swfdr

[SiminaB]

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[bioc-issue-bot]

Hi @SiminaB

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: swfdr
Title: Science-wise false discovery rate estimation
Version: 0.99.0
Author: Jeffrey T. Leek, Simina M. Boca
Maintainer: Simina M. Boca <smb310@georgetown.edu>, Jeffrey T. Leek <jtleek@gmail.com>
Description: This package allows users to estimate the science-wise false discovery rate from Jager and Leek, 
    "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach
    due to the presence of rounding and censoring. It also allows users to estimate the proportion of true null
    hypotheses in the presence of covariates, using a regression framework, as per Boca and Leek, "A regression
    framework for the proportion of true null hypotheses," 2015, bioRxiv preprint.
Depends:
    R (>= 3.3.0)
Imports:
    MASS, splines, stats4, genefilter, lme4, reshape2
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr,
    rmarkdown
VignetteBuilder: knitr

[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
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[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, 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/swfdr_buildreport_20161209151659.html

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION
file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to
do anything. If you did want to start a build, increment
the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION
file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to
do anything. If you did want to start a build, increment
the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION
file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to
do anything. If you did want to start a build, increment
the Version: field and try again.

[bioc-issue-bot]

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

b0e5d70 Incremented version to 0.99.1

[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, 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/swfdr_buildreport_20161209230745.html

[bioc-issue-bot]

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

0077a2f Fixed some errors, incremented version to 0.99.2

[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, 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/swfdr_buildreport_20161210004014.html

[bioc-issue-bot]

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

38a712d Fixed some warnings, incremented to 0.99.3

[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, 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/swfdr_buildreport_20161210201234.html

[bioc-issue-bot]

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

74f36ad Removed files from inst/doc and upgraded to 0.99.4

[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: "WARNINGS, 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/swfdr_buildreport_20161210205522.html

[bioc-issue-bot]

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

bce8f54 Changes to vignette header, incremented to 0.99.5

[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, 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/swfdr_buildreport_20161211000638.html

[bioc-issue-bot]

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

b3107cd Changed vignette to html, incremented to 0.99.6

[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, 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/swfdr_buildreport_20161211003244.html

[bioc-issue-bot]

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

817b1cd Compressed data file, incremented to 0.99.7

[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: "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/swfdr_buildreport_20161212011808.html

[bioc-issue-bot]

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

206c77c Removed 2 variables, incremented to 0.99.8 Remove...

[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/swfdr_buildreport_20161213162644.html

[SiminaB]

Hi Herve @hpages ,
It looks like the ERROR issue with the MAC build on oaxaca is common to other folks as well, for example here http://bioconductor.org/spb_reports/ChIPexoQual_buildreport_20161207193202.html #79
I have a Windows machine and I cannot reproduce the error - it looks like pdflatex is just not installed on oaxaca though.

Thanks so much!
Best,
Simina

[bioc-issue-bot]

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

12b532b Incremented version to 0.99.9 to test Mac 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.

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/swfdr_buildreport_20161221233157.html

[mtmorgan]

I'm really sorry for the delay in getting this review to you. The package looks in great shape, and I have only one suggestion

• include the script for generating journals_pVals.Rd as a script,
  inst/script/getPvalues.R instead of referencing a github url.

Please respond and if you change your package include a version bump, and I'll be happy to accept the revision.

[bioc-issue-bot]

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

4c41bd6 Small changes in DESCRIPTION, add inst/script

[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/swfdr_buildreport_20170127111624.html

[SiminaB]

Thank you so much @mtmorgan ! I just made the change you suggested.

[mtmorgan]

Great, I've marked your package as accepted. It will be added to the Bioconductor SVN repository and additional information forwarded over the next couple of days.