Hi Ar,
On 03/15/2017 12:57 AM, Aayush Raman wrote:
Hello Everyone,
I have developed a Bioconductor package and submit the issue to build and
check. I have some questions regarding on the build and BioCheck of the
package. Here are the questions:
1. It has passed the build and check on Mac OS and Windows. However, when I
am checking it on linux, I am getting the following error:
"ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package
‘DASC’"
Although, I know the NMF and cvxclustr are not present in the linux
machine, I would like to know if it possible to build the package by
installing other packages that my package depends on ? I am already
mentioned it on DESCRIPTION file. Do I need to do anything else before
submitting my package ?
You have these packages listed in your Imports field so they will be
automatically installed by the Single Package Builder on the 3 build
machines if they are not already present.
2. After successfully building (using R CMD build) and checking (R CMD
check), I did a BiocCheck on my package. I got 2 warnings:
a. WARNING: Use FALSE instead of F (found in 1 files)
I am using a function called norm (from base package) where I need to
specify the type. The type I would like to use is Frobenius norm which is
specified by "F/f". How can I remove this warning ? or infom bioconductor
about this warning prior to their checks ?
I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz.
Have you addressed this already? Please note that the way to specify
the type in base::norm() is with a 1-letter *string* ("O", "I", "F",
"M", or "2"). This has nothing to do with the use of F (unquoted) for
specifying the single logical value FALSE.
b. WARNING: Add non-empty \value sections to the following man pages:
data.Rd:
data.Rd is a dataset that I will be uploading with our package. I would
like to know how can I remove this error ?
Man pages for data sets need a \format section instead of a \value
section. If you have one, and R CMD BiocCheck still complains about
the lack of a \value section, please ignore the warning.
Hope this helps,
H.
Any help or advice would be much appreciated.
Thanks,
-Ar
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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