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isarnassiri commented 7 years ago

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Repository: https://github.com/isarnassiri/CMEA

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bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

Dear Package contributor,

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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:

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bioc-issue-bot commented 7 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: "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.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 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: "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.

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bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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hpages commented 7 years ago

Hi Isar,

Thanks for updating your package. There are still important issues that will need to be addressed before we can add it to Bioconductor. Some of these issues were already reported to you but you apparently ignored them.

The vignette is still static i.e. the code chunks in it don't get evaluated and the output produced by the commands was just copy-paste'd from an interactive R session to the code chunk.
The Mapping() function doesn't take any argument. What datasets to use for input is hard-coded in the function itself. So it will always produce the same output. The situation is similar with all the other functions in the package: they all take as input the 3 datasets included in the package and the user has no control on this. Wouldn't the package be much more useful if one could use it on its own datasets?
The description of the value returned by your functions is too minimalist: "Repository of gene sets" for CellMorphologyEnrichmentAnalysis() or "gene-gene interaction network" for GRN(). You need to provide more details about the data structure that is returned e.g. what its type (matrix or data.frame etc...), what are the dimensions, what are the rows, what are the columns, are they named, what are names, etc... The user needs to know exactly what to expect.
After calling Mapping(), the vignette says:
```
You can find the results in your current directory.
```
However, after doing this, I don't see any results in my current directory.
When you have more than one entry in the references section of a man page, please separate them with a blank line. Otherwise they get displayed in a single paragraph and that hurts readability. See for example ?Cell_Morphology_Profile.
Please remove the 2 following lines from the DESCRIPTION file:
```
Packaged: 2016-06-02 15:29:15 UTC; inassiri1
Author: Isar Nassiri [aut, cre], Matthew McCall [aut, cre]
```
These lines will be automatically added to the DESCRIPTION file of the source tarball produced by R CMD build (the Author line will be generated from the Authors@R line so you will need to add Matthew McCall in the latter if you want him to be credited as one of the authors of the package).
The CMEA.html file does not belong to the package source tree. Please remove it. The HTML version of the vignette will be built and added to the package source tarball by R CMD build.
Please use camelCase style for the name of the CellMorphologyEnrichmentAnalysis() function i.e. start its name with a lower case c.
Please find a more specific name for the Mapping() function. The current name is too generic. Also please avoid starting function names with a capital letter.

Thanks, H.

hpages commented 6 years ago

Hi Isar, Are you planning to follow up on this submission? If we don't hear back from you in the next couple of weeks, we'll close this issue. Regards, H.

isarnassiri commented 6 years ago

Hello, Sorry for my delay to response. I have moved from URMC, and my university email was terminated. Therefore, I did receive your email. Please open this issue, and I revise the package based on your comments this week. Best regards, Isar

isarnassiri commented 6 years ago

Hello, I used an up to date and accessible email address. Best regards, Isar

bioc-issue-bot commented 6 years ago

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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: "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/CMEA_buildreport_20171112084842.html

bioc-issue-bot commented 6 years ago

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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: "WARNINGS, 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/CMEA_buildreport_20171112090305.html

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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: "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/CMEA_buildreport_20171112091742.html

bioc-issue-bot commented 6 years ago

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Bioconductor / Contributions

(inactive) #344