pcxn

[BioSok]

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[bioc-issue-bot]

Hi @BioSok

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: pcxn
Type: Package
Version: 0.99.0
Title: Pathway correlation coefficients and p values between pre-defined gene sets
Description: PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively.
Author: Sokratis Kariotis, Yered Pita-Juarez, Winston Hide, Wenbin Wei
Maintainer: Sokratis Kariotis <s.kariotis@sheffield.ac.uk>
License: MIT + file LICENSE
biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, OneChannelData, PathwayInteractionDatabase
NeedsCompilation: no
Suggests: org.Hs.eg.db, pheatmap, igraph, annotate
Imports: methods, grDevices, utils
Depends: R (>= 3.4)
LazyData: true
Encoding: UTF-8
RoxygenNote: 6.0.1

[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: "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 following build report for more details:

http://bioconductor.org/spb_reports/pcxn_buildreport_20171002071128.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/pcxn_buildreport_20171002080754.html

[BioSok]

Dear @vobencha , I believe the ERROR concerns the turned-off Tcl/Tk (and X11?) during compilation on Linux and OSX. I believe they are TRUE by default on the Windows server where the package builds fine.

[bioc-issue-bot]

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

ec678f8 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: "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/pcxn_buildreport_20171004044821.html

[bioc-issue-bot]

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

51896d4 commented image line

[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/pcxn_buildreport_20171004060838.html

[bioc-issue-bot]

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

d2bcc08 commented image line

[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/pcxn_buildreport_20171004063205.html

[bioc-issue-bot]

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

98f50d0 commented image line

[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/pcxn_buildreport_20171004064725.html

[bioc-issue-bot]

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

de7e3a8 commented image line

[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/pcxn_buildreport_20171004065441.html

[vobencha]

Hi,

It looks like we have a mixture of a software and experimental data package.

• In general, experimental data packages do not contain R code. Functions that manipulate the data object belong in a software package that defines the class of the data object.
• I would not recommend setting so many global variables. This usually means the existing functions don't have the proper input arguments to create the desired outcome. Please explain why you feel you need these:
  utils::globalVariables(c("pathprint.Hs.gs","pheatmap",
  "pathCor_pathprint_v1.2.3_dframe",
  "pathCor_CPv5.1_dframe", "gobp_gs_v5.1",
  "PathCor", "p.value", "Pathway.A", "Pathway.B"))
• The name of the vignette file is inconsistent with the name of the package (PCxN vs pcxn).
• I don't see the need to create the pxcn object. It is a matrix with a list. Why not reuse objects from Biobase, GSEABase, or SummarizedExperiment? Please consider re-packaging the data in an existing class and using the getters/setters already in place for that class.

Please explain a little more about what you want to accomplish with this package. Once that's cleared up I can give better guidance on how to restructure.

Valerie

[BioSok]

Dear @vobencha ,

This package is meant to carry the functionality (mostly as queries) of the included functions using the present data. In the future this package will be extended and we want to build around the pcxn object and that is the reason we want to differentiate it. The specific fields of this object also coincide with other forms of existing pcxn (like a web-tool). This object should be plugged in future R packages which are part of a pipeline along with pcxn.

The global variables were used as it was the only successful way to gain access to those data from within the functions without encountering the NOTE: no visible binding for global variable. After your comment I will try to find the proper way to do this.

Thank you for your time and help!

With regards,
Sokratis

[vobencha]

Hi,

The data should be separate from the software functions unless you can pair it down to the required size which is <=4MB on disk: http://www.bioconductor.org/developers/package-guidelines/#correctness

Can you reduce the size and should we go ahead with pcxn as a software package?

Valerie

[BioSok]

Hi,

Unfortunately all included data are necessary and cannot be loaded from another place, so I cant remove them. I will split the current package to a software (named pcxn) and a data package (named pcxnData). If I do the split (within few days) will both packages be included in the coming release? Thanks!

-Sokratis

[vobencha]

We'll do our best but there are no guarantees. Both packages must meet the guidelines and go through the full review process.

The process is described in detail here: https://github.com/Bioconductor/Contributions. The key steps are,

• close this issue
• open a new issue for the data package; once the data package passes build/check then
• submit the software package to the same issue

Valerie