Closed BioSok closed 6 years ago
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: pcxnData
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: pcxn
Depends: R (>= 3.4)
Encoding: UTF-8
RoxygenNote: 6.0.1
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.
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/pcxnData_buildreport_20171010120025.html
Received a valid push; starting a build. Commits are:
32193b6 first fix
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/pcxnData_buildreport_20171010122037.html
Assign to self.
@BioSok go ahead and add the software package as described in https://github.com/Bioconductor/Contributions#submitting-related-packages
AdditionalPackage: https://github.com/hidelab/pcxn
Dear @BioSok ,
You (or someone) has already posted that repository to our tracker.
See https://github.com/Bioconductor/Contributions/issues/501
You cannot post the same repository more than once.
AdditionalPackage: https://github.com/hidelab/pcxn
Dear @BioSok ,
You (or someone) has already posted that repository to our tracker.
See https://github.com/Bioconductor/Contributions/issues/501
You cannot post the same repository more than once.
AdditionalPackage: https://github.com/hidelab/pcxn
Dear @BioSok ,
You (or someone) has already posted that repository to our tracker.
See https://github.com/Bioconductor/Contributions/issues/501
You cannot post the same repository more than once.
Dear @vobencha ,
I have the pcxn package ready but it seems that the old (combined) pcxn package is already in your tracker, therefore I cant add this new software pcxn package. How can I remove the old package from the tracker?
-Sokratis
AdditionalPackage: https://github.com/hidelab/pcxn
Dear @BioSok ,
You (or someone) has already posted that repository to our tracker.
See https://github.com/Bioconductor/Contributions/issues/501
You cannot post the same repository more than once.
Did you remove the webhook from pcxn when you closed the old issue?
Yes. I even deleted and remade it with the same name.
On Wed, Oct 11, 2017 at 2:03 PM, vobencha notifications@github.com wrote:
Did you remove the webhook from pcxn when you closed the old issue?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/526#issuecomment-335802305, or mute the thread https://github.com/notifications/unsubscribe-auth/AQWOuZ7XNV6g2XYKfT17NepRoAgiV_FYks5srLyhgaJpZM4P0HnQ .
@lshep can you help us out? @BioSok had this previous submission: https://github.com/Bioconductor/Contributions/issues/501
We decided to break the original submission into a data and software package. AFAIK, the approach is to submit the data package, get a clean build, then add the software to the same issue. The software package has the same name as the original issue and we keep getting this error:
https://github.com/Bioconductor/Contributions/issues/526#issuecomment-335796673
Thoughts? Direction? Thanks. Val
This had to be corrected on our end. I have manually pushed a build and you should receive a report shortly. Please ensure the webhook is re-established for updates.
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_20171011105634.html
Thanks @lshep .
Thank you @lshep ! I re-established the web-hook for updating through github. The present error is the one I got previously and posted in Bioc-devel:
Hi all, Today I submitted a new package called "pcxn" in bioconductor and I got the following Abnormal built >result:
Warning in fun(libname, pkgname) : no display name and no $DISPLAY environment variable
Error: processing vignette 'usingPCxNdb.Rnw' failed with diagnostics: chunk 4 (label = pcxn.network) Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : [tcl] invalid command name "font".
The pcxn.network function uses igraph::tkplot to return a network, which works every time on several > local machines. After searching for a while it seems that whenever this problem arises its because of > the igraph package installation. How can I deal with this? Thanks in advance.
To which I got the answer (from Shepherd, Lori):
Yes, this seems to be a problem on our side. We are looking into it. For now you can ignore this ERROR.
There was a similar post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011773.html
As a temporary solution I can comment the problematic line in man files and vignette.
Yes. This ERROR is a problem on our end and we are still in the process of coming up with a solution so please ignore for now.
Received a valid push; starting a build. Commits are:
f51b814 Temp network solution
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_20171011171103.html
Received a valid push; starting a build. Commits are:
6f8d8db fix pcxn.analyze.R
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_20171011171921.html
Received a valid push; starting a build. Commits are:
0ad966c fix vignette
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_20171011173037.html
Received a valid push; starting a build. Commits are:
63b1395 fix vignette
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_20171011173505.html
Received a valid push; starting a build. Commits are:
1e0a6fb fix vignette
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_20171011174209.html
Received a valid push; starting a build. Commits are:
ba8978e fixing package
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_20171012051006.html
Received a valid push; starting a build. Commits are:
3056159 setting lib in analyze
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_20171012052211.html
Received a valid push; starting a build. Commits are:
ead453d setting lib in analyze
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_20171012052607.html
Received a valid push; starting a build. Commits are:
15b3c41 setting lib in analyze
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_20171012053240.html
Received a valid push; starting a build. Commits are:
4314729 setting lib in analyze
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_20171012054938.html
Received a valid push; starting a build. Commits are:
a3f2781 setting lib in analyze
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_20171012062925.html
Received a valid push; starting a build. Commits are:
dfd6802 setting lib in analyze
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_20171012063904.html
Dear @vobencha ,
regarding the pcxn package, my builds come out with various errors although they are clear in my local checks and biocChecks. In windows it fails to locate the 'texi2pdf' output file for my vignette. In the other two servers it cannot find my datasets (again this doesnt happen in my local checks, biocChecks). Thanks for any advice on that.
-Sokratis
Received a valid push; starting a build. Commits are:
9fd4043 adding depends
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