Closed qxdu closed 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
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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: "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.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 96205701f354d8245f3d1d70e477cc7effddd832
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push on git.bioconductor.org; starting a build for commit id: baf6f68a304124f03152c333d7a64b2e205dd656
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 69a2caedf035bebb895c403fb1e2bef17679bb12
Received a valid push on git.bioconductor.org; starting a build for commit id: 7e6d63ced4dbf50ba3689b13f900e530dddf69c3
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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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.
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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?
I'm also not sure why you are adding this to your Makefile.
https://github.com/Carla-Radames/Rhisat/blob/master/src/Makefile#L4
Received a valid push on git.bioconductor.org; starting a build for commit id: 7b9c028f9800f01b63b9c0c854faf94acad8db00
Received a valid push on git.bioconductor.org; starting a build for commit id: 0cd59b9143a5697dd4a5cf70d1f0161512f0fbac
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.
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.
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.
@nturaga I forgot to @ you in time. Sir can you see my new submission?
Elaborate the Description to be more like a paper abstract.
Is the email of the maintainer correct? The details of the maintainer in the vignette are different from that in the DESCRIPTION file.
contact:{wei-z14,w-zhang16}(at)mails.tsinghua.edu.cn
No usage of Bioconductor infrastructure at all.
ok
use system2
instead of system
in your call to the hisat library.
I've noticed that not every functionality of hisat is captured in this package. I've got some reservations about that.
hisat is very extensive and very little of the functionality is encapsulated in the package.
Overall, the package just allows the building of the index, adapter removal, and alignment.
ok
ok
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.
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.
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.
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
.
👋🏻 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
).
Thank you @csoneson for your valuable comments on this contribution.
I would appreciate it if @Carla-Radames would answer the questions posed here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7bc7492e2d43f0fdb544a043b1b0e1fa69f2cbe5
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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.
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 21a33af76c3e829bc4852ec61360c12ec698e9ec
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Your package has been built on Linux, Mac, and Windows.
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Remember: if you submitted your package after July 7th, 2020,
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Received a valid push on git.bioconductor.org; starting a build for commit id: 4dcfce6746c8b9e48e41aebcfe8136d3034a4ef2
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,
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@Carla-Radames please respond to the previously posted questions/concerns.
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: c54fee63c1524e2fc1a749dd3ea5c4cb16d1eb0b
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 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.
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.
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.
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.
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.
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