IMMAN

[jafarilab]

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

• Repository: https://github.com/jafarilab/IMMAN

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.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @jafarilab

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: IMMAN
Title: Interlog protein network reconstruction by Mapping and Mining ANalysis
Version: 1.0.0
Description: Reconstructing Interlog Protein Network (IPN) integrated from several 
   Protein protein Interaction Networks (PPINs). Using this package, 
   overlaying different PPINs to mine conserved common networks between diverse 
   species will be applicable.
Author: Payman Nickchi, 
        Abdollah Safari,
        Minoo Ashtiani,
        Mohieddin Jafari
Maintainer: Minoo Ashtiani <m_ashtiani@pasteur.ac.ir>
biocViews: SequenceMatching, Alignment, SystemsBiology, GraphAndNetwork,  
 Network, Proteomics
RoxygenNote: 6.0.1
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Imports: STRINGdb, seqinr, Biostrings, igraph

[mtmorgan]

There is no reason to use seqinr and Biostrings; Biostrings is sufficient. Your package should have a 'vignettes' directory with markdown or latex vignette. The version number is incorrect, it should be 0.99.0 for the start of a submission.

I'm very concerned that this is your 'first attempt' at writing an R package, and I strongly encourage you to consider NOT submitting it to Bioconductor, but rather use it as a learning experience for developing better programming practices.

[jafarilab]

Dear Martin, I fixed all the mentioned problems and uploaded the files again. As this package usage is in biological fields, more specifically protein protein interactions, I am intend to submit it on Bioconductor repository. I would be really grateful, if you locate this repository to be linked to issue number: 565

Bests, Minoo

On Sun, Nov 26, 2017 at 2:39 PM, Martin Morgan notifications@github.com wrote:

There is no reason to use seqinr and Biostrings; Biostrings is sufficient. Your package should have a 'vignettes' directory with markdown or latex vignette. The version number is incorrect, it should be 0.99.0 for the start of a submission.

I'm very concerned that this is your 'first attempt' at writing an R package, and I strongly encourage you to consider NOT submitting it to Bioconductor, but rather use it as a learning experience for developing better programming practices.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/564#issuecomment-347000650, or mute the thread https://github.com/notifications/unsubscribe-auth/AbZocv3e-sLmlLTEYsXO-vdjfcbPoNw4ks5s6UbfgaJpZM4Qqs-J .

-- آزمایشگاه زیست شناسی سامانه گرای محاسباتی انستیتو پاستور ایران

[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: "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/IMMAN_buildreport_20171128074601.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.

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/IMMAN_buildreport_20171128081359.html

[jafarilab]

Dear @dvantwisk I fixed the problem. Would you please recheck it again?

[bioc-issue-bot]

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

071b005 version updated

[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/IMMAN_buildreport_20171129040958.html

[jafarilab]

@dvantwisk I tried to remove errors. Would you please recheck it?

[mtmorgan]

Note that version numbering in supposed to go 9.99.0, 0.99.1, 0.99.2, ... until your package is accepted. I am unsure whether you will now be able to change to that sequence -- version numbers must always go 'up'. So I suggest 1.1.0, 1.1.1, 1.1.2, 1.1.3, ..., 1.1.9, 1.1.10, 1.1.11, .... See http://bioconductor.org/developers/how-to/version-numbering/ for version numbering if your package is accepted.

[bioc-issue-bot]

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

9f2b78c change the version number

[jafarilab]

@mtmorgan Thanks in advance for your advice, I fixed it.

[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/IMMAN_buildreport_20171129080211.html

[bioc-issue-bot]

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

96851e5 version update

[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/IMMAN_buildreport_20171129081323.html

[bioc-issue-bot]

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

8dda472 version update

[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/IMMAN_buildreport_20171129081954.html

[bioc-issue-bot]

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

68b9b52 version update

[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, TIMEOUT, 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/IMMAN_buildreport_20171129084721.html

[bioc-issue-bot]

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

1089066 version update

[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/IMMAN_buildreport_20171129092324.html

[bioc-issue-bot]

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

f385c4f version update

[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/IMMAN_buildreport_20171129130645.html

[bioc-issue-bot]

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

2ffe5a0 version update

[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/IMMAN_buildreport_20171130041838.html

[jafarilab]

@mtmorgan I think the below error is an error of build system. As this problem has not happened in OS and I can properly access the mentioned link.

* checking for file IMMAN/DESCRIPTION ... OK
* preparing IMMAN:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 80-88 (IMMAN.Rmd) 
Error: processing vignette 'IMMAN.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.uniprot.org/uniprot/Q09508.fasta'
Execution halted

[mtmorgan]

@jafarilab this is likely a transient error and will go away on your next version bump, perhaps when you address the issue with the undefined variable tem.

[bioc-issue-bot]

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

8c66b07 update version

[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, TIMEOUT". 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/IMMAN_buildreport_20171130073303.html

[bioc-issue-bot]

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

8aeaf15 version update

[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: "TIMEOUT". 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/IMMAN_buildreport_20171130075825.html

[bioc-issue-bot]

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

6f1f0c6 version update

[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/IMMAN_buildreport_20171130081412.html

[jafarilab]

Dear @mtmorgan , Thanks a lot for all of your helps. Now, shall I do anything else? How long does it take to be downloadable for users?

[mtmorgan]

It needs to be reviewed (by @dvantwisk) and then added to the Bioconductor build system. The review may require further changes on your part, and can take several weeks. Remember that the package is added to the 'devel' version of Bioconductor, so your users will need to be using that until the next release, typically in April.

[jafarilab]

Dear @dvantwisk, Would you please review my package for any possible mistake, if you had time please? I would be glad for your kind help.

[dvantwisk]

Hello,

This package is currently being reviewed. I will try to have it to you by early next week.

[dvantwisk]

Hello,

We've reviewed you package! Please address the following issues and message us back when you are finished!

GENERAL:

• [REQUIRED] place .Rproj.user and IMMAN.Rproj into .gitignore

R/IMMAN.R

• [REQUIRED] L126, and multiple other locations: use seq_len() instead of 1:. Faster and avoids edge case where 1:0 returns unexpected 1 0.
• [REQUIRED] L212: and multiple other locations: paste() not needed in message()
• [REQUIRED] L352, and multiple other locations: Do not use the word "Error" in stop(), it is redundant.
• [REQUIRED] L453-499, 648-690, 772-808: Inefficient copy and append pattern specifically at L496-497, L687-688, L805-806.
• [CONSIDER] L453-499, 648-690, 772-808: These blocks are very similar. Consider writing a function to encapsulate it and thereby reuse code.

Tests:

• [CONSIDER] adding tests to your package using the testthat package.

[dvantwisk]

Hello,

I haven't heard back from you in a while. Have you been making the above changes to your package?

[jafarilab]

Hi Daniel,

Sorry for being late. We are working on the code to fix the problems, and make the performance time shorter. Is there any deadline for making the changes? I think it will be complete within 2 weeks.

On Thu, Jan 11, 2018 at 7:17 PM, Daniel Van Twisk notifications@github.com wrote:

Hello,

I haven't heard back from you in a while. Have you been making the above changes to your package?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/564#issuecomment-356967950, or mute the thread https://github.com/notifications/unsubscribe-auth/AbZociytlvQvso4Nw_xinhsd5e3JZMioks5tJi0jgaJpZM4Qqs-J .

-- آزمایشگاه زیست شناسی سامانه گرای محاسباتی انستیتو پاستور ایران

[dvantwisk]

There's no deadline. Just checking in to make sure that this submission is still active.

[bioc-issue-bot]

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

7f7ab19 version bump

[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 build report for more details.

[bioc-issue-bot]

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

a6d89cc add testthat

[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: "TIMEOUT". 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.

[bioc-issue-bot]

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

c07b37c change files

[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: "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.

[bioc-issue-bot]

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

c311f37 change example

[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 build report for more details.