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(inactive) Rhisat #2426

Closed qxdu closed 2 years ago

qxdu commented 2 years ago

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

Confirm the following by editing each check box to '[x]'

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For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 2 years ago

Hi @Carla-Radames

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: Rhisat
Type: Package
Title: An R Wrapper for Hisat and AdapterRemoval
Version: 0.99.0
Date: 2021-10-31
Author: Zheng Wei, Qixiu Du
Maintainer: Qixiu Du <dqx18@mails.tsinghua.edu.cn>
Description: This package provides an R wrapper of the popular hisat sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging.
License: GPL (>= 3)
Depends: R (>= 3.5)
Encoding: UTF-8
Suggests: knitr
SystemRequirements: C++11, GNU make
Archs: x64
RoxygenNote: 7.1.2
biocViews: Sequencing, Alignment, Preprocessing
VignetteBuilder: knitr
git_url: https://github.com/Carla-Radames/Rhisat.git
git_branch: RELEASE_3_13
git_last_commit: f15bc6e
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: yes
Packaged: 2021-10-27 03:36:40 UTC; qxdu
bioc-issue-bot commented 2 years ago

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IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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bioc-issue-bot commented 2 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: "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. 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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 96205701f354d8245f3d1d70e477cc7effddd832

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 015e53ecd887886a24474588a1ffdaf891879a18

bioc-issue-bot commented 2 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: "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. 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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: baf6f68a304124f03152c333d7a64b2e205dd656

bioc-issue-bot commented 2 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: "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. 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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 69a2caedf035bebb895c403fb1e2bef17679bb12

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7e6d63ced4dbf50ba3689b13f900e530dddf69c3

bioc-issue-bot commented 2 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: "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. 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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 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: "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. 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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: dfbe28efa89da80bb462207aa438c61351110ac9

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

nturaga commented 2 years ago

Hi @Carla-Radames

I cannot seem to build and install your package locally on my Mac (Intel x86)

R CMD build Rhisat 

I've truncated the error, but it looks like this...

   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:511:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:179:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:649:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/initializer_list:46:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:37:
   ./version:1:1: error: expected unqualified-id
   0.1.6-beta
   ^
   ...
      0.1.6-beta
   ^
   In file included from tinythread.cpp:25:
   In file included from ./tinythread.h:87:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:139:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:199:
   ./version:1:1: error: expected unqualified-id
   0.1.6-beta
   ^
   In file included from tinythread.cpp:25:
   In file included from ./tinythread.h:87:
   In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:142:
   ./version:1:1: error: expected unqualified-id
   0.1.6-beta
   ^
   fatal error: too many errors emitted, stopping now [-ferror-limit=]
   20 errors generated.
   make[1]: *** [hisat-inspect-s] Error 1
   make: *** [all] Error 2
   ERROR: compilation failed for package ‘Rhisat’
─  removing ‘/private/var/folders/1w/xf7rrsr1483d4rg7vwbkdy780000gp/T/Rtmpgvgqrm/Rinst105d92834588a/Rhisat’
         -----------------------------------
   ERROR: package installation failed
Error in (function (command = NULL, args = character(), error_on_status = TRUE,  :
  System command 'R' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occurred

I run into this issue and I'm unable to figure out the issue. It seems it's only happening with your Rhisat package on my machine and not other packages which have Rcpp code in them.

Any suggestions?

nturaga commented 2 years ago

I'm also not sure why you are adding this to your Makefile.

https://github.com/Carla-Radames/Rhisat/blob/master/src/Makefile#L4

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7b9c028f9800f01b63b9c0c854faf94acad8db00

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0cd59b9143a5697dd4a5cf70d1f0161512f0fbac

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

qxdu commented 2 years ago

Thank you sir. I have made some corrections for the package, I would be grateful if you could check it again. For the first error, it may because I named a file "VERSION", maybe it cause some conflicts , now I have renamed it as "HISAT_VERSION". For https://github.com/Carla-Radames/Rhisat/blob/master/src/Makefile#L4 , This line I wrote is to refer to the format of other R packages. I found that maybe it could be commented. Sorry for not being able to reply you in time, I have submitted another edition.

qxdu commented 2 years ago

@nturaga I forgot to @ you in time. Sir can you see my new submission?

nturaga commented 2 years ago

Review

DESCRIPTION

NAMESPACE

ok

NEWS

R

inst

man

ok

tests

vignettes

ok

nturaga commented 2 years ago

We are also not sure the licensing is handled properly for AdapterRemoval (something would need to be in the package root folder); likely the same for hisat itself.

The way the vignette does a replication of the help text for the binaries is not very useful. The vignette is mostly consumed by replication of help text from the utilities, it makes one wonder exactly what is being added by wrapping in R and submitting to Bioconductor?

Please explain to the reviewers the logic behind the design. It would also be helpful to do this in the vignette.

Take a look at Rsubread package as an example of a package solving a related problem.

qxdu commented 2 years ago

We are also not sure the licensing is handled properly for AdapterRemoval (something would need to be in the package root folder); likely the same for hisat itself.

The way the vignette does a replication of the help text for the binaries is not very useful. The vignette is mostly consumed by replication of help text from the utilities, it makes one wonder exactly what is being added by wrapping in R and submitting to Bioconductor?

Please explain to the reviewers the logic behind the design. It would also be helpful to do this in the vignette.

Take a look at Rsubread package as an example of a package solving a related problem.

dear Nitesh, thanks for your kind reminder. I am fixing it now and modifying it with reference to your suggestion. And It will be resubmitted in the next or two week.

nturaga commented 2 years ago

Hi,

It’s not just the vignette. There are other issues with this package as well.

The other big issue is you don’t have “any” usage of existing Bioconductor packages to make it interoperable with the larger package ecosystem we provide. Please address this concern as pointed out in the documentation here - http://contributions.bioconductor.org/description.html#depends-imports-suggests-enhances.

I’m trying to understand if you’ve contacted the hisat authors and had any input from them regarding your package? If I were you, I’d contact them and see if they have any valuable suggestions on the package and it’s functionality.

Best,

Nitesh

On Jan 22, 2022, at 10:18 AM, Qixiu Du @.***> wrote:

We are also not sure the licensing is handled properly for AdapterRemoval (something would need to be in the package root folder); likely the same for hisat itself.

The way the vignette does a replication of the help text for the binaries is not very useful. The vignette is mostly consumed by replication of help text from the utilities, it makes one wonder exactly what is being added by wrapping in R and submitting to Bioconductor?

Please explain to the reviewers the logic behind the design. It would also be helpful to do this in the vignette.

Take a look at Rsubread package as an example of a package solving a related problem.

dear Nitesh, thanks for your kind reminder. I am fixing it now and modifying it with reference to your suggestion. And It will be resubmitted in the next or two week.

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you were mentioned.

nturaga commented 2 years ago

There is also a Rhisat2 package in Bioconductor. https://bioconductor.org/packages/release/bioc/html/Rhisat2.html

Please note the differences as well between what you are submitting and Rhisat2.

csoneson commented 2 years ago

👋🏻 Rhisat2 developer here. I don't think this is a duplicate (since the underlying hisat and hisat2 are different software packages), but note that the developers of hisat explicitly recommend that users switch to hisat2.

The other thing I was wondering about is the inclusion of adapterremoval. This seems to be already wrapped in the Rbowtie2 package, and the collection of files (as well as the version) look the same. Does it need to be included here as well? Btw, it looks like the version_info.cpp file was accidentally copied from Rbowtie2 (it refers to the version of bowtie2, but not of hisat).

nturaga commented 2 years ago

Thank you @csoneson for your valuable comments on this contribution.

I would appreciate it if @Carla-Radames would answer the questions posed here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7bc7492e2d43f0fdb544a043b1b0e1fa69f2cbe5

bioc-issue-bot commented 2 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: "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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 86b116a6bcd539d77d0eb17a9d1513acd37e5f41

bioc-issue-bot commented 2 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: "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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a29c294d9346053ce0cb8925062d9c6f3e041873

bioc-issue-bot commented 2 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: "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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cccd3af47fdf1bd92dec32df83cfba03fd15e2b4

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 21a33af76c3e829bc4852ec61360c12ec698e9ec

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4dcfce6746c8b9e48e41aebcfe8136d3034a4ef2

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 2 years ago

@Carla-Radames please respond to the previously posted questions/concerns.

qxdu commented 2 years ago

Thank you @csoneson for your valuable comments on this contribution.

I would appreciate it if @Carla-Radames would answer the questions posed here.

Thank you sir. Sorry for not being able to answer you in time. I have been busy with my graduation thesis, and also not able to get the advice from the author of Hisat. I have fixed major problems, including your advice on tests file, functionality and so on. But I haven't added the User-guide file. I have check the Rbowtie2 and sure that I should remove AdapterRemoval. But I could only fix the last 2 bugs only in this weekend. All the other bugs have been fixed.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c54fee63c1524e2fc1a749dd3ea5c4cb16d1eb0b

bioc-issue-bot commented 2 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.

Congratulations! The package built without errors or warnings on all platforms.

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/Rhisat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

qxdu commented 2 years ago

@nturaga I forgot to @ you before. I have fixed the problem you said. But about vignettes, I'm little bit not sure because I only wrap the Hisat package as a R format, without new functions added. I've emailed the author of hisat asking for suggestions, but still haven't gotten any response so far. Therefore I did not extend new functionality. Thanks for your kindness.

nturaga commented 2 years ago

Thanks for your reply. I'm specifically looking for answers to the questions posted by @csoneson, and it seems like they have not been answered to the degree I would like.

Good luck with your thesis. We can wait till you have more time to respond.

bioc-issue-bot commented 2 years ago

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.

bioc-issue-bot commented 2 years ago

Dear @Carla-Radames ,

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.

nturaga commented 2 years ago

Hi @Carla-Radames ,

I'm guessing your package will be inactive for a while? Please confirm and I'll close the issue. You can always reopen later.

There is no point leaving it open.