[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

----- Original Message -----

From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Cc: "bioc-devel" <bioc-devel at r-project.org>
Sent: Tuesday, March 29, 2016 12:05:03 PM
Subject: Re: [Bioc-devel] 49 software packages either have no vignettes

or their vignettes are not built by R CMD build!

Thank you,
I am in devel branch (git checkout devel) .

when I "git svn rebase" I get all changed files with message: needs

update.

This doesn't happen with me:

clone https://github.com/kmezhoud/canceR.git
cd canceR/
../mirror/update_remotes.sh
git checkout devel
git svn rebase


No error. You might try doing a fresh clone in another directory.

Dan

How can I update.
km




On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- Original Message -----

From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "bioc-devel" <bioc-devel at r-project.org>
Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Sent: Tuesday, March 29, 2016 6:11:15 AM
Subject: Re: [Bioc-devel] 49 software packages either have no

vignettes

or their vignettes are not built by R CMD build!

Dear Dr Dan,
Thank you for this note.
In my case (canceR), I am using sweave and having:

checking PDF version of manual ... [8s/19s]   OK

during R CMD Check.

I need to sync devel version using git-mirrors (
https://www.bioconductor.org/developers/how-to/git-mirrors/).
I am following scenario 2.
When I fork bioc-mirror/canceR I get two repo with the same name in my
github.

It sounds like you already had a github repository before the fork. In
this case, do not fork, just run the update_remotes.sh script.
Dan

at step 4 of tutorial, I can not push some changes:

error: unable to read askpass response from 'rpostback-askpass'
fatal: could not read Username for 'https://github.com': Device not
configured

1- How can I configure access to bioc-mirror/canceR.

2- What is the utility of the fork if we can commit directly to
bioc-mirror/canceR?

Thank you
Karim


On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum <

dtenenba at fredhutch.org>

wrote:

Attention package maintainers,

When building an R package, if R thinks there is a vignette, it will

emit

this line during R CMD build:

* creating vignettes ... OK

If there is either no vignette, or in the case of non-sweave

vignettes,

something is not set up correctly (there are many things that can go
wrong), you won't see that line of output.

This means your vignette will not be available on our web site, nor

to

end

users who install your package.

So going to the build system and looking through all R CMD build

output

to

see which output files do NOT have that line, returns 49 matches:

$ grep -L "creating vignettes ..." *.buildsrc-out.txt
a4Base.buildsrc-out.txt
a4Classif.buildsrc-out.txt
a4Core.buildsrc-out.txt
a4Preproc.buildsrc-out.txt
a4Reporting.buildsrc-out.txt
affxparser.buildsrc-out.txt
affyio.buildsrc-out.txt
AffyTiling.buildsrc-out.txt
aroma.light.buildsrc-out.txt
arrayQuality.buildsrc-out.txt
bigmemoryExtras.buildsrc-out.txt
BiocCaseStudies.buildsrc-out.txt
BiocGenerics.buildsrc-out.txt
BiocInstaller.buildsrc-out.txt
BufferedMatrixMethods.buildsrc-out.txt
canceR.buildsrc-out.txt
CGHbase.buildsrc-out.txt
CoCiteStats.buildsrc-out.txt
daMA.buildsrc-out.txt
dcGSA.buildsrc-out.txt
DynDoc.buildsrc-out.txt
ExperimentHub.buildsrc-out.txt
flipflop.buildsrc-out.txt
GraphAT.buildsrc-out.txt
HDF5Array.buildsrc-out.txt
hypergraph.buildsrc-out.txt
Icens.buildsrc-out.txt
impute.buildsrc-out.txt
mcaGUI.buildsrc-out.txt
microRNA.buildsrc-out.txt
minet.buildsrc-out.txt
MSstats.buildsrc-out.txt
multtest.buildsrc-out.txt
netresponse.buildsrc-out.txt
nondetects.buildsrc-out.txt
normalize450K.buildsrc-out.txt
oligoClasses.buildsrc-out.txt
parglms.buildsrc-out.txt
plier.buildsrc-out.txt
preprocessCore.buildsrc-out.txt
ProtGenerics.buildsrc-out.txt
QUALIFIER.buildsrc-out.txt
RPA.buildsrc-out.txt
scde.buildsrc-out.txt
seqplots.buildsrc-out.txt
SJava.buildsrc-out.txt
spotSegmentation.buildsrc-out.txt
stepNorm.buildsrc-out.txt
XVector.buildsrc-out.txt

Some of these (a4Base, a4Classif and many more) just have no

vignettes/

directory so no vignettes at all.


Others (ExperimentHub for example) have an empty vignettes directory.

But others (QUALIFIER for example) have a vignettes directory with
vignette files.

If any packages you maintain do not have a vignette, please add one.

If your package has a vignette in the vignettes/ directory but is in

the

above list, then you need to fix it.

This page is a good place to start tracking down the problem:

http://yihui.name/knitr/demo/vignette/

For non-sweave (usually knitr) vignettes, the important things to

check

are:

- knitr should be in the Suggests field in DESCRIPTION
  (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown

are

  also in Suggests).
- VignetteBuilder: knitr should be in DESCRIPTION
- The actual vignette file should have a %\VignetteEngine line; see

link

above
  for more information.

How can you tell if you've fixed the problem?
run R CMD build on your package and look for the line

* creating vignettes ... OK

In the output. If you don't see that line, your vignette has not been
built.

If you've tried all these things and are still running into problems,
contact bioc-devel.

Dan