Closed genesofeve closed 5 years ago
Hi @genesofeve
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: projectoR
Type: Package
Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
correlation, and clustering
Version: 0.99.0
Date: 2016-11-22
Author: Genevieve Stein-O'Brien
Maintainer: Genevieve Stein-O'Brien <gsteinobrien@gmail.com>
Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
License: GPL (==2)
Imports:
RColorBrewer (>= 1.0.5),
gplots (>= 2.8.0),
graphics,
grDevices,
methods,
cluster,
shiny,
stats,
utils,
doParallel,
foreach,
iterators,
parallel,
ggplot2,
reshape2,
limma,
MASS
Suggests:
CoGAPS,
BiocStyle,
gridExtra,
grid,
testthat,
devtools,
lintr,
knitr,
rmarkdown,
testthat,
ComplexHeatmap
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
biocViews: Software
BugReports: https://support.bioconductor.org/t/projectoR/
URL: https://github.com/genesofeve/projectoR/
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/projectoR_buildreport_20170728161529.html
Received a valid push; starting a build. Commits are:
1fff4ba .99.1
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/projectoR_buildreport_20170728174522.html
Hello!
Just a friendly reminder that your package is still building with errors. We cannot begin our review of your package until you adjust it so that it clears build and check on all platforms.
so I've having some trouble isolating the source of the errors. The package builds just fine on my computer and on travis (https://travis-ci.org). I am trying to get my hands on a windows machine, but since no compilation is required I'm not sure why cross platform usage would be a problem. I know that people have installed the GitHub repo and it works just fine, which makes me think it may be something to do with the vignette. Any suggestions where to look or common problems of this nature would be greatly appreciated. I hope to have it figured out soon.
On Mon, Aug 7, 2017 at 2:48 PM, Daniel Van Twisk notifications@github.com wrote:
Hello!
Just a friendly reminder that your package is still building with errors. We cannot begin our review of you adjust your package so that it clears build and check on all platforms.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/433#issuecomment-320748103, or mute the thread https://github.com/notifications/unsubscribe-auth/APZDpDa9w3OZHfvVmMGvE0IWlLPcIETBks5sV1vpgaJpZM4OnBUG .
-- Genevieve Stein-O'Brien
Postdoctoral fellow
Division of Oncology Biostatistics and Bioinformatics The Sidney Kimmel Comprehensive Cancer Johns Hopkins University School of Medicine
550 N. Broadway, Suite 1101
Baltimore, MD 21205-2013
Department of Neuroscience & Institute of Genomic Medicine
733 N. Broadway, MRB 515, Baltimore, MD 21205
email: gsteino1@jhmi.edu twitter: genesofeve GitHub: genesofeve
Hello,
Just a few suggestions:
devtools::install_github()
doesn't run any of the checks that our system requires. It is important that you run R CMD build <your_package>
, then R CMD check <your_package>_0.00.0.tar.gz
, and finally R CMD BiocCheck <your_package>_0.00.0.tar.gz
(where 0.00.0 is your package's current version). This should show all the errors that our build system is experiencing.Let me know if this helps or if you have any more questions!
@genesofeve you could try using http://johnmuschelli.com/neuroc/getting_ready_for_submission/index.html#62_appveyor for testing on a windows machine
It doesn't appear that the build problems with the package are related to windows as check
and BiocCheck
is producing the same errors on both Linux and windows machines. These warnings and errors appear to be related mostly to issues with documentation of the package and Bioconductor specific preferences that the package isn't following. The most recent package build report can be accessed at: http://bioconductor.org/spb_reports/projectoR_buildreport_20170728174522.html
Hello, This issue has been pretty quiet for the last month. Just a friendly reminder that if you wish for this package to be reviewed, you must first modify it so that it builds without warnings, errors, or timeouts. Feel free to ask for any help if you need it!
Thank you so much. I'm terribly sorry for the delay, but will be returning to this directly.
Just another friendly reminder that this package must first pass builds and checks on our single package builder before we can review it. If you wish for your package to be included in the 3.6 release of Bioconductor, we would recommend you make changes soon so that we can review it. Again, if you need any help, don't hesitate to leave us a message!
How can I check the build issues? I updated the version but didn't see the corresponding link to see if it passed the checks.
Thanks, Genevieve
On Fri, Sep 29, 2017 at 2:16 PM, Daniel Van Twisk notifications@github.com wrote:
Just another friendly reminder that this package must first pass builds and checks on our single package builder before we can review it. If you wish for your package to be included in the 3.6 release of Bioconductor, we would recommend you make changes soon so that we can review it. Again, if you need any help, don't hesitate to leave us a message!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/433#issuecomment-333200152, or mute the thread https://github.com/notifications/unsubscribe-auth/APZDpO-D2G9CqYw7ItZZzAvON1AvOd2vks5snTQbgaJpZM4OnBUG .
-- Genevieve Stein-O'Brien
Postdoctoral fellow
Division of Oncology Biostatistics and Bioinformatics The Sidney Kimmel Comprehensive Cancer Johns Hopkins University School of Medicine
550 N. Broadway, Suite 1101
Baltimore, MD 21205-2013
Department of Neuroscience & Institute of Genomic Medicine
733 N. Broadway, MRB 515, Baltimore, MD 21205
email: gsteino1@jhmi.edu twitter: genesofeve GitHub: genesofeve
Looks like you changed the name of the package and the GitHub repo https://github.com/genesofeve/projectR/commit/02e8b9860c66a8e2cf0f34fb446cbb744d6f68ba from projectoR
to projectR
. I bet that messed up the single package builder system.
What should I do to fix this (other than change it back, which I would prefer not to do)?
Thanks, Genevieve
On Fri, Sep 29, 2017 at 3:44 PM, Leonardo Collado-Torres < notifications@github.com> wrote:
Looks like you changed the name of the package and the GitHub repo genesofeve/projectR@02e8b98 https://github.com/genesofeve/projectR/commit/02e8b9860c66a8e2cf0f34fb446cbb744d6f68ba from projectoR to projectR. I bet that messed up the single package builder system.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/433#issuecomment-333221092, or mute the thread https://github.com/notifications/unsubscribe-auth/APZDpIpVdgwFnJu3x0MMnKVos9LMAkNeks5snUizgaJpZM4OnBUG .
-- Genevieve Stein-O'Brien
Postdoctoral fellow
Division of Oncology Biostatistics and Bioinformatics The Sidney Kimmel Comprehensive Cancer Johns Hopkins University School of Medicine
550 N. Broadway, Suite 1101
Baltimore, MD 21205-2013
Department of Neuroscience & Institute of Genomic Medicine
733 N. Broadway, MRB 515, Baltimore, MD 21205
email: gsteino1@jhmi.edu twitter: genesofeve GitHub: genesofeve
If you want the new name, I guess that you could close this issue and then open a new one via https://github.com/Bioconductor/Contributions/issues/new. Just double check with the assigned reviewer so that they know/approve this before you do it.
You should probably double check your web-hooks to be sure that they are configured correctly: https://github.com/Bioconductor/Contributions#adding-a-web-hook. If you make any changes to the web-hook, you should perform a version bump to see if it is working. Changing the name of the package shouldn't effect the web-hook's functionality. Message back if this isn't working.
Renaming the repository actually did effect our build system. We had to do some manual work on our end. It should be straightened out and as long as the webhook is still initialized, doing another version bump should trigger a rebuild of your package.
I'll try now. I had previously checked the web hook and it seemed to be in order, but that was over a week ago at this point so I will recheck that as well. Thanks for all of your efforts on this.
On Mon, Oct 2, 2017 at 11:51 AM, lshep notifications@github.com wrote:
Renaming the repository actually did effect our build system. We had to do some manual work on our end. It should be straightened out and as long as the webhook is still initialized, doing another version bump should trigger a rebuild of 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/433#issuecomment-333577146, or mute the thread https://github.com/notifications/unsubscribe-auth/APZDpEydA3TOhfZ_Y5Qy7ujZXy4TBSr1ks5soQaUgaJpZM4OnBUG .
-- Genevieve Stein-O'Brien
Postdoctoral fellow
Division of Oncology Biostatistics and Bioinformatics The Sidney Kimmel Comprehensive Cancer Johns Hopkins University School of Medicine
550 N. Broadway, Suite 1101
Baltimore, MD 21205-2013
Department of Neuroscience & Institute of Genomic Medicine
733 N. Broadway, MRB 515, Baltimore, MD 21205
email: gsteino1@jhmi.edu twitter: genesofeve GitHub: genesofeve
Received a valid push; starting a build. Commits are:
b31164b version bump to test webhook
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/projectR_buildreport_20171002123558.html
Received a valid push; starting a build. Commits are:
8142608 updated biocViews
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/projectR_buildreport_20171002141409.html
Received a valid push; starting a build. Commits are:
087942c change examples to runnable examples in man files
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/projectR_buildreport_20171002154607.html
Received a valid push; starting a build. Commits are:
d726a35 strange build report, rebuilding
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/projectR_buildreport_20171002155420.html
Received a valid push; starting a build. Commits are:
9e9c648 vignette running examples
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/projectR_buildreport_20171006133006.html
Received a valid push; starting a build. Commits are:
519fb35 fixed intersectoR examples to run
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/projectR_buildreport_20171006180330.html
Hello,
I'm glad to see you are now able to make changes. I do need to note that, if you want this package to be included in the next release, it must build without warnings by Wednesday the 18th of October. Message us back if you need any help!
Hello,
It's been a while since this package has seen any activity. Are you still working on this package? Please respond within the next two weeks or I am going to close this issue.
Received a valid push; starting a build. Commits are:
1947d41 test for warnings
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/projectR_buildreport_20171110165909.html
Sorry, I was sidelined by another project. I will get back to it now. Any help you can offer would be greatly appreciated. Although, I have a feeling it is a matter of tracking down some very banal missed details.
Thanks, Genevieve
On Fri, Nov 10, 2017 at 2:32 PM, Daniel Van Twisk notifications@github.com wrote:
Hello,
It's been a while since this package has seen any activity. Are you still working on this package? Please respond within the next two weeks or I am going to close this issue.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/433#issuecomment-343565206, or mute the thread https://github.com/notifications/unsubscribe-auth/APZDpKSTLd44FSo9Phpy_z-Z9ACSLWXRks5s1KTSgaJpZM4OnBUG .
-- Genevieve Stein-O'Brien
Postdoctoral fellow
Division of Oncology Biostatistics and Bioinformatics The Sidney Kimmel Comprehensive Cancer Johns Hopkins University School of Medicine
550 N. Broadway, Suite 1101
Baltimore, MD 21205-2013
Department of Neuroscience & Institute of Genomic Medicine
733 N. Broadway, MRB 515, Baltimore, MD 21205
email: gsteino1@jhmi.edu twitter: genesofeve GitHub: genesofeve
Received a valid push; starting a build. Commits are:
0791303 fix clusterPlotR
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/projectR_buildreport_20171110174243.html
Received a valid push; starting a build. Commits are:
1905378 removed stray file
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/projectR_buildreport_20171110175053.html
Received a valid push; starting a build. Commits are:
9f833b9 update version
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/projectR_buildreport_20171110180207.html
Received a valid push; starting a build. Commits are:
5143e44 update version
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/projectR_buildreport_20171110182720.html
Hello,
Since your package is running without error, I assume that your are ready for a review. As your package stands right now, it uses S3 dispatch in its user facing functions. This is not allowed for Bioconductor packages, user facing functions must cannot use S3dispatch. I need to ask that you use S4 methods for any user facing functionality.
Hello,
Just another reminder that the above change must be made before we can provide you with a more detailed review.
Hello,
Just another reminder about fixing the suggestion we made on Nov. 21. We will be happy to help you with any issues you are having, but we need a response just to be sure that this issue is still active. Please leave a message soon about what you are doing with the package. If you do not respond within two weeks, we will close this issue and you will need to resubmit your package.
My understanding is that I need to completely recode the package to S4 standards. I would welcome any help, suggestion, etc that people may have on that front as this is a nontrivial undertaking and I am currently a one person development team with numerous other obligations (also the reason for the lag between updates).
Thanks in advance, G
On Fri, Dec 22, 2017 at 2:33 PM, Daniel Van Twisk notifications@github.com wrote:
Hello,
Just another reminder about fixing the suggestion we made on Nov. 21. We will be happy to help you with another issues you are having, but we need a response just to be sure that this issue is still active. Please leave a message soon about what you are doing with the package. If you do not respond within two weeks, we will close this issue and you will need to resubmit 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/433#issuecomment-353661959, or mute the thread https://github.com/notifications/unsubscribe-auth/APZDpOuoWmISUyzGR9Ln7HH2-CHd0h3qks5tDAQNgaJpZM4OnBUG .
-- Genevieve Stein-O'Brien
Postdoctoral fellow
Division of Oncology Biostatistics and Bioinformatics The Sidney Kimmel Comprehensive Cancer Johns Hopkins University School of Medicine
550 N. Broadway, Suite 1101
Baltimore, MD 21205-2013
Department of Neuroscience & Institute of Genomic Medicine
733 N. Broadway, MRB 452, Baltimore, MD 21205
email: gsteino1@jhmi.edu twitter: genesofeve GitHub: genesofeve
Sorry for the delay. I've sent you a pull request for your package giving an example on how to convert your S3 methods to S4 methods for the cluster2pattern()
method. Please implement similar changes to the rest of your S3 methods so that we can continue the review. Feel free to message me back if you have any questions.
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