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(inactive) #344

Closed isarnassiri closed 6 years ago

isarnassiri commented 7 years ago

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

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bioc-issue-bot commented 7 years ago

Hi @isarnassiri

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: CMEA
Title: CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
Version: 0.99.0
Authors@R: c(person("Isar", "Nassiri", email = "isar_nassiri@urmc.rochester.edu", role = c("aut", "cre")))
Description: CMEA is a tool for cell morphology enrichment analysis and link transcriptomic alterations with cell morphological phenotypes. In our approach we (1) map the transcriptomic profile of a query against the L1000 LINCS repository, (2) create a gene set repository for cell morphological features (CM), (3) identify the top CMs associated with alterations and analyze their direction of regulation, and (4) model a regulatory network of cell morphological phenotypes. 
Depends: R (>= 3.3.1), plotly, clusterSim, netbenchmark, qgraph, data.table, glmnet, PANR, Hmisc, caret, arules, arulesViz, vegan, ggplot2, gridExtra, plotrix, netbenchmark, igraph
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
biocViews: Software, StatisticalMethod, Regression
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-02 15:29:15 UTC; inassiri1
Author: Isar Nassiri [aut, cre], Matthew McCall [aut, cre]
Maintainer: Isar Nassiri <isar_nassiri@urmc.rochester.edu>
bioc-issue-bot commented 7 years ago

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.

isarnassiri commented 7 years ago

Hello,

  1. I uploaded the CMEA package, including the complete repositories of cell morphology and transcriptomic profiles to the Github (https://github.com/isarnassiri/CMEA) through the Bitbucket.

  2. I submitted the CMEA package to the Bioconductor.

Best regards, Isar

From: bioc-issue-bot [mailto:notifications@github.com] Sent: Friday, April 07, 2017 8:49 PM To: Bioconductor/Contributions Cc: Nassiri, Isar; Mention Subject: Re: [Bioconductor/Contributions] CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile (#344)

Hi @isarnassirihttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_isarnassiri&d=DQMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E-oniHbGv_UHjPSrRjRIX5Oxoyh1VH3wE7UxwyHhNAU&m=dY8OxdQrJIfKCwuv1CQVMnSL3runatRFuwxw-ab-KlQ&s=ZO5cHTQyB-Pic4iqx8lfnkEe76FWXXPdzcLRolYb8pA&e=

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: CMEA

Title: CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile

Version: 0.99.0

Authors@R: c(person("Isar", "Nassiri", email = "isar_nassiri@urmc.rochester.edumailto:isar_nassiri@urmc.rochester.edu", role = c("aut", "cre")))

Description: CMEA is a tool for cell morphology enrichment analysis and link transcriptomic alterations with cell morphological phenotypes. In our approach we (1) map the transcriptomic profile of a query against the L1000 LINCS repository, (2) create a gene set repository for cell morphological features (CM), (3) identify the top CMs associated with alterations and analyze their direction of regulation, and (4) model a regulatory network of cell morphological phenotypes.

Depends: R (>= 3.3.1), plotly, clusterSim, netbenchmark, qgraph, data.table, glmnet, PANR, Hmisc, caret, arules, arulesViz, vegan, ggplot2, gridExtra, plotrix, netbenchmark, igraph

License: GPL-2

Encoding: UTF-8

LazyData: true

RoxygenNote: 5.0.1.9000

biocViews: Software, StatisticalMethod, Regression

Suggests: knitr, rmarkdown

VignetteBuilder: knitr

NeedsCompilation: no

Packaged: 2016-06-02 15:29:15 UTC; inassiri1

Author: Isar Nassiri [aut, cre], Matthew McCall [aut, cre]

Maintainer: Isar Nassiri isar_nassiri@urmc.rochester.edu<mailto:isar_nassiri@urmc.rochester.edu>

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_344-23issuecomment-2D292683011&d=DQMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E-oniHbGv_UHjPSrRjRIX5Oxoyh1VH3wE7UxwyHhNAU&m=dY8OxdQrJIfKCwuv1CQVMnSL3runatRFuwxw-ab-KlQ&s=loZ-v2naPETqFPiKUTayoofJD6nIzI5cib_mzOdJRsI&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AZxqFencscTfdexnpyWSPCXNR1Vb-2Dlidks5rttmRgaJpZM4M3iZG&d=DQMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E-oniHbGv_UHjPSrRjRIX5Oxoyh1VH3wE7UxwyHhNAU&m=dY8OxdQrJIfKCwuv1CQVMnSL3runatRFuwxw-ab-KlQ&s=onP6Tjwa5LtVs3WrPwPD3Fgb0rRUPa7pgB9tHYbtdS0&e=.

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170407211958.html

isarnassiri commented 7 years ago

Hello, I revised the code, and fixed the warnings. I have pushed the code to git. Best regards, Isar

bioc-issue-bot commented 7 years ago

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

f98a91e Add files via upload bc63181 Merge pull request #10 from isarnassiri/isarnassir...

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170419133721.html

bioc-issue-bot commented 7 years ago

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

4d5f911 Add files via upload 7421c30 Merge pull request #11 from isarnassiri/isarnassir...

bioc-issue-bot commented 7 years ago

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

c5c39c9 Add files via upload 10a8f50 Merge pull request #14 from isarnassiri/isarnassir...

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170419193859.html

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170419193931.html

bioc-issue-bot commented 7 years ago

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

f4e8d50 Add files via upload a358a31 Merge pull request #16 from isarnassiri/isarnassir...

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170420091133.html

bioc-issue-bot commented 7 years ago

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

2b3e992 Add files via upload 7b325a5 Merge pull request #18 from isarnassiri/isarnassir...

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170420115928.html

bioc-issue-bot commented 7 years ago

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

72c4bea Add files via upload

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170420122644.html

bioc-issue-bot commented 7 years ago

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

35d724b Add files via upload Revised.

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170420131315.html

isarnassiri commented 7 years ago

Hello,

The "WARNINGS" is " 'rgl_init' failed, running with rgl.useNULL = TRUE", and is a problem with the build system itself.

Best regards, Isar

hpages commented 7 years ago

Hi Isar,

Thanks for submitting the CMEA package. Please take the time to read carefully our package guidelines here. CMEA fails to satisfy 2 important criteria from these guidelines: it's too big and the vignette has no real code chunks. Also, the package has usability issues that are so severe that it's almost impossible for me to test it and judge its usefulness. Overall it will need a lot of work to reach an acceptable level. See details below.

Regards, H.

  1. Package is too big: 73M. That's because it contains big data sets of experimental data. The source tarball of a Bioconductor software package should occupy less than 4MB on disk. Please check our package guidelines (at https://bioconductor.org/developers/package-guidelines/) and make sure CMEA satisfies them. One way to reduce the size is to move all the experimental data to a separate data experiment package. Let's call this solution 1. If the data is not too big, another way to reduce the size of the package is to explicitly download the data in the examples or vignette. Let's call this solution 2.

  2. Your data sets are poorly documented. We need to know exactly where the data is coming from and how it was retrieved. For example the man page for Cell_Morphology_Profile only says that the data comes from the LINCS database but it doesn't say what data it is exactly from this database or how it was extracted from it. Also the man page doesn't say what the row names of the data frame are. So if you opt for solution 1, make sure the data sets are well documented in the data experiment package. If you opt for solution 2, then things will be more transparent and reproducible because you'll provide the code for downloading the data sets. Even if you opt for solution 1, I would strongly suggest that you make available the code you used to generate the data sets in the data experiment package.

  3. Your vignette doesn't contain any real code chunks i.e. code chunks that are evaluated by R CMD build. This is called a static vignette. Bioconductor vignettes should never be static i.e. they must contain real code chunks. See our package guidelines for more information on this.

  4. None of your functions have arguments. The input they take is unclear. Some of it seems to come from some user defined variables (e.g. number_of_features for Cell_Morphology_Enrichment_Analysis()). But they also seem to take as input some files produced by other functions. This is very poor software design. Besides, none of this is documented. This makes the package barely usable.

  5. One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features() function:

    > library(CMEA)
> example(Ranking_Cell_Morphological_features)

R_C_M_> {
R_C_M_+ data(Transcriptomic_Profile)
R_C_M_+ data(Cell_Morphology_Profile)
R_C_M_+ TOP=20
R_C_M_+ Ranking_Cell_Morphological_features() 
R_C_M_+ }
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt':
No such file or directory

    That's probably because it requires other things from other examples to run before it. All the examples should work independently from each others.

  6. Some of your functions (e.g. Cell_Morphology_Enrichment_Analysis()) write their output to the package installation folder. This is a very bad idea. The package installation folder should always be treated as a read-only place.

  7. Please use camelCase style for your function names e.g. crossTabulation() instead of crosstabulation() or rankCellMorphologicalFeatures() instead of Ranking_Cell_Morphological_features() etc... (Also note that you could use "rank" instead of "ranking".)

  8. The examples provided in the man pages are all inside curly brackets ({ ... }). These curly brackets have no purpose and should be removed.

  9. Use <- instead of = for assignments.

bioc-issue-bot commented 7 years ago

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

e3b5811 Add files via upload

bioc-issue-bot commented 7 years ago

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

ef83dfc Revised.

bioc-issue-bot commented 7 years ago

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

e5c0286 R.

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, 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_20170613155321.html

bioc-issue-bot commented 7 years ago

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

59fa2b4 Revised.

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, 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_20170613165922.html

bioc-issue-bot commented 7 years ago

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

55fce9f

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, 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_20170614164030.html

bioc-issue-bot commented 7 years ago

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

8058bde Revised.

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, 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_20170614180949.html

bioc-issue-bot commented 7 years ago

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

7a394d4 Revised.

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, 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_20170614184324.html

bioc-issue-bot commented 7 years ago

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

84898b1 Revised.

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, 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_20170616153246.html

bioc-issue-bot commented 7 years ago

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

6330096

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, 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_20170616154242.html

bioc-issue-bot commented 7 years ago

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

18322a0 Revised.

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, 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_20170617140505.html

bioc-issue-bot commented 7 years ago

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

148164c

bioc-issue-bot commented 7 years ago

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

1d4fed4

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, 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_20170619161235.html

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, 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_20170619161307.html

isarnassiri commented 7 years ago

Hello,

I am pleased to resubmit the revised version of CMEA package. I appreciated the constructive criticisms of the reviewer. I have addressed each of his concerns as outlined below.

  1. Package is too big: 73M. That's because it contains big data sets of experimental data. The source tarball of a Bioconductor software package should occupy less than 4MB on disk. Please check our package guidelines (at ) and make sure CMEA satisfies them. One way to reduce the size is to move all the experimental data to a separate data experiment package. Let's call this solution 1. If the data is not too big, another way to reduce the size of the package is to explicitly download the data in the examples or vignette. Let's call this solution 2.

We moved the files of complete experimental data to a separate data experiment package, and used subset of the complete dataset as an example input. The package size now is 2.22MB.

  1. Your data sets are poorly documented. We need to know exactly where the data is coming from and how it was retrieved. For example the man page for Cell_Morphology_Profile only says that the data comes from the LINCS database but it doesn't say what data it is exactly from this database or how it was extracted from it. Also the man page doesn't say what the row names of the data frame are. So if you opt for solution 1, make sure the data sets are well documented in the data experiment package. If you opt for solution 2, then things will be more transparent and reproducible because you'll provide the code for downloading the data sets. Even if you opt for solution 1, I would strongly suggest that you make available the code you used to generate the data sets in the data experiment package.

The input data were explained in vignette/documents with more details. We explained the origin of data with proper citations.

  1. Your vignette doesn't contain any real code chunks i.e. code chunks that are evaluated by R CMD build. This is called a static vignette. Bioconductor vignettes should never be static i.e. they must contain real code chunks. See our package guidelines for more information on this.

We added some real code chunks to the vignette, and improved it thoroughly.

  1. None of your functions have arguments. The input they take is unclear. Some of it seems to come from some user defined variables (e.g. number_of_features for Cell_Morphology_Enrichment_Analysis()). But they also seem to take as input some files produced by other functions. This is very poor software design. Besides, none of this is documented. This makes the package barely usable.

The name of the functions were revised. We added arguments with comprehensive explanations. All functions return the R objects in the global environment after running them.

  1. One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features() function:

    library(CMEA)

    example(Ranking_Cell_Morphological_features)

    R_CM> {

    R_CM+ data(Transcriptomic_Profile)

    R_CM+ data(Cell_Morphology_Profile)

    R_CM+ TOP=20

    R_CM+ Ranking_Cell_Morphological_features()

    R_CM+ }

    Error in file(file, "rt") : cannot open the connection

    In addition: Warning message:

    In file(file, "rt") :

    cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt':

    No such file or directory

That's probably because it requires other things from other examples to run before it. All the examples should work independently.

Revised. All the examples work independently, and return the R objects in the global environment after running them.

  1. Some of your functions (e.g. Cell_Morphology_Enrichment_Analysis()) write their output to the package installation folder. This is a very bad idea. The package installation folder should always be treated as a read-only place.

Revised. All functions return their outputs to the global environment.

  1. Please use camelCase style for your function names e.g. crossTabulation() instead of crosstabulation() or rankCellMorphologicalFeatures() instead of Ranking_Cell_Morphological_features() etc... (Also note that you could use "rank" instead of "ranking".)

Thanks for the comment. We used CamelCase symbol names for function names.

  1. The examples provided in the man pages are all inside curly brackets ({ ... }). These curly brackets have no purpose and should be removed.

Unessential curly brackets in the man pages were removed.

  1. Use <- instead of = for assignments.

Revised. Best regards, Isar

From: hpages [mailto:notifications@github.com] Sent: Thursday, May 25, 2017 3:11 AM To: Bioconductor/Contributions Cc: Nassiri, Isar; Manual Subject: Re: [Bioconductor/Contributions] CMEA: An R Package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile (#344)

Hi Isar,

Thanks for submitting the CMEA package. Please take the time to read carefully our package guidelines here . CMEA fails to satisfy 2 important criteria from these guidelines: it's too big and the vignette has no real code chunks. Also, the package has usability issues that are so severe that it's almost impossible for me to test it and judge its usefulness. Overall it will need a lot of work to reach an acceptable level. See details below.

Regards, H.

  1. Package is too big: 73M. That's because it contains big data sets of experimental data. The source tarball of a Bioconductor software package should occupy less than 4MB on disk. Please check our package guidelines (at ) and make sure CMEA satisfies them. One way to reduce the size is to move all the experimental data to a separate data experiment package. Let's call this solution 1. If the data is not too big, another way to reduce the size of the package is to explicitly download the data in the examples or vignette. Let's call this solution 2.

  2. Your data sets are poorly documented. We need to know exactly where the data is coming from and how it was retrieved. For example the man page for Cell_Morphology_Profile only says that the data comes from the LINCS database but it doesn't say what data it is exactly from this database or how it was extracted from it. Also the man page doesn't say what the row names of the data frame are. So if you opt for solution 1, make sure the data sets are well documented in the data experiment package. If you opt for solution 2, then things will be more transparent and reproducible because you'll provide the code for downloading the data sets. Even if you opt for solution 1, I would strongly suggest that you make available the code you used to generate the data sets in the data experiment package.

  3. Your vignette doesn't contain any real code chunks i.e. code chunks that are evaluated by R CMD build. This is called a static vignette. Bioconductor vignettes should never be static i.e. they must contain real code chunks. See our package guidelines for more information on this.

  4. None of your functions have arguments. The input they take is unclear. Some of it seems to come from some user defined variables (e.g. number_of_features for Cell_Morphology_Enrichment_Analysis()). But they also seem to take as input some files produced by other functions. This is very poor software design. Besides, none of this is documented. This makes the package barely usable.

  5. One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features() function:

    library(CMEA)

    example(Ranking_Cell_Morphological_features)

    R_CM> {

    R_CM+ data(Transcriptomic_Profile)

    R_CM+ data(Cell_Morphology_Profile)

    R_CM+ TOP=20

    R_CM+ Ranking_Cell_Morphological_features()

    R_CM+ }

    Error in file(file, "rt") : cannot open the connection

    In addition: Warning message:

    In file(file, "rt") :

    cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt':

    No such file or directory

That's probably because it requires other things from other examples to run before it. All the examples should work independently from each others.

  1. Some of your functions (e.g. Cell_Morphology_Enrichment_Analysis()) write their output to the package installation folder. This is a very bad idea. The package installation folder should always be treated as a read-only place.

  2. Please use camelCase style for your function names e.g. crossTabulation() instead of crosstabulation() or rankCellMorphologicalFeatures() instead of Ranking_Cell_Morphological_features() etc... (Also note that you could use "rank" instead of "ranking".)

  3. The examples provided in the man pages are all inside curly brackets ({ ... }). These curly brackets have no purpose and should be removed.

  4. Use <- instead of = for assignments.

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bioc-issue-bot commented 7 years ago

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

3a5e5d2

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, 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_20170621094451.html

bioc-issue-bot commented 7 years ago

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

5b6a512 Revised.

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170621095637.html

bioc-issue-bot commented 7 years ago

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

1c0ba9b Revised.

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.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/CMEA_buildreport_20170624120925.html