[R-pkg-devel] SystemRequirements: Berkeley DB STL

[Hong Ooi]

This looks like a similar situation to the C++ Boost headers, which are packaged up for easy R consumption in the boost package. You could try doing that with BerkeleyDB.

There's another issue though: looking at your FAQ page, you seem to rely on a bunch of tools written by UCSC. These tools aren't available for Windows, or at least I didn't see a download link. What are Windows users supposed to do?


-----Original Message-----
From: R-package-devel <r-package-devel-bounces using r-project.org> On Behalf Of Toby Hocking
Sent: Wednesday, 24 October, 2018 5:03 AM
To: r-package-devel using r-project.org
Subject: [R-pkg-devel] SystemRequirements: Berkeley DB STL

I would like to put the https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftdhock%2FPeakSegDisk&data=02%7C01%7Chongooi%40microsoft.com%7C8a2dca6e52e844d5f38808d6392ba1c3%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636759256910869612&sdata=bxglS4I%2BlPieYCAjiZHIAvnkOLqCIwxj%2BPocGrfRR2Q%3D&reserved=0 package on
CRAN. This package needs Berkeley DB C++ Standard Template Library. What do
I need to do to get this package (with compiled mac/windows binaries) on
CRAN?

This C++ library is relatively easy to install
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftdhock%2FPeakSegPipeline%2Fwiki%2FFAQ%23installing-berkeleydb-stl&data=02%7C01%7Chongooi%40microsoft.com%7C8a2dca6e52e844d5f38808d6392ba1c3%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636759256910869612&sdata=%2FGQgkzrA7bveVJkRGcfr4swCsZ5EoQUzqRcW%2BGR8lS0%3D&reserved=0
but probably too big (tar.gz source code is 43MB) to include in the R
package, so I have indicated this external library dependency in the
SystemRequirements field of DESCRIPTION. I have also put PKG_LIBS=-ldb_stl
in my src/Makevars. Is that OK?

My Linux travis builds pass CRAN checks just fine
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftravis-ci.org%2Ftdhock%2FPeakSegDisk%2Fjobs%2F442813478&data=02%7C01%7Chongooi%40microsoft.com%7C8a2dca6e52e844d5f38808d6392ba1c3%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636759256910869612&sdata=RGv3KjWuWcp7mR2JVBZzFj7mQErYHceC2cweRwWD93E%3D&reserved=0 because I have
installed the libdb5.1-stl-dev package which provides -ldb_stl.

Usually I check my packages on win-builder prior to CRAN submission. When I
check PeakSegDisk on win-builder, I get a linker error (db_stl not found)
because presumbly it is not installed on the win-builder machine. So
presumably my package would not pass checks on CRAN.

I have emailed Uwe Ligges to ask to install BerkeleyDB STL on win-builder
but I have got no response. Is there anybody else I should ask?

Is there anything else I should do?

FYI I believe that I have done my homework. From a search of
"systemrequirements" on r-package-devel I saw that there are several
related threads, for example a message on Feb 4 from Dirk who explains how
to use PKG_LIBS. However I did not see any specific explanation of how to
get a package with dependent compiled code on CRAN. Maybe the officially
accepted method should be added to Writing R Extensions or CRAN Repository
policies?

Thanks in advance for any help/advice you can provide.
Toby Dylan Hocking

	[[alternative HTML version deleted]]

______________________________________________
R-package-devel using r-project.org mailing list
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-package-devel&data=02%7C01%7Chongooi%40microsoft.com%7C8a2dca6e52e844d5f38808d6392ba1c3%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636759256910869612&sdata=JHyirFiiFY9zonR9p2CgeQh2EuP3YBsi%2FZLG2NFv%2FDA%3D&reserved=0