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

Fri, Apr 1, 2016 8:27 AM

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

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

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