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

From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org>
Sent: Friday, April 1, 2016 2:25:56 PM
Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

git clone https://github.com/Bioconductor-mirror/canceR
cd canceR/
bash ../update_remotes.sh
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Rebuilding
.git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
...
r100351 = 942469704de53586b277926f1b3d358ffd808152
r100809 = 0aa2b86471d49cace7d4baa504684c2e86f47830
r100810 = 3940d764844e9051172fd1d05fe606ee56764e67
r100984 = 55fba8349ef754fc51a78367c19a8bc8f29b881e
r100985 = b313b60029281d2c8486d0dc9e6a34c2f68fd9be
r100987 = a8cd3e44badee5b04548fff7a9faeca2f8448489
r101023 = f625ce6a1d225016103768be2e051593ba785832
r102448 = a2c8236451c5e04cc1e43f4568472de8ea8361ba
r102571 = f6fc58dd50aa611f3b1930fd850df9c5471c7f94
r102584 = fdd1ce259835d1325645a17e80affa4f0656fc41
r102591 = 2e2874d3ad1d00f3599dcdc6ef7347199dc8b651
r102594 = 363ea15b52e2c00cc063c1bffeb167c70390769c
r102693 = 535c658791a5218ad341b329c2e049c4b04c9584
r102694 = 26c26df43c2ddf12008543e4f647f135bde63cf7
r102695 = af7cd2771d0695bb92c4d6a433b545cf63940463
r102854 = 954b8510e0fe68211fc315787a1c866ad237e8a5
r103140 = f042db172a7f04f00c04ca9e233df54bbc1746a1
r103142 = efb740a41e489809c91cd6f3a42516adddb6b050
r103607 = 1b9435efea2dd8d14593ad500f59623bcecbe155
r106326 = c9a8e4f83e33c277e26b58b03848c8bb304b9571
r106461 = 9726cf88862426c96fbbd238321599e99444fd12
r109589 = 88ef0e88bb6ab106d53100787d698672d6f44bac
r109592 = a8299618231a8ce2891e20310f4cbf2fddc24526
r115378 = 1da8432c11ae9cbc38950c22e16093fc4c97853f
r115379 = 2592b6a5ac7c41003611ce44b93ff9b6ac8c5a54
r115385 = 7fbc307287b25ff7efe7235001921791f2668898
r115387 = 1fe033d9fdd765f6c7e6a2a884053721bbd5691a
r115608 = 025a596f5f717b527b9a5c92612d48a09e93f0a8
Done rebuilding
.git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
Current branch master is up to date.
Commit to git as normal, when you want to push your commits to svn
 1. `git svn rebase` to get the latest SVN changes.
 2. `git svn dcommit --add-author-from` to commit your changes to SVN.


add files/forder to /vignette
pump version DESCRIPTION

git commit -m "fix vignette"
git svn rebase
Current branch master is up to date.

git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
   A    vignettes/canceR.Rnw
   A    vignettes/canceR.latex
   A    vignettes/image/BrstPrstGSEAlm.png
   A    vignettes/image/whichMSigDB2.jpeg
   A    vignettes/image/workspace.png
   M    vignettes/.gitignore

ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
 File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 283, in <module>
   myexit(0)
TypeError: myexit() takes exactly 2 arguments (1 given)

W: 35d29461f59277e54461a31161c6522053c666ad and refs/remotes/git-svn
differ, using rebase:
:040000 040000 e29c612e777ebd221293caaccbfb810b293addd0
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M    vignettes
Current branch master is up to date.
ERROR: Not all changes have been committed into SVN, however the committed
ones (if any) seem to be successfully integrated into the working tree.
Please see the above messages for details.

git diff


No thing



On Fri, Apr 1, 2016 at 9:48 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

Sorry, about that, please try again.

Dan


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

From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Sent: Friday, April 1, 2016 1:36:30 PM
Subject: Re: [Bioc-devel] 49 software packages either have no vignettes

or their vignettes are not built by R CMD build!

git reset --hard HEAD~
bash ../update_remotes.sh

add files/folder  to / vignette
pump version in DESCRIPTION
check all change
git commit -m "fix vignette"
git svn rebase
git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
   A    vignettes/canceR.Rnw
   A    vignettes/canceR.latex
   A    vignettes/image/BrstPrstGSEAlm.png
   A    vignettes/image/BrstPrstGSEAlm1.jpeg
   A    vignettes/image/BrstPrstGSEAlm2.jpeg
   A    vignettes/image/BrstPrstGSEAlm3.jpeg
   A    vignettes/image/BrstPrstGSEAlm4.jpeg
   A    vignettes/image/Circos.png
   A    vignettes/image/Coxph.png
   A    vignettes/image/stadGSEAlm2.jpeg
   A    vignettes/image/stadGSEAlm3.jpeg
   A    vignettes/image/stadGSEAlm4.jpeg
   A    vignettes/image/stadGSEAlm5.jpeg
   A    vignettes/image/stadGSEAlm6.jpeg
   A    vignettes/image/stadGSEAlm7.jpeg
   A    vignettes/image/stadGSEAlm8.jpeg
   A    vignettes/image/stadGSEAlm9.jpeg
   A    vignettes/image/stadGSEAlmCNA.png
   A    vignettes/image/starting.png
   A    vignettes/image/starting.svg
   A    vignettes/image/startingWindow.jpeg
   A    vignettes/image/whichMSigDB.png
   A    vignettes/image/whichMSigDB1.jpeg
   A    vignettes/image/whichMSigDB2.jpeg
   A    vignettes/image/workspace.png
   M    DESCRIPTION

ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
 File

"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",

line 283, in <module>
   process_diff(diff)
 File

"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",

line 118, in process_diff
   filename = segs0[1]
IndexError: list index out of range

W: 989187ef342a32768b73a4a852bf20aaee9f2dec and refs/remotes/git-svn
differ, using rebase:
:100755 100755 47dcc306473ddd67eb11ec42423b30991b72099c
6b7df529709f10184b376d69d5ea9f3ae9e1d3fe M    DESCRIPTION
:040000 040000 056451883aa9ba2af9e19f8dd2a285d412b9ae60
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M    vignettes
Current branch master is up to date.
ERROR: Not all changes have been committed into SVN, however the

committed

ones (if any) seem to be successfully integrated into the working tree.
Please see the above messages for details.

MBP-de-MacBook:canceR Mezhoud$ git diff
MBP-de-MacBook:canceR Mezhoud$

NO THING IN DIFF


On Fri, Apr 1, 2016 at 8:13 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

[removing bioc-devel from the thread]

Please try the git svn dcommit again, I have modified the post commit

hook.

Dan


----- 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: Friday, April 1, 2016 12:08:45 PM
Subject: Re: [Bioc-devel] 49 software packages either have no

vignettes

or their vignettes are not built by R CMD build!

NO thing in the file

On Fri, Apr 1, 2016 at 6:24 PM, Dan Tenenbaum <dtenenba at fredhutch.org

wrote:

Can  you send me the output of

git diff?

So:

git diff > diff.txt

and send me diff.txt?

Dan


----- 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: Friday, April 1, 2016 9:27:52 AM
Subject: Re: [Bioc-devel] 49 software packages either have no

vignettes

or their vignettes are not built by R CMD build!

Hi,
I tried the scenario 1:
git clone https://github.com/Bioconductor-mirror/canceR
cd canceR

bash ../update_remotes.sh
add files/dir  in /vignette
pump version in DESCRIPTION

commit -m "fix vignette"
git svn rebase
git svn dcommit --add-author-from


MBP-de-MacBook:canceR Mezhoud$ git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR

...

   A    inst/doc/canceR.pdf
   A    vignettes/canceR.Rnw
   A    vignettes/canceR.latex
   A    vignettes/image/BrstPrstGSEAlm.png
   A    vignettes/image/BrstPrstGSEAlm1.jpeg
   A    vignettes/image/BrstPrstGSEAlm2.jpeg
   A    vignettes/image/BrstPrstGSEAlm3.jpeg
   A    vignettes/image/BrstPrstGSEAlm4.jpeg
   A    vignettes/image/Circos.png
   A    vignettes/image/Coxph.png
   A    vignettes/image/GSEA-R.png
   A    vignettes/image/Mutation1.png
   A    vignettes/image/clinicalDataDialog.png
   A    vignettes/image/dialogCircos.png
   A    vignettes/image/gct_cls.png
..............
   A    vignettes/image/setWorkspace.jpeg
   A    vignettes/image/stadGSEAlm4.jpeg
   A    vignettes/image/stadGSEAlm5.jpeg
   A    vignettes/image/stadGSEAlm6.jpeg
   A    vignettes/image/stadGSEAlm7.jpeg
   A    vignettes/image/stadGSEAlm8.jpeg
   A    vignettes/image/stadGSEAlm9.jpeg
   A    vignettes/image/stadGSEAlmCNA.png
   A    vignettes/image/starting.png
   A    vignettes/image/starting.svg
   A    vignettes/image/startingWindow.jpeg
   A    vignettes/image/whichMSigDB.png
   A    vignettes/image/whichMSigDB1.jpeg
   A    vignettes/image/whichMSigDB2.jpeg
   A    vignettes/image/workspace.png
   M    DESCRIPTION

ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit

code 1)

with output:
Traceback (most recent call last):
 File

"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",

line 277, in <module>
   process_diff(diff)
 File

"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",

line 112, in process_diff
   filename = segs0[1]
IndexError: list index out of range

W: e980c09a87a818a1736f38304e18325b7c0362f5 and

refs/remotes/git-svn

differ, using rebase:
:100755 100755 d4a308bbf85b4f0ba06ee27af51f1e76804bad2a
6b7df529709f10184b376d69d5ea9f3ae9e1d3fe M    DESCRIPTION
:040000 040000 de5dbdd606d8758565afcadbaf04e5821e71b461
870588b10784e8f5169b2f7bf6377985edd3a735 M    inst
:040000 040000 056451883aa9ba2af9e19f8dd2a285d412b9ae60
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M    vignettes
Current branch master is up to date.
ERROR: Not all changes have been committed into SVN, however the

committed

ones (if any) seem to be successfully integrated into the working

tree.

Please see the above messages for details.


On Fri, Apr 1, 2016 at 4:27 PM, Dan Tenenbaum <

dtenenba at fredhutch.org

wrote:

Just because git tells you to push, doesn't mean you should push!

;)

In the devel branch, the upstream repository is an svn

repository, so

instead of pushing you want to do

git svn dcommit --add-author-from

I'll take a look at your earlier email later today.

Dan


----- 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: Friday, April 1, 2016 5:17:32 AM
Subject: Re: [Bioc-devel] 49 software packages either have no

vignettes

or their vignettes are not built by R CMD build!

Hi,
What is the meaning of this? Thanks

git checkout devel

Previous HEAD position was 1fe033d... add /image
Switched to branch 'devel'
Your branch is ahead of 'bioc/master' by 49 commits.
 (use "git push" to publish your local commits)

git push

fatal: The upstream branch of your current branch does not match
the name of your current branch.  To push to the upstream branch
on the remote, use

   git push bioc HEAD:master

To push to the branch of the same name on the remote, use

git push HEAD:master


ssh: Could not resolve hostname head: nodename nor servname

provided,

or

not known
fatal: Could not read from remote repository.

Please make sure you have the correct access rights



On Fri, Apr 1, 2016 at 1:09 AM, Karim Mezhoud <

kmezhoud at gmail.com>

wrote:

Hi,
I repeated several times the clone ....And I success for one

time

the

commit but with mistakes. I can't repeat the steps again.

git merge master --log

And I had a conflict between versions. I omit conflicts and I

git svn dcommit --add-author-from

##############################
A....
A.....
A.....
All files are added


ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook

(exit

code

1)

with output:
Traceback (most recent call last):
  File

"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",

line 277, in <module>
    process_diff(diff)
  File

"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",

line 112, in process_diff
    filename = segs0[1]
IndexError: list index out of range

W: bc9bed01f7b03d6da5b345d2699822d197b202b4 and

refs/remotes/git-svn-devel

differ, using rebase:
:100644 100644 d4a2ec80b4623bc866606de39e06ff33e60056a8
cea7fa70e88adf9033fce5d7a846944c3431ee85 M    .gitignore
:100755 100755 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe
15ac213b3484b967cceabc0c0e22bda2d654b27a M    DESCRIPTION
:040000 040000 e2c182ee6256b99e4c83e2dac8e7576fedeef302
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M    vignettes

It seems that there is already a rebase-apply directory, and
I wonder if you are in the middle of another rebase.  If that

is

the

case, please try
    git rebase (--continue | --abort | --skip)
If that is not the case, please
    rm -fr

"/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"

and run me again.  I am stopping in case you still have

something

valuable there.
rebase refs/remotes/git-svn-devel: command returned error: 1
@#####################################




I removed


rm -fr /Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply

and

git svn rebase

###########################
First, rewinding head to replay your work on top of it...
Applying: canceR0.99.1
Using index info to reconstruct a base tree...
.git/rebase-apply/patch:102: trailing whitespace.

.git/rebase-apply/patch:103: trailing whitespace.

.git/rebase-apply/patch:106: trailing whitespace.

.git/rebase-apply/patch:113: trailing whitespace.

.git/rebase-apply/patch:120: trailing whitespace.

warning: squelched 7388 whitespace errors
warning: 7393 lines add whitespace errors.
Falling back to patching base and 3-way merge...
error: The following untracked working tree files would be

overwritten

by

merge:
    vignettes/._canceR.pdf
Please move or remove them before you can merge.
Aborting
error: Failed to merge in the changes.
Patch failed at 0001 canceR0.99.1
The copy of the patch that failed is found in:

.git/rebase-apply/patch

When you have resolved this problem, run "git rebase

--continue".

If you prefer to skip this patch, run "git rebase --skip"

instead.

To check out the original branch and stop rebasing, run "git

rebase

--abort".

rebase refs/remotes/git-svn-devel: command returned error: 128
###############################

I did not found any whitespace in path file line: 102, 103,

106,

113,

120

patch file from 112 to 120:

*@@ -0,0 +1,73 @@*

*+Match_GeneList_MSigDB <- function(){*

*+    *

*+    *

*+    ttdialogMSigDB<-tktoplevel()*

*+    tktitle(ttdialogMSigDB) <- "Setting MSigDB Directory"*

*+    *

*+    fromDir <- function(){*

*+        ##Select directory which has MSigDB*

*+        myGlobalEnv$dirMSigDBPath <- tk_choose.dir()*

*+        tkdestroy(ttdialogMSigDB)*

*+        #return(dirMSigDBPath)*

*+    }*

*+    *

*+    fromExample <- function(){*

*+        ##Or select MSigDB from package*

*+        myGlobalEnv$dirMSigDBPath <-
paste(path.package("canceR"),"/extdata/MSigDB/",sep="")*

*+        tkdestroy(ttdialogMSigDB)*

*+        #return(dirMSigDBPath)*



 after I    git svn rebase

It seems that there is already a rebase-apply directory, and
I wonder if you are in the middle of another rebase.  If that

is

the

case, please try
    git rebase (--continue | --abort | --skip)
If that is not the case, please
    rm -fr

"/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"

and run me again.  I am stopping in case you still have

something

valuable there.
rebase refs/remotes/git-svn-devel: command returned error: 1

On Tue, Mar 29, 2016 at 8:12 PM, Dan Tenenbaum <

dtenenba at fredhutch.org>

wrote:

----- 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