering #810

Closed yycunc closed 6 years ago

yycunc commented 6 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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bioc-issue-bot commented 6 years ago

Hi @yycunc

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: SAFEclustering
Type: Package
Title: SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
Version: 0.99.0
Authors@R: c(person("Yuchen", "Yang", email = "yangyuchensysu@gmail.com", role = c("aut", "cre")),
   person("Ruth", "Huh", email = "rhuh@live.unc.edu", role = c("aut")),
   person("Yun", "Li", email = "yunli@med.unc.edu", role = c("aut")))
Maintainer: Yuchen Yang <yangyuchensysu@gmail.com>
Description: SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data
Depends: R (>= 3.4.4)
License: GPL-3
Imports: ADPclust, Matrix, Rtsne, SAVER, SC3, Seurat, e1071, SingleCellExperiment, SummarizedExperiment, parallel, S4Vectors, doParallel, doRNG, foreach, methods, bit64, cidr, dplyr, stringr, utils, graphics, stats
Suggests: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
VignetteBuilder: knitr
biocViews: Software, Clustering, Classification, SingleCell, Transcription, GUI, RNASeq, Transcriptomics
bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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.

bioc-issue-bot commented 6 years ago

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.

nturaga commented 6 years ago

Hi @yycunc

Please make sure that your package build report is clean. That means, no errors, no warnings, and as few notes as possible.

I can review it once it's a clean build.

yycunc commented 6 years ago

Hi Nitesh,

Sorry for the inconvenience. However, there is no error or warning in my code, when I did check and BiocCheck. I think the problem is that, my code requires two compiled C codes for computing. And these two programs need to be put into the working directory or define the exact directory where they are. So, there may be an error when you run the example without these two programs.

Do you have any ideas how to deal with such a case?

Thanks for your help!

Bests,

Yuchen

Yuchen Yang, Ph.D. Postdoctoral Fellow, Department of Genetics 5100 Genetic Medicine Building University of North Carolina at Chapel Hill 120 Mason Farm Road Chapel Hill, NC, 27599

On Jul 26, 2018, at 3:43 PM, Nitesh Turaga notifications@github.com wrote:

Hi @yycunc https://github.com/yycunc Please make sure that your package build report is clean. That means, no errors, no warnings, and as few notes as possible

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/810#issuecomment-408213024, or mute the thread https://github.com/notifications/unsubscribe-auth/Al90-cStAphsyBzJblDTL3xS9z_tnD7yks5uKhvpgaJpZM4VdJl8.

nturaga commented 6 years ago

Hi @yycunc

I have to point out, that by including third-party code the package maintainer assumes responsibility for maintenance of that code. Part of the maintenance responsibility includes keeping the code up to date as bug fixes and updates are released for the mainline third-party project.

Have you taken a look at the following two links?

https://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces

http://bioconductor.org/developers/package-guidelines/#ccode

It's not common to populate your package directory with the two folders(gpmetis_and_shmetis_for_Linux etc..) you have. C code usually lives in the src directory. The other issue is it seems like your package is supported on only two platforms.

Another point is, the build report shows

ERROR: dependencies 'SAVER', 'cidr' are not available for package 'SAFEclustering'
* removing 'C:/Users/pkgbuild/AppData/Local/Temp/RtmpyMZLJM/Rinst1e604bff4200/SAFEclustering'
In R CMD INSTALL

The packages cidr and SAVER are not available through CRAN or Bioconductor. This should not be the case.

@mtmorgan Do you have any more comments regarding this issue @yycunc is having?

Best,

Nitesh

yycunc commented 6 years ago

Hi Nitesh,

I have tried to compile the C code by command MAKEFLAGS="CFLAGS=-O3" R CMD SHLIB gpmetis.c, however, I met the error that the library used in gpmetis.c can not be found. Actually, there are many library required by this program.

include

include

include

include

include

include

include

include

include

include

include

include

include

I don’t know how to deal with this problem.

Thanks for your kindly help!

Bests,

Yuchen

Yuchen Yang, Ph.D. Postdoctoral Fellow, Department of Genetics 5100 Genetic Medicine Building University of North Carolina at Chapel Hill 120 Mason Farm Road Chapel Hill, NC, 27599

On Jul 27, 2018, at 11:21 AM, Nitesh Turaga notifications@github.com wrote:

Hi @yycunc https://github.com/yycunc I have to point out, that by including third-party code the package maintainer assumes responsibility for maintenance of that code. Part of the maintenance responsibility includes keeping the code up to date as bug fixes and updates are released for the mainline third-party project.

Have you taken a look at the following two links?

https://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces https://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces http://bioconductor.org/developers/package-guidelines/#ccode http://bioconductor.org/developers/package-guidelines/#ccode It's not common to populate your package directory with the two folders(gpmetis_and_shmetis_for_Linux etc..) you have. C code usually lives in the src directory. The other issue is it seems like your package is supported on only two platforms.

@mtmorgan https://github.com/mtmorgan Do you have any more comments regarding this issue @yycunc https://github.com/yycunc is having?

Best,

Nitesh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/810#issuecomment-408451573, or mute the thread https://github.com/notifications/unsubscribe-auth/Al90-UUho0yi2BHDdl2Eqql3iDFbx875ks5uKzAIgaJpZM4VdJl8.

mtmorgan commented 6 years ago

Let me interject here and say also that there seem to be two R packages (SAVER, cidr) that are not on CRAN or Bioconductor; these cannot be dependencies of your package. My feeling is that there is significant technical work that needs to be done before the package can be reviewed, and that the level of support you're asking of Nitesh is too much for the review process. I'd encourage you to close this issue and to work on the package further, perhaps through questions on the bioc-devel mailing list but also through independent effort at incorporating the library code and modifying your package to only use CRAN or Bioconductor functionality.

When your package is ready for review, then post a comment here asking to re-open the issue.