hicrep

[TaoYang-dev]

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

• Repository: https://github.com/MonkeyLB/hicrep

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

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

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• [x] The 'devel' branch for new packages and features.
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For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @MonkeyLB

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: hicrep
Title: Measuring the reproducibility of Hi-C data
Version: 0.99.0
Authors@R: person("Tao", "Yang", email = "xadmyangt@gmail.com", role = c("aut", "cre"))
Description: This package evaluate the reproducibility of Hi-C intra-chromosome Hi-C data.
Depends:
    R (>= 3.0.1)
License: GPL (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr,
    rmarkdown
VignetteBuilder: knitr

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

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]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170123162723.html

[mtmorgan]

@hpages will review this package but it is very surprising that it does not use or provide interoperability with any of the Bioconductor infrastructure for working with genomic ranges and related infrastructure infrastructure specifically designed to work with interaction data HiC biocViews, e.g., InteractionSet

[TaoYang-dev]

I follow the instruction to set the webhook, but it seems not working. I get "Invalid HTTP Response: 400" warning.

I have done a lot changes and modification to my package. Please help me to push them to your end for review. Thanks!

[mtmorgan]

Look at https://github.com/Bioconductor/Contributions/#additional-actions and see if the 'Response' reads 'Failed to parse JSON'.

[TaoYang-dev]

@mtmorgan I followed instruction, but still not working. Here is the response I got: Connection: close Content-Length: 57 Content-Type: text/html;charset=utf-8 Date: Wed, 01 Feb 2017 02:56:24 GMT Server: Apache/2.4.18 (Ubuntu) Status: 400 Bad Request X-Content-Type-Options: nosniff X-Frame-Options: SAMEORIGIN X-Powered-By: Phusion Passenger 5.0.30 X-XSS-Protection: 1; mode=block

[mtmorgan]

What is the content (both 'Headers' and 'Payload') of the request?

[TaoYang-dev]

Header: Request URL: http://issues.bioconductor.org/ Request method: POST content-type: application/json Expect: User-Agent: GitHub-Hookshot/baf7d6b X-GitHub-Delivery: 8b8d7780-e80a-11e6-8d2e-0cccfb4ddf9e X-GitHub-Event: ping

Payload: { "zen": "Favor focus over features.", "hook_id": 11846802, "hook": { "type": "Repository", "id": 11846802, "name": "web", "active": true, "events": [ "push" ], "config": { "content_type": "json", "insecure_ssl": "0", "url": "http://issues.bioconductor.org" }, "updated_at": "2017-01-31T23:11:07Z", "created_at": "2017-01-31T23:11:07Z", "url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks/11846802", "test_url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks/11846802/test", "ping_url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks/11846802/pings", "last_response": { "code": null, "status": "unused", "message": null } }, "repository": { "id": 75767357, "name": "hicrep", "full_name": "MonkeyLB/hicrep", "owner": { "login": "MonkeyLB", "id": 20000491, "avatar_url": "https://avatars.githubusercontent.com/u/20000491?v=3", "gravatar_id": "", "url": "https://api.github.com/users/MonkeyLB", "html_url": "https://github.com/MonkeyLB", "followers_url": "https://api.github.com/users/MonkeyLB/followers", "following_url": "https://api.github.com/users/MonkeyLB/following{/other_user}", "gists_url": "https://api.github.com/users/MonkeyLB/gists{/gist_id}", "starred_url": "https://api.github.com/users/MonkeyLB/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/MonkeyLB/subscriptions", "organizations_url": "https://api.github.com/users/MonkeyLB/orgs", "repos_url": "https://api.github.com/users/MonkeyLB/repos", "events_url": "https://api.github.com/users/MonkeyLB/events{/privacy}", "received_events_url": "https://api.github.com/users/MonkeyLB/received_events", "type": "User", "site_admin": false }, "private": false, "html_url": "https://github.com/MonkeyLB/hicrep", "description": "R package to evaluate the reproducibility of Hi-C data", "fork": false, "url": "https://api.github.com/repos/MonkeyLB/hicrep", "forks_url": "https://api.github.com/repos/MonkeyLB/hicrep/forks", "keys_url": "https://api.github.com/repos/MonkeyLB/hicrep/keys{/key_id}", "collaborators_url": "https://api.github.com/repos/MonkeyLB/hicrep/collaborators{/collaborator}", "teams_url": "https://api.github.com/repos/MonkeyLB/hicrep/teams", "hooks_url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks", "issue_events_url": "https://api.github.com/repos/MonkeyLB/hicrep/issues/events{/number}", "events_url": "https://api.github.com/repos/MonkeyLB/hicrep/events", "assignees_url": "https://api.github.com/repos/MonkeyLB/hicrep/assignees{/user}", "branches_url": "https://api.github.com/repos/MonkeyLB/hicrep/branches{/branch}", "tags_url": "https://api.github.com/repos/MonkeyLB/hicrep/tags", "blobs_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/blobs{/sha}", "git_tags_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/tags{/sha}", "git_refs_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/refs{/sha}", "trees_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/trees{/sha}", "statuses_url": "https://api.github.com/repos/MonkeyLB/hicrep/statuses/{sha}", "languages_url": "https://api.github.com/repos/MonkeyLB/hicrep/languages", "stargazers_url": "https://api.github.com/repos/MonkeyLB/hicrep/stargazers", "contributors_url": "https://api.github.com/repos/MonkeyLB/hicrep/contributors", "subscribers_url": "https://api.github.com/repos/MonkeyLB/hicrep/subscribers", "subscription_url": "https://api.github.com/repos/MonkeyLB/hicrep/subscription", "commits_url": "https://api.github.com/repos/MonkeyLB/hicrep/commits{/sha}", "git_commits_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/commits{/sha}", "comments_url": "https://api.github.com/repos/MonkeyLB/hicrep/comments{/number}", "issue_comment_url": "https://api.github.com/repos/MonkeyLB/hicrep/issues/comments{/number}", "contents_url": "https://api.github.com/repos/MonkeyLB/hicrep/contents/{+path}", "compare_url": "https://api.github.com/repos/MonkeyLB/hicrep/compare/{base}...{head}", "merges_url": "https://api.github.com/repos/MonkeyLB/hicrep/merges", "archive_url": "https://api.github.com/repos/MonkeyLB/hicrep/{archive_format}{/ref}", "downloads_url": "https://api.github.com/repos/MonkeyLB/hicrep/downloads", "issues_url": "https://api.github.com/repos/MonkeyLB/hicrep/issues{/number}", "pulls_url": "https://api.github.com/repos/MonkeyLB/hicrep/pulls{/number}", "milestones_url": "https://api.github.com/repos/MonkeyLB/hicrep/milestones{/number}", "notifications_url": "https://api.github.com/repos/MonkeyLB/hicrep/notifications{?since,all,participating}", "labels_url": "https://api.github.com/repos/MonkeyLB/hicrep/labels{/name}", "releases_url": "https://api.github.com/repos/MonkeyLB/hicrep/releases{/id}", "deployments_url": "https://api.github.com/repos/MonkeyLB/hicrep/deployments", "created_at": "2016-12-06T20:15:28Z", "updated_at": "2016-12-07T20:25:56Z", "pushed_at": "2017-01-31T23:08:11Z", "git_url": "git://github.com/MonkeyLB/hicrep.git", "ssh_url": "git@github.com:MonkeyLB/hicrep.git", "clone_url": "https://github.com/MonkeyLB/hicrep.git", "svn_url": "https://github.com/MonkeyLB/hicrep", "homepage": null, "size": 1053, "stargazers_count": 0, "watchers_count": 0, "language": "R", "has_issues": true, "has_downloads": true, "has_wiki": true, "has_pages": false, "forks_count": 0, "mirror_url": null, "open_issues_count": 0, "forks": 0, "open_issues": 0, "watchers": 0, "default_branch": "master" }, "sender": { "login": "MonkeyLB", "id": 20000491, "avatar_url": "https://avatars.githubusercontent.com/u/20000491?v=3", "gravatar_id": "", "url": "https://api.github.com/users/MonkeyLB", "html_url": "https://github.com/MonkeyLB", "followers_url": "https://api.github.com/users/MonkeyLB/followers", "following_url": "https://api.github.com/users/MonkeyLB/following{/other_user}", "gists_url": "https://api.github.com/users/MonkeyLB/gists{/gist_id}", "starred_url": "https://api.github.com/users/MonkeyLB/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/MonkeyLB/subscriptions", "organizations_url": "https://api.github.com/users/MonkeyLB/orgs", "repos_url": "https://api.github.com/users/MonkeyLB/repos", "events_url": "https://api.github.com/users/MonkeyLB/events{/privacy}", "received_events_url": "https://api.github.com/users/MonkeyLB/received_events", "type": "User", "site_admin": false } }

[TaoYang-dev]

@mtmorgan Hi, do you see the problem from the above messege content?

[mtmorgan]

I can't see a problem. Please try to remove the web hook and re-apply it. Then commit a version bump to your package. Please report the Header: and Payload: of BOTH the request and response.

[TaoYang-dev]

@mtmorgan I did what you suggested.

Request:

header: Request URL: http://issues.bioconductor.org Request method: POST content-type: application/json Expect: User-Agent: GitHub-Hookshot/786bab5 X-GitHub-Delivery: 163fef00-ebdc-11e6-8c79-a9bb58053dc6 X-GitHub-Event: ping

Payload: { "zen": "Encourage flow.", "hook_id": 11929425, "hook": { "type": "Repository", "id": 11929425, "name": "web", "active": true, "events": [ "push" ], "config": { "content_type": "json", "insecure_ssl": "0", "url": "http://issues.bioconductor.org" }, "updated_at": "2017-02-05T19:48:38Z", "created_at": "2017-02-05T19:48:38Z", "url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks/11929425", "test_url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks/11929425/test", "ping_url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks/11929425/pings", "last_response": { "code": null, "status": "unused", "message": null } }, "repository": { "id": 75767357, "name": "hicrep", "full_name": "MonkeyLB/hicrep", "owner": { "login": "MonkeyLB", "id": 20000491, "avatar_url": "https://avatars.githubusercontent.com/u/20000491?v=3", "gravatar_id": "", "url": "https://api.github.com/users/MonkeyLB", "html_url": "https://github.com/MonkeyLB", "followers_url": "https://api.github.com/users/MonkeyLB/followers", "following_url": "https://api.github.com/users/MonkeyLB/following{/other_user}", "gists_url": "https://api.github.com/users/MonkeyLB/gists{/gist_id}", "starred_url": "https://api.github.com/users/MonkeyLB/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/MonkeyLB/subscriptions", "organizations_url": "https://api.github.com/users/MonkeyLB/orgs", "repos_url": "https://api.github.com/users/MonkeyLB/repos", "events_url": "https://api.github.com/users/MonkeyLB/events{/privacy}", "received_events_url": "https://api.github.com/users/MonkeyLB/received_events", "type": "User", "site_admin": false }, "private": false, "html_url": "https://github.com/MonkeyLB/hicrep", "description": "R package to evaluate the reproducibility of Hi-C data", "fork": false, "url": "https://api.github.com/repos/MonkeyLB/hicrep", "forks_url": "https://api.github.com/repos/MonkeyLB/hicrep/forks", "keys_url": "https://api.github.com/repos/MonkeyLB/hicrep/keys{/key_id}", "collaborators_url": "https://api.github.com/repos/MonkeyLB/hicrep/collaborators{/collaborator}", "teams_url": "https://api.github.com/repos/MonkeyLB/hicrep/teams", "hooks_url": "https://api.github.com/repos/MonkeyLB/hicrep/hooks", "issue_events_url": "https://api.github.com/repos/MonkeyLB/hicrep/issues/events{/number}", "events_url": "https://api.github.com/repos/MonkeyLB/hicrep/events", "assignees_url": "https://api.github.com/repos/MonkeyLB/hicrep/assignees{/user}", "branches_url": "https://api.github.com/repos/MonkeyLB/hicrep/branches{/branch}", "tags_url": "https://api.github.com/repos/MonkeyLB/hicrep/tags", "blobs_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/blobs{/sha}", "git_tags_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/tags{/sha}", "git_refs_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/refs{/sha}", "trees_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/trees{/sha}", "statuses_url": "https://api.github.com/repos/MonkeyLB/hicrep/statuses/{sha}", "languages_url": "https://api.github.com/repos/MonkeyLB/hicrep/languages", "stargazers_url": "https://api.github.com/repos/MonkeyLB/hicrep/stargazers", "contributors_url": "https://api.github.com/repos/MonkeyLB/hicrep/contributors", "subscribers_url": "https://api.github.com/repos/MonkeyLB/hicrep/subscribers", "subscription_url": "https://api.github.com/repos/MonkeyLB/hicrep/subscription", "commits_url": "https://api.github.com/repos/MonkeyLB/hicrep/commits{/sha}", "git_commits_url": "https://api.github.com/repos/MonkeyLB/hicrep/git/commits{/sha}", "comments_url": "https://api.github.com/repos/MonkeyLB/hicrep/comments{/number}", "issue_comment_url": "https://api.github.com/repos/MonkeyLB/hicrep/issues/comments{/number}", "contents_url": "https://api.github.com/repos/MonkeyLB/hicrep/contents/{+path}", "compare_url": "https://api.github.com/repos/MonkeyLB/hicrep/compare/{base}...{head}", "merges_url": "https://api.github.com/repos/MonkeyLB/hicrep/merges", "archive_url": "https://api.github.com/repos/MonkeyLB/hicrep/{archive_format}{/ref}", "downloads_url": "https://api.github.com/repos/MonkeyLB/hicrep/downloads", "issues_url": "https://api.github.com/repos/MonkeyLB/hicrep/issues{/number}", "pulls_url": "https://api.github.com/repos/MonkeyLB/hicrep/pulls{/number}", "milestones_url": "https://api.github.com/repos/MonkeyLB/hicrep/milestones{/number}", "notifications_url": "https://api.github.com/repos/MonkeyLB/hicrep/notifications{?since,all,participating}", "labels_url": "https://api.github.com/repos/MonkeyLB/hicrep/labels{/name}", "releases_url": "https://api.github.com/repos/MonkeyLB/hicrep/releases{/id}", "deployments_url": "https://api.github.com/repos/MonkeyLB/hicrep/deployments", "created_at": "2016-12-06T20:15:28Z", "updated_at": "2016-12-07T20:25:56Z", "pushed_at": "2017-02-05T19:45:23Z", "git_url": "git://github.com/MonkeyLB/hicrep.git", "ssh_url": "git@github.com:MonkeyLB/hicrep.git", "clone_url": "https://github.com/MonkeyLB/hicrep.git", "svn_url": "https://github.com/MonkeyLB/hicrep", "homepage": null, "size": 1153, "stargazers_count": 0, "watchers_count": 0, "language": "R", "has_issues": true, "has_downloads": true, "has_wiki": true, "has_pages": false, "forks_count": 0, "mirror_url": null, "open_issues_count": 0, "forks": 0, "open_issues": 0, "watchers": 0, "default_branch": "master" }, "sender": { "login": "MonkeyLB", "id": 20000491, "avatar_url": "https://avatars.githubusercontent.com/u/20000491?v=3", "gravatar_id": "", "url": "https://api.github.com/users/MonkeyLB", "html_url": "https://github.com/MonkeyLB", "followers_url": "https://api.github.com/users/MonkeyLB/followers", "following_url": "https://api.github.com/users/MonkeyLB/following{/other_user}", "gists_url": "https://api.github.com/users/MonkeyLB/gists{/gist_id}", "starred_url": "https://api.github.com/users/MonkeyLB/starred{/owner}{/repo}", "subscriptions_url": 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Response:

headers: Connection: close Content-Length: 57 Content-Type: text/html;charset=utf-8 Date: Sun, 05 Feb 2017 19:48:38 GMT Server: Apache/2.4.18 (Ubuntu) Status: 400 Bad Request X-Content-Type-Options: nosniff X-Frame-Options: SAMEORIGIN X-Powered-By: Phusion Passenger 5.0.30 X-XSS-Protection: 1; mode=block

body:

Only push, issue, and issue comment event hooks supported

[mtmorgan]

How are you bumping the version number? You should have a local repository, edit the DESCRIPTION file, commit to your local git, then push to github.

Actually, the event, 'ping', looks like what is triggered when the web hook is created. What happens when you push a change to your repository?

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9f923ed version bump test a827902 Merge pull request #1 from MonkeyLB/MonkeyLB-patch...

[TaoYang-dev]

I think it pushes through successfully now.

[mtmorgan]

It looks you've figured out the problem. Any guess as to what it was, so that we can help others more quickly?

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205150118.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

1ac1219 version 0.99.4

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205153321.html

[TaoYang-dev]

@mtmorgan changes on the master brunch will not trigger the push. That was what happened to me.

[mtmorgan]

Do you mean only changes on the master branch will trigger a build? Because the last build was triggered by a commit (https://github.com/MonkeyLB/hicrep/commit/1ac1219a6051c4827dedd4ce458ddb6e7ab43dab) on master...

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9ab60fd version bump e6613b6 Merge pull request #25 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205162611.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

6379f1e version bump and biocViews editted ab0631c Merge pull request #26 from MonkeyLB/MonkeyLB-patc...

[TaoYang-dev]

@mtmorgan I mean, the changes on master branch will NOT trigger push. I did the changes on master branch initially, but they were not pushed through. Then I did version bump on a side branch, and it works.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

b4d2d06 version bump a9684e1 Merge pull request #29 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205172148.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

4605b0b version bump 2a488e5 Merge pull request #30 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205174204.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

df49376 version bump d7406aa Merge pull request #31 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205181109.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

6def8f7 version bump 0896569 Merge pull request #34 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205190123.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

778613d version bump 38719fa Merge pull request #35 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205190559.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

3354051 version bump 3b90508 Merge pull request #36 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170205234746.html

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170206071618.html

[TaoYang-dev]

@mtmorgan Hi, I wonder what is the typical length review time for the package? I saw the notice that my package has been built withou errors or warnings on all platforms, but not sure what should be the next step. Is it just wait for further review? Is there anything I should do?

[mtmorgan]

I'm sorry for the delay, I will try to review this in the next day or so.

[mtmorgan]

DESCRIPTION

• Provide additional detail in the Description: field, more like a paper abstract describing the method, merits, and maybe comparison with alternative solutinos.

• Likely 'stats' should be in the Imports: field (used internally by the package) rather than Depends: field (essential for the end user of your package.

R

• avoid use of : for sequences, e..g., 1:nrow(). Use seq_len() or seq_along() instead (code is robust to 1:0)

• sample(1:nrow(temp)) can be written more efficiently as sample(nrow(temp)).

• indent code for readability, e.g., get.scc.R:46-60.

• avoid 'copy-and-append', e.g., get.scc()

  corr = cov = wei = n = array()
  ...
  corr[i] = ...

  in favor of 'pre-allocate and fill'

• This algorithm

  for (i in 1:ub){
      idx = which(gdist == i*resol)

  has complexity ub * length(gdist), whereas something like (untested!)

  grp <- match(gdist, seq_len(ub) * resol)
  idx <- split(gdist, grp)

  has linear complexity so scales much better. Investigate such implementations for more efficient code.

• Use message() rather than print() to communicate with users during function execution, e.g., htrain.R:36. Use warning() rather than print() to indicate unusual conditions, e.g., htrain.R:51

• copy-and-append again appears at MatToVec.R:45

  tmp = NULL
  for (i in as.double(colnames(mat))){
      tmp = c(tmp, rep(i, rc))
  }

  instead tmp = rep(as.double(colnames(mat)), each=rc)

• vectorize calculations rather than iterate, 'hoist' constant cacluations outside loops to avoid unnecessary re-caclucation, e.g., , e.g., smoothMat.R:40

  for (i in 1:r){
      for (j in 1:c){
          rlb = ifelse(i-h > 0, i-h, 1)
          rrb = ifelse(i+h < r, i+h, r)
          clb = ifelse(j-h > 0, j-h, 1)
          crb = ifelse(j+h < c, j+h, c)
          smd_matr[i,j] = mean(matr[rlb:rrb, clb:crb])
      }
  }

  becomes

  i <- seq_len(r)
  rlb <- ifelse(i - h > 0, i - h, 1)
  rrb <- ifelse(i + h < r, i + h, r)
  
  j <- seq_len(c)
  clb <- ifelse(j - h > 0, j - h, 1)
  crb <- ifelse(j + h < c, j +  h, c)
  
  for (i in seq_len(r)){
      for (j in seq_len(c)){
          smd_matr[i,j] = mean(matr[rlb[i]:rrb[i], clb[j]:crb[j]])
      }
  }

vignette

• no need to include vignette products (.R, .html files) in git.

• indicate correct way to install package once accepted to Bioconductor

  source("https://bioconductor.org/biocLite.R")
  biocLite("hicrep")

• Rather than using r Sys.Date() for date:, consider a fixed date representing 'last revision'.

• In a final code chunk, include the output of sessionInfo() to help with reproducibility.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

8338110 bump to 0.99.13 e1196b6 Merge pull request #48 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170302161855.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

178b636 bump to 0.99.14 ab616e0 Merge pull request #50 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170302162901.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

748e53e Update DESCRIPTION 9db7213 Merge pull request #53 from MonkeyLB/MonkeyLB-patc...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/hicrep_buildreport_20170302164623.html

[TaoYang-dev]

@mtmorgan Hi, Thank you very much for your kind suggestions. I have revised my code accordingly, and the system checks returned OK. Please let me know if I need to do further polishing or something. Again, thank you very much for your comments and insights.

[mtmorgan]

Thank you I have marked the package as accepted. It will be added to the Bioconductor svn repository and nightly builds over the next few days, with additional information available then.