Re: [Bioc-devel] error in loading pbdMPI on tokay2

[Armen Abnousi]

Hi Valerie,

Thanks for your reply. I can make it work using snow I believe. But the
problem is that all functions in these packages that you have suggested
(including snow; as far as I have seen) return the answer to one node and
then if I want all nodes to have the same answer I will need to broadcast
it to all nodes or repeat the same operation. This is very prohibitive,
requiring a lot of communication. On the other hand if I could use MPI
functionality, allGather would cut the operation to half (if not more,
given the size of the communication that will be needed. I haven't been
able to find a package with a functionality similar to allGather that will
work without MPI. With larger dataset sizes, this problem becomes more
threatening and that is just the opposite of what drives us to use
parallelism. I don't know if there is any other option, maybe we can't do
better, but I thought I'll let you know what my problem is and maybe you'll
suggest a better way to deal with it. Thank you again.

Thanks,
Armen

On Wed, Jan 31, 2018 at 2:37 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Armen,
>
> MPI is not installed on the Windows builders so pbdMPI is not supported.
> Was there a specific reason you chose pbdMPI? There are several other
> options for parallel evaluation which are supported across all 3 platforms,
> e.g., BiocParallel, doParallel and batchtools.
>
> I took a brief look at what naddaR is importing from pdbMPI and didn't see
> anything unusual - I believe you can find all functionality in one of the
> alternatives. Please have a look and let us know if one of these will work
> for you.
>
> Thanks.
> Valerie
>
>
>
> On 01/27/2018 12:35 PM, Armen Abnousi wrote:
>
> Hi,
>
> I'm submitting a package for build, but for windows it goes to tokay2 and
> fails during the build with the following message:
>
> --
>
> * checking for file 'naddaR/DESCRIPTION' ... OK
> * preparing 'naddaR':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
>   ---
> * installing *source* package 'naddaR' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : .onLoad failed in loadNamespace() for 'pbdMPI', details:
>   call: inDL(x, as.logical(local), as.logical(now), ...)
>   error: unable to load shared object
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/626/R-libs/pbdMPI/libs/x64/pbdMPI.dll':
>   LoadLibrary failure:  The specified module could not be found.
>
> ERROR: lazy loading failed for package 'naddaR'
> * removing 
> 'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp4kcgED/Rinst1ffc2775216d/naddaR'
> In R CMD INSTALL
>   ---
> ERROR: package installation failed
>
> 
> ---
>
> How can I change this? It builds for Linux and Mac on Merida2 and Malbec2.
>
> Thanks,
> Armen
>
>   [[alternative HTML version deleted]]
>
> ___bioc-de...@r-project.org 
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>
>
>
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Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see this on the 
rsvg landing page:

https://cran.r-project.org/web/packages/rsvg/index.html

Nothing we can do until CRAN makes them available.

Valerie


On 02/07/2018 08:29 AM, Kevin Horan wrote:


The ChemmineR build is failing on the mac due to a new dependency not
being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


Kevin

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[Bioc-devel] release build of ChemmineR failing

[Kevin Horan]

The release version of ChemmineR is failing on windows. It seems to be a
build script issue though, possibly something on your side. The package
was building fine a few weeks ago and I have not modified it. Can you
please have a look? Thanks.

"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "library(rmarkdown); 
library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
'C:\Users\BIOCBU˜1\BBS-3˜1.6-B\R\bin\x64\Rscript.exe" -e "library' is 
not recognized as an internal or external command,operable program or 
batch file.


http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-buildsrc.html


Kevin

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[Bioc-devel] rsvg on mac

[Kevin Horan]

The ChemmineR build is failing on the mac due to a new dependency not 
being available, the package "rsvg". Would it be possible to install 
that on the mac build machine? Thanks.


http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


Kevin

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Re: [Bioc-devel] Nightly builds

[Leonardo Collado Torres]

On Wed, Feb 7, 2018 at 10:36 AM, Leonardo Collado Torres
 wrote:
> Hi,
>
> I try to follow all the best practices but sometimes I end up relying
> on the Bioc nightly build.
>
> Anyhow, I personally use r-travis** for quick checks to detect broken
> commits instead of running R CMD check/build on my laptop. This way I
> can submit a new commit that fixes a broken commit before the Bioc
> nightly build in about the same time as using my laptop. r-travis
> doesn't always work as Bioc might have newer versions of dependencies
> or other issues (cache, timing, installation of deps), but it helps
> most of the time. A scenario where I definitely rely on the Bioc
> nightly build is when I can't reproduce the error/warning on my
> machine (with the latest setup). For example, Windows issues***.
>
> Note that I do run a quick local test of whatever bug I'm solving, but
> I might miss how my changes affected another unit test.
>
> Best,
> Leonardo
>
> ** Example setup
> https://github.com/leekgroup/derfinderPlot/blob/master/.travis.yml
> *** You can also use r-hub for testing in other OS including Windows
> but maybe not with the R version that bioc-devel needs and/or without
> being able to set useDevel(). Example
> https://github.com/LieberInstitute/jaffelab/blob/master/.travis.yml#L17-L18
> I've only used it for that non-bioc package.

More on r-hub and Bioc https://github.com/r-hub/rhub/issues/38 which I
just found

>
> On Wed, Feb 7, 2018 at 9:51 AM, Martin Morgan
>  wrote:
>>
>>
>> Bioc developers!
>>
>> I've been exploring the Bioconductor nightly builds
>>
>>   http://bioconductor.org/checkResults/
>>
>> a bit using this in-development package.
>>
>>   https://github.com/mtmorgan/BiocBuildReports
>>
>> This
>>
>>   rpt <- report()
>>   filter_recent(rpt) %>% print(n = n())
>>
>> summarizes the packages changed in the 24 hours before the current build 
>> snapshot, and their fate on the nightly builds
>>
>> > filter_recent(rpt) %>% print(n=nrow(.))
>> # A tibble: 18 x 5
>>package   buildsrc checksrc push txt
>> 
>>  1 AllelicImbalance  ERRORskipped  skipped  skipped
>>  2 ChIPpeakAnno  ERRORskipped  skipped  skipped
>>  3 GenomicScores ERRORskipped  skipped  skipped
>>  4 genphen   ERRORskipped  skipped  skipped
>>  5 metavizr  ERRORskipped  skipped  skipped
>>  6 QUBIC ERRORskipped  skipped  skipped
>>  7 Repitools OK   ERRORskipped  skipped
>>  8 rtracklayer   OK   WARNINGS UNNEEDED same version exists in 
>> interna…
>>  9 genoset   OK   WARNINGS YES  new version is higher than 
>> in …
>> 10 IRanges   OK   WARNINGS YES  new version is higher than 
>> in …
>> 11 LOLA  OK   WARNINGS YES  new version is higher than 
>> in …
>> 12 DAPAR OK   OK   UNNEEDED same version exists in 
>> interna…
>> 13 AnnotationHubData OK   OK   YES  new version is higher than 
>> in …
>> 14 BEARscc   OK   OK   YES  new version is higher than 
>> in …
>> 15 ChemmineR OK   OK   YES  new version is higher than 
>> in …
>> 16 DESeq2OK   OK   YES  new version is higher than 
>> in …
>> 17 Onassis   OK   OK   YES  new version is higher than 
>> in …
>> 18 synergyfinder OK   OK   YES  new version is higher than 
>> in …
>>
>> A couple of things strike me about this.
>>
>>   - All the packages with 'ERROR' in the buildsrc or checksrc column failed 
>> to propagate because the commit, or a previous version, does not build or 
>> check. It is not a very productive development model to push broken commits 
>> to git.bioconductor.org, especially if the developer doesn't realize that 
>> the commits are broken. The best practice is to build and check packages 
>> locally, and then commit.
>>
>>   R CMD build 
>>   R CMD check >
>> An even more robust approach is to clone the repository locally, so that the 
>> build and check are against only the committed changes and not miscellaneous 
>> files or versions hanging out in your source directory
>>
>>   cd /tmp
>>   git clone /path/to/
>>   R CMD build 
>>   ...
>>
>> I would not suggest using devtools during this final stage; the build system 
>> doesn't use devtools, as devtools has its own ideas about options etc with 
>> which to build packages. The very careful would also use the build and check 
>> options found on the build report of each package, e.g., from
>>
>>
>> http://bioconductor.org/checkResults/3.7/bioc-LATEST/rtracklayer/malbec2-buildsrc.html
>>
>> one might
>>
>>   R CMD build --keep-empty-dirs --no-resave-data rtracklayer
>>
>> A common problem is that packages are built and checked locally using the 
>> wrong version of R and / or Bioconductor -- commits to the devel branch 
>> should be against 

Re: [Bioc-devel] Nightly builds

[Leonardo Collado Torres]

Hi,

I try to follow all the best practices but sometimes I end up relying
on the Bioc nightly build.

Anyhow, I personally use r-travis** for quick checks to detect broken
commits instead of running R CMD check/build on my laptop. This way I
can submit a new commit that fixes a broken commit before the Bioc
nightly build in about the same time as using my laptop. r-travis
doesn't always work as Bioc might have newer versions of dependencies
or other issues (cache, timing, installation of deps), but it helps
most of the time. A scenario where I definitely rely on the Bioc
nightly build is when I can't reproduce the error/warning on my
machine (with the latest setup). For example, Windows issues***.

Note that I do run a quick local test of whatever bug I'm solving, but
I might miss how my changes affected another unit test.

Best,
Leonardo

** Example setup
https://github.com/leekgroup/derfinderPlot/blob/master/.travis.yml
*** You can also use r-hub for testing in other OS including Windows
but maybe not with the R version that bioc-devel needs and/or without
being able to set useDevel(). Example
https://github.com/LieberInstitute/jaffelab/blob/master/.travis.yml#L17-L18
I've only used it for that non-bioc package.

On Wed, Feb 7, 2018 at 9:51 AM, Martin Morgan
 wrote:
>
>
> Bioc developers!
>
> I've been exploring the Bioconductor nightly builds
>
>   http://bioconductor.org/checkResults/
>
> a bit using this in-development package.
>
>   https://github.com/mtmorgan/BiocBuildReports
>
> This
>
>   rpt <- report()
>   filter_recent(rpt) %>% print(n = n())
>
> summarizes the packages changed in the 24 hours before the current build 
> snapshot, and their fate on the nightly builds
>
> > filter_recent(rpt) %>% print(n=nrow(.))
> # A tibble: 18 x 5
>package   buildsrc checksrc push txt
> 
>  1 AllelicImbalance  ERRORskipped  skipped  skipped
>  2 ChIPpeakAnno  ERRORskipped  skipped  skipped
>  3 GenomicScores ERRORskipped  skipped  skipped
>  4 genphen   ERRORskipped  skipped  skipped
>  5 metavizr  ERRORskipped  skipped  skipped
>  6 QUBIC ERRORskipped  skipped  skipped
>  7 Repitools OK   ERRORskipped  skipped
>  8 rtracklayer   OK   WARNINGS UNNEEDED same version exists in 
> interna…
>  9 genoset   OK   WARNINGS YES  new version is higher than in 
> …
> 10 IRanges   OK   WARNINGS YES  new version is higher than in 
> …
> 11 LOLA  OK   WARNINGS YES  new version is higher than in 
> …
> 12 DAPAR OK   OK   UNNEEDED same version exists in 
> interna…
> 13 AnnotationHubData OK   OK   YES  new version is higher than in 
> …
> 14 BEARscc   OK   OK   YES  new version is higher than in 
> …
> 15 ChemmineR OK   OK   YES  new version is higher than in 
> …
> 16 DESeq2OK   OK   YES  new version is higher than in 
> …
> 17 Onassis   OK   OK   YES  new version is higher than in 
> …
> 18 synergyfinder OK   OK   YES  new version is higher than in 
> …
>
> A couple of things strike me about this.
>
>   - All the packages with 'ERROR' in the buildsrc or checksrc column failed 
> to propagate because the commit, or a previous version, does not build or 
> check. It is not a very productive development model to push broken commits 
> to git.bioconductor.org, especially if the developer doesn't realize that the 
> commits are broken. The best practice is to build and check packages locally, 
> and then commit.
>
>   R CMD build 
>   R CMD check 
> An even more robust approach is to clone the repository locally, so that the 
> build and check are against only the committed changes and not miscellaneous 
> files or versions hanging out in your source directory
>
>   cd /tmp
>   git clone /path/to/
>   R CMD build 
>   ...
>
> I would not suggest using devtools during this final stage; the build system 
> doesn't use devtools, as devtools has its own ideas about options etc with 
> which to build packages. The very careful would also use the build and check 
> options found on the build report of each package, e.g., from
>
>
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/rtracklayer/malbec2-buildsrc.html
>
> one might
>
>   R CMD build --keep-empty-dirs --no-resave-data rtracklayer
>
> A common problem is that packages are built and checked locally using the 
> wrong version of R and / or Bioconductor -- commits to the devel branch 
> should be against the devel version of Bioconductor and (for the current 
> release cycle) the devel version of R.
>
>   http://bioconductor.org/developers/how-to/useDevel/
>
>   - two packages (rtracklayer, DAPAR) built and checked successfully, but did 
> not propagate to the public repository. This is because they did not bump 

Re: [Bioc-devel] Nightly builds

[Michael Love]

I've found this Makefile from Laurent et al makes it a lot easier to
do build/check, getting closer to the ease of devtools while still
building and checking from command line:

https://github.com/ComputationalProteomicsUnit/maker

You do:

git clone g...@github.com:ComputationalProteomicsUnit/maker.git
ln -s maker/Makefile .

Then configure maker/Makefile for your package and point it to your
local R-devel

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[Bioc-devel] Nightly builds

[Martin Morgan]

Bioc developers!

I've been exploring the Bioconductor nightly builds

  http://bioconductor.org/checkResults/

a bit using this in-development package.

  https://github.com/mtmorgan/BiocBuildReports

This

  rpt <- report()
  filter_recent(rpt) %>% print(n = n())

summarizes the packages changed in the 24 hours before the current build 
snapshot, and their fate on the nightly builds


> filter_recent(rpt) %>% print(n=nrow(.))
# A tibble: 18 x 5
   package   buildsrc checksrc push txt 

 

 1 AllelicImbalance  ERRORskipped  skipped  skipped 

 2 ChIPpeakAnno  ERRORskipped  skipped  skipped 

 3 GenomicScores ERRORskipped  skipped  skipped 

 4 genphen   ERRORskipped  skipped  skipped 

 5 metavizr  ERRORskipped  skipped  skipped 

 6 QUBIC ERRORskipped  skipped  skipped 

 7 Repitools OK   ERRORskipped  skipped 

 8 rtracklayer   OK   WARNINGS UNNEEDED same version exists in 
interna…
 9 genoset   OK   WARNINGS YES  new version is higher 
than in …
10 IRanges   OK   WARNINGS YES  new version is higher 
than in …
11 LOLA  OK   WARNINGS YES  new version is higher 
than in …
12 DAPAR OK   OK   UNNEEDED same version exists in 
interna…
13 AnnotationHubData OK   OK   YES  new version is higher 
than in …
14 BEARscc   OK   OK   YES  new version is higher 
than in …
15 ChemmineR OK   OK   YES  new version is higher 
than in …
16 DESeq2OK   OK   YES  new version is higher 
than in …
17 Onassis   OK   OK   YES  new version is higher 
than in …
18 synergyfinder OK   OK   YES  new version is higher 
than in …


A couple of things strike me about this.

  - All the packages with 'ERROR' in the buildsrc or checksrc column 
failed to propagate because the commit, or a previous version, does not 
build or check. It is not a very productive development model to push 
broken commits to git.bioconductor.org, especially if the developer 
doesn't realize that the commits are broken. The best practice is to 
build and check packages locally, and then commit.


  R CMD build 
  R CMD check 

Re: [Bioc-devel] cannot git (the package Pi)

[Turaga, Nitesh]

We name our release branches in the manner `RELEASE_3_6`. There is no branch 
`1.6.0`. As a maintainer you can only push to `master` and `RELEASE_3_6`.

You need to do something like, 

git checkout RELEASE_3_6

## Fix the bugs

git commit 

git push origin RELEASE_3_6


Maintainers are not allowed to create random branches on the Bioconductor git 
repository like `1.6.0`. It’s a hook that is rejecting your push.

Best,

Nitesh 


> On Feb 7, 2018, at 5:58 AM, Hai Fang  wrote:
> 
> Hi Nitesh
> 
> Following the instructions at 
> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have 
> successfully made changes to the development version (1.7.0 in my case). 
> 
> However, following the instructions at 
> https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/, 
> I am unable to make change to the release version (1.6.0 in my case)
> 
> $ git checkout 1.6.0
> Switched to branch '1.6.0'
> $ git push origin 1.6.0
> Counting objects: 3, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 332 bytes | 0 bytes/s, done.
> Total 3 (delta 2), reused 0 (delta 0)
> remote: FATAL: W refs/heads/1.6.0 packages/Pi h.fang DENIED by fallthru
> remote: error: hook declined to update refs/heads/1.6.0
> To g...@git.bioconductor.org:packages/Pi
>  ! [remote rejected] 1.6.0 -> 1.6.0 (hook declined)
> error: failed to push some refs to 'g...@git.bioconductor.org:packages/Pi'
> 
> The error message shows it is denied by fallthru. Any ideas?
> 
> Best wishes,
> Hai
> 
> 
>> On 5 Feb 2018, at 15:00, Turaga, Nitesh  
>> wrote:
>> 
>> Hi,
>> 
>> We have that key on file for you. But if you never got access using that 
>> key, it is possible because you submitted an “ssh-dss” key instead of an 
>> “ssh-rsa”. 
>> 
>> To solve this, please submit another key, with 
>> https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/.
>>  The “-t rsa” tells keygen to create an RSA key instead of a DDS.
>> 
>> ssh-keygen -t rsa -b 4096 -C "your_em...@example.com"
>> 
>> It’s either that, or you are using the wrong private key which corresponds 
>> to that public key.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Feb 2, 2018, at 11:58 AM, Hai Fang  wrote:
>>> 
>>> Dear Lori,
>>> I have an issue accessing my package called ‘Pi’.
>>> Following the instruction detailed at 
>>> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have 
>>> submit my SSH public key (shown in red):
>>> 
>>> $ cat ~/.ssh/id_dsa.pub
>>> ssh-dss 
>>> 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
>>>  
>>> hf...@eduroam-219-092.nomadic.bris.ac.uk
>>> 
>>> When clone it into my local machine (OS X EI Capitan version 10.11.6), it 
>>> said the permission denied (shown in pink).
>>> 
>>> $ git clone g...@git.bioconductor.org:packages/Pi
>>> Cloning into 'Pi'...
>>> Permission denied (publickey).
>>> fatal: Could not read from remote repository.
>>> 
>>> Please make sure you have the correct access rights
>>> and the repository exists.
>>> 
>>> I wonder whether my SSH was indeed added into the system or should I 
>>> regenerate the key or something else.
>>> 
>>> Many thanks,
>>> Hai
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
>> 
>> This email message may contain legally privileged and/or confidential 
>> information.  If you are not the intended recipient(s), or the employee or 
>> agent responsible for the delivery of this message to the intended 
>> recipient(s), you are hereby notified that any disclosure, copying, 
>> distribution, or use of this email message is prohibited.  If you have 
>> received this message in error, please notify the sender immediately by 
>> e-mail and delete this email message from your computer. Thank you.
> 
> 



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have 

Re: [Bioc-devel] cannot git (the package Pi)

[Hai Fang]

Hi Nitesh

Following the instructions at 
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have 
successfully made changes to the development version (1.7.0 in my case).

However, following the instructions at 
https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/, I 
am unable to make change to the release version (1.6.0 in my case)

$ git checkout 1.6.0
Switched to branch '1.6.0'
$ git push origin 1.6.0
Counting objects: 3, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 332 bytes | 0 bytes/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: FATAL: W refs/heads/1.6.0 packages/Pi h.fang DENIED by fallthru
remote: error: hook declined to update refs/heads/1.6.0
To g...@git.bioconductor.org:packages/Pi
 ! [remote rejected] 1.6.0 -> 1.6.0 (hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:packages/Pi'

The error message shows it is denied by fallthru. Any ideas?

Best wishes,
Hai


On 5 Feb 2018, at 15:00, Turaga, Nitesh 
> wrote:

Hi,

We have that key on file for you. But if you never got access using that key, 
it is possible because you submitted an “ssh-dss” key instead of an “ssh-rsa”.

To solve this, please submit another key, with 
https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/.
 The “-t rsa” tells keygen to create an RSA key instead of a DDS.

ssh-keygen -t rsa -b 4096 -C 
"your_em...@example.com"

It’s either that, or you are using the wrong private key which corresponds to 
that public key.

Best,

Nitesh

On Feb 2, 2018, at 11:58 AM, Hai Fang 
> wrote:

Dear Lori,
I have an issue accessing my package called ‘Pi’.
Following the instruction detailed at 
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have 
submit my SSH public key (shown in red):

$ cat ~/.ssh/id_dsa.pub
ssh-dss 
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
 
hf...@eduroam-219-092.nomadic.bris.ac.uk

When clone it into my local machine (OS X EI Capitan version 10.11.6), it said 
the permission denied (shown in pink).

$ git clone g...@git.bioconductor.org:packages/Pi
Cloning into 'Pi'...
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

I wonder whether my SSH was indeed added into the system or should I regenerate 
the key or something else.

Many thanks,
Hai

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