Re: [Bioc-devel] Need help for debug on palomino3

[Jianhong Ou, Ph.D.]

Thank you Hervé. I will take a try. Looks like the first year is free.

J.

From: Hervé Pagès 
Date: Thursday, March 24, 2022 at 1:36 PM
To: Jianhong Ou, Ph.D. , bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Need help for debug on palomino3
Hi Jianhong,

Is there any possibility that you can rent time on the Azure cloud via your 
organization? Cost should be reasonable if you shutdown the VM when you're not 
actively using it.

Best,
H.


On 24/03/2022 06:36, Jianhong Ou, Ph.D. wrote:
> Hi all,
>
> The package I maintained got error in Windows Server 2022 Datacenter / x64. 
> However I don�t have any windows system to debug.
> What is the best way to repeat the errors in palomino3? Any suggestion is 
> welcome.
> Thank you for your help.
>
> Jianhong.
>
>[[alternative HTML version deleted]]
>
>
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[Bioc-devel] Need help for debug on palomino3

[Jianhong Ou, Ph.D.]

Hi all,

The package I maintained got error in Windows Server 2022 Datacenter / x64. 
However I don�t have any windows system to debug.
What is the best way to repeat the errors in palomino3? Any suggestion is 
welcome.
Thank you for your help.

Jianhong.

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Re: [Bioc-devel] ENCODExplorer is not available in release and development version

[Jianhong Ou, Ph.D.]

Hi Lori,

Thank you so much for letting me know that. I will have a try.

Jianhong.

From: Kern, Lori 
Sent: Wednesday, June 23, 2021 8:34 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org 

Subject: Re: ENCODExplorer is not available in release and development version

Instead of using the bioc-de...@bioconductor.org mailing list I might also 
suggest you reach out to the ENCODExplorer maintainers directly.

Bioconductor has tried to reach out to the package maintainers several times 
with no response. As the package has been failing for an extended period of 
time and there has been no repsonse from the maintainers,  it is also marked as 
deprecated in devel with the intention to remove in 3.15 if the current 
maintainers do not fix and request un-deprecation.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Wednesday, June 23, 2021 8:29 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] ENCODExplorer is not available in release and development 
version

Dear Charles and maintainers of ENCODEExplorer,

The ENCODExplorer package is not available in release and development version. 
ENCODExplorer package is an important package for my current work. I hope it 
can be fixed as soon as possible. Thank you for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] ENCODExplorer is not available in release and development version

[Jianhong Ou, Ph.D.]

Dear Charles and maintainers of ENCODEExplorer,

The ENCODExplorer package is not available in release and development version. 
ENCODExplorer package is an important package for my current work. I hope it 
can be fixed as soon as possible. Thank you for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] Question about IRanges for coordinates greater than 536870912

[Jianhong Ou, Ph.D.]

Hi All,

Recently I encountered issues with IRanges that the coordinates greater than 
536870912. Is there any easy solution to extract the information from bam file 
for the range greater than 2^29 via Rsamtools or GenomicAlignments?

And does Rsamtools support CRAI or CSI index formats?

Thank you in advance for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

[Jianhong Ou, Ph.D.]

Hi Lori,

Thank you so much for the message.

Jianhong.

From: Kern, Lori 
Sent: Thursday, May 6, 2021 8:09 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org 

Subject: Re: How to repeat the error: shape of 'skeleton' is not compatible 
with 'NROW(flesh)'

This is a known issue with a recent push to IRanges.  The maintainers are aware 
and working on a fix.  You can follow the reported issue
https://<https://urldefense.com/v3/__https://github.com/Bioconductor/IRanges/issues/40__;!!OToaGQ!_eO94R27TcuA_bkDidtRGMe0b0MHs7Hpe74v7Mqlz_FUllmSPP5O3G3eNbFhkv_MfZE$>github.com/Bioconductor/IRanges/issues/40<https://urldefense.com/v3/__https://github.com/Bioconductor/IRanges/issues/40__;!!OToaGQ!_eO94R27TcuA_bkDidtRGMe0b0MHs7Hpe74v7Mqlz_FUllmSPP5O3G3eNbFhkv_MfZE$>

It should get resolved on its own shortly.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Thursday, May 6, 2021 7:50 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] How to repeat the error: shape of 'skeleton' is not 
compatible with 'NROW(flesh)'

Hi all,

In most recent build I got error message:

shape of 'skeleton' is not compatible with 'NROW(flesh)'

And I have trouble in repeating the error by 
Bioconductor/bioconductor_docker:devel.

I am asking will the bioconductor_docker will update soon or I should install 
the newest development version R by myself.

Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

[Jianhong Ou, Ph.D.]

Hi all,

In most recent build I got error message:

shape of 'skeleton' is not compatible with 'NROW(flesh)'

And I have trouble in repeating the error by 
Bioconductor/bioconductor_docker:devel.

I am asking will the bioconductor_docker will update soon or I should install 
the newest development version R by myself.

Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] How to proper write documentation (Rd) file for setReplaceMethod

[Jianhong Ou, Ph.D.]

Thank you Lori for the information.

Best!

Your sincerely,

Jianhong Ou

On Apr 15, 2021, at 8:38 AM, Kern, Lori  wrote:


Please see this related post

https://stat.ethz.ch/pipermail/bioc-devel/2021-January/017587.html<https://urldefense.com/v3/__https://stat.ethz.ch/pipermail/bioc-devel/2021-January/017587.html__;!!OToaGQ!4XrX3E6xOnpagfnr-ZLZzRMlV3IOQFFqmg8u0M-yfwtfk83Ld8SdOsTjuoL85gNxz8g$>

I believe you can ignore the window warnings for now as it is a product of the 
way we are building/checking the packages.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Wednesday, April 14, 2021 3:11 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] How to proper write documentation (Rd) file for 
setReplaceMethod

Hi All,

I got warning message in windows building like:


Rd warning: cannot open file 
'D:/biocbuild/bbs-3.13-bioc/meat/trackViewer.buildbin-libdir/00LOCK-trackViewer/00new/trackViewer/help/$<-,track-method.html':
 Invalid argument

I used RoxygenNote to create the Rd file and the note I wrote like this:

#' Method $<-
#' @rdname trackStyle-class
#' @exportMethod $<-
#' @aliases $<-,track-method

Any help will be appreciated. Thanks in advance.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] How to proper write documentation (Rd) file for setReplaceMethod

[Jianhong Ou, Ph.D.]

Hi All,

I got warning message in windows building like:


Rd warning: cannot open file 
'D:/biocbuild/bbs-3.13-bioc/meat/trackViewer.buildbin-libdir/00LOCK-trackViewer/00new/trackViewer/help/$<-,track-method.html':
 Invalid argument

I used RoxygenNote to create the Rd file and the note I wrote like this:

#' Method $<-
#' @rdname trackStyle-class
#' @exportMethod $<-
#' @aliases $<-,track-method

Any help will be appreciated. Thanks in advance.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] Ask for help to debug the error on riesling1

[Jianhong Ou, Ph.D.]

Hi Martin,

Thank you for going so deep. I tried

R -d "valgrind --leak-check=full --track-origins=yes" -f plotInteractionData.R

to locate the exact line where initialed the possible leak.

Is there any other possibility that killed the process and did not leave any 
error log information?

Jianhong.

From: Martin Morgan 
Sent: Wednesday, April 7, 2021 2:16 PM
To: Jianhong Ou, Ph.D. ; Hervé Pagès 
; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1

I followed these steps, more or less, to configure and use valgrind on the 
Bioconductor docker image.

  
https://urldefense.com/v3/__https://gist.github.com/mtmorgan/77f9d92d81830eeb7f254809b445874d__;!!OToaGQ!-g840WABoFzxZ4_VS8wWp_YSW6KeHVFxX66mQcS2nGxeHwk8XlzjCnonGt7rnWeMU0g$

For this particular use I

- added the valgrind system dependency
- installed trackViewer and it's 'Suggests' dependencies in a standard R session
- made a git clone --depth 1 
https://urldefense.com/v3/__https://git.bioconductor.org/packages/trackViewer__;!!OToaGQ!-g840WABoFzxZ4_VS8wWp_YSW6KeHVFxX66mQcS2nGxeHwk8XlzjCnonGt7rzc3RP4s$
- made an R script from the vignette via cd vignettes && R CMD Stangle...
- ran once with

  root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -f plotInteractionData.R

  as a sanity check, then

  root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -d valgrind -f 
plotInteractionData.R

This lead to a single suspicious valgrind message

> importGInteractions(file=hic, format="hic",
+ ranges=GRanges("22", IRanges(5000, 1)),
+ out = "GInteractions")
==29679== Conditional jump or move depends on uninitialised value(s)
==29679==at 0x48428EC: memset (in 
/usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==29679==by 0x212D08FF: memset (string_fortified.h:71)
==29679==by 0x212D08FF: select_hits (Hits_class.c:324)
==29679==by 0x4944EB3: R_doDotCall (dotcode.c:614)
==29679==by 0x4945464: do_dotcall (dotcode.c:1281)
==29679==by 0x498AC35: bcEval (eval.c:7072)
==29679==by 0x4999DA7: Rf_eval (eval.c:727)
==29679==by 0x499BBDE: R_execClosure (eval.c:1897)
==29679==by 0x499CAD1: Rf_applyClosure (eval.c:1823)
==29679==by 0x4987DBD: bcEval (eval.c:7083)
==29679==by 0x4999DA7: Rf_eval (eval.c:727)
==29679==by 0x499BBDE: R_execClosure (eval.c:1897)
==29679==by 0x499CAD1: Rf_applyClosure (eval.c:1823)
==29679==

Hits_class.c:324 is in S4Vectors

if (nodup0) {
is_used = _new_CharAE(get_nnode(nRnode, "R"));
memset(is_used->elts, 0, is_used->_buflength);
}

I re-ran under gdb

  root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -d valgrind -f 
plotInteractionData.R
  ...
  (gdb) break Hits_class.c:324
  (gdb) run
  ...
  (gdb) continue
  ...
  > importGInteractions(file=hic, format="hic",
  + ranges=GRanges("22", IRanges(5000, 1)),
  + out = "GInteractions")

Thread 1 "R" hit Breakpoint 1, select_hits (from=,
  to=, nLnode=, nRnode=0x56071b51d5e8,
  select=, nodup=) at Hits_class.c:327
  327   in Hits_class.c
  (gdb) p *is_used
  $2 = {_buflength = 0, _nelt = 0, elts = 0x0}

I guess the complaint is about elts = 0x0, but I'm not really sure if this is 
enough to cause a fault during package build -- it seems like the code writes 
nothing nowhere, but ...

Martin Morgan

On 4/7/21, 8:08 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

Hi Herv�,

Thank you for the information. I will try to figure out.

Jianhong.
    
From: Herv� Pag�s 
Sent: Wednesday, April 7, 2021 1:54 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1

Hi Jianhong,

Memory leaks and other memory errors are bugs in native code that often
exist on all platforms but typically manifest themselves in different
ways depending on the platform where it runs. Running your code thru a
tool like Valgrind should reveal these problems even if you do this on a
non-Windows machine. See

https://urldefense.com/v3/__https://bioconductor.org/developers/how-to/c-debugging/__;!!OToaGQ!6X7J1i17XSPaKkNmZMcdEY24rEjchLfeQ8YTdhLB68dZII3WDxYfoPTTpGr2AOjQ4ds$
for more information.

Best,
H.


On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> The trackViewer package got error on Windows Server since version 1.27.4. 
I am totally lost to figure it out by myself. The current error message listed 
in building system is:
>
>
> * creating vignettes ... ERROR
> --- re-building 'changeTracksStyles.Rmd' using rmarkdown
> --- finished re-building 'changeTracksStyles.Rmd

Re: [Bioc-devel] Ask for help to debug the error on riesling1

[Jianhong Ou, Ph.D.]

Hi Herv�,

Thank you for the information. I will try to figure out.

Jianhong.

From: Herv� Pag�s 
Sent: Wednesday, April 7, 2021 1:54 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1

Hi Jianhong,

Memory leaks and other memory errors are bugs in native code that often
exist on all platforms but typically manifest themselves in different
ways depending on the platform where it runs. Running your code thru a
tool like Valgrind should reveal these problems even if you do this on a
non-Windows machine. See
https://urldefense.com/v3/__https://bioconductor.org/developers/how-to/c-debugging/__;!!OToaGQ!6X7J1i17XSPaKkNmZMcdEY24rEjchLfeQ8YTdhLB68dZII3WDxYfoPTTpGr2AOjQ4ds$
for more information.

Best,
H.


On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> The trackViewer package got error on Windows Server since version 1.27.4. I 
> am totally lost to figure it out by myself. The current error message listed 
> in building system is:
>
>
> * creating vignettes ... ERROR
> --- re-building 'changeTracksStyles.Rmd' using rmarkdown
> --- finished re-building 'changeTracksStyles.Rmd'
>
> --- re-building 'dandelionPlot.Rmd' using rmarkdown
> --- finished re-building 'dandelionPlot.Rmd'
>
> --- re-building 'lollipopPlot.Rmd' using rmarkdown
> --- finished re-building 'lollipopPlot.Rmd'
>
> --- re-building 'plotInteractionData.Rmd' using rmarkdown
>
> I suppose this is a memory leak error. But I don't have windows server to 
> repeat the error. What is the best way to fix the issue? Thank you in advance 
> for your help.
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
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>

--
Herv� Pag�s

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[Jianhong Ou, Ph.D.]

Hi Alan,

Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging. 
Hope this help.

You may want to add one more step after check and before pkgdown to push to 
your dockerhub by:

- name: push to docker
- uses: docker/build-push-action@v1
with:
  username: ${{ secrets.DOCKER_USERNAME }}
  password: ${{ secrets.DOCKER_TOKEN }}
  repository: your/docker/path
  tag_with_ref: true
  tag_with_sha: true
  tags: latest
[https://avatars.githubusercontent.com/u/5640707?s=400=4]
jianhong/HMMtBroadPeak
call broad peak by a modified Baum_Welch algorithm that supports 
multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak
github.com



From: Bioc-devel  on behalf of Murphy, Alan E 

Sent: Tuesday, April 6, 2021 10:24 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi all,

I'm working on the development of 
(EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$
 ] and have a question regarding a reviewer note. My package currently uses 
pkgdown to create a website through the master branch. I also create and push a 
new docker image from the main branch when the package successfully builds on 
travis.

My reviewer has asked to remove the related files 
_pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues 
with these external configurations and Bioconductor. My reviewer has suggested 
to put these in another branch. It's not clear to me how best to do this? 
Ideally, if they are in a separate branch, is there a way to run them once 
there is an update and successful build on the master branch? If this isn't 
possible, is there a way to avoid manually duplicating new changes in the 
master branch in this separate branch and instead, just push the changes from 
master to this separate branch and trigger pkgdown and docker build that way? 
Sorry, I realise this last part more so relates to github commands but I was 
thinking someone else has probably already foudn a way around this issue.

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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[Bioc-devel] Ask for help to debug the error on riesling1

[Jianhong Ou, Ph.D.]

Hi,

The trackViewer package got error on Windows Server since version 1.27.4. I am 
totally lost to figure it out by myself. The current error message listed in 
building system is:


* creating vignettes ... ERROR
--- re-building 'changeTracksStyles.Rmd' using rmarkdown
--- finished re-building 'changeTracksStyles.Rmd'

--- re-building 'dandelionPlot.Rmd' using rmarkdown
--- finished re-building 'dandelionPlot.Rmd'

--- re-building 'lollipopPlot.Rmd' using rmarkdown
--- finished re-building 'lollipopPlot.Rmd'

--- re-building 'plotInteractionData.Rmd' using rmarkdown

I suppose this is a memory leak error. But I don't have windows server to 
repeat the error. What is the best way to fix the issue? Thank you in advance 
for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] How to handle Empty reply from server from httr package

[Jianhong Ou, Ph.D.]

Hi all,

Sometime my package got "Empty reply from server" error when I using httr 
package.
The pseudo-code I used to handle error is like this:

library(httr)
APIurl <- 
"https://www.ebi.ac.uk/proteins/api/features?offset=0=-1=true=DNA_BIND%2CMOTIF%2CDOMAIN=9606=K7PPA8%2CP04637%2CQ53GA5%2CH2EHT1%2CA0A087X1Q1%2CA0A087WXZ1%2CA0A087WT22;
tryCatch({
response <- GET(featureURL)
if(!http_error(response)){content <- httr::content(response)}
}, error=function(e){
  message(e)
},warning=function(w){
  message(w)
},interrupt=function(i){
  message(i)
})

But I did not get the error handled. What is the correct way to handle the curl 
52 error?
Thank you for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi Hervé,

Thank you! You saved me.

Best!

Your sincerely,

Jianhong Ou

> On Apr 24, 2020, at 5:59 PM, Hervé Pagès  wrote:
> 
> Hi Jianhong,
> 
> I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the good 
> news is that I no longer get a TIMEOUT with this new R:
> 
> machv2:meat biocbuild$ time R CMD build motifStack
> * checking for file ‘motifStack/DESCRIPTION’ ... OK
> * preparing ‘motifStack’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files and shell scripts
> * checking for empty or unneeded directories
> * building ‘motifStack_1.31.2.tar.gz’
> 
> 
> real1m33.576s
> user1m26.714s
> sys0m3.815s
> 
> So maybe it was a temporary issue with early Mac builds of R 4.0.
> 
> Please keep an eye on tomorrow's report (Saturday) and let me know if the 
> TIMEOUT is still there.
> 
> Thanks,
> H.
> 
> 
>> On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:
>> Hi Herve,
>> Thank you for your help.
>> Jianhong.
>> On 4/17/20, 4:14 PM, "Hervé Pagès"  wrote:
>> For some reasons the generation of the plots in the vignette is VERY
>> slow on machv2. 'R CMD build' actually completed... after 6h! This is
>> still under investigation.
>>  Best,
>> H.
>>   On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
>> > Hi,
>> >
>> > I got timeout for my package motifStack in machv2. But I don't know 
>> what cuased the issue.
>> >
>> > Any help would be greatly appreciated.
>> >
>> > Jianhong.
>> > 
>> > From: Jianhong Ou, Ph.D.
>> > Sent: Wednesday, April 15, 2020 7:53 AM
>> > To: bioc-devel@r-project.org 
>> > Subject: Got timeout for machv2 BUILD
>> >
>> > Hi,
>> >
>> > Hope you are doing well.
>> >
>> > I got timeout for my package motifStack in machv2. The ellapsedTime is 
>> 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 
>> seconds. I have limited information how to debug.
>> > Could you share your suggestion? Thank you.
>> >
>> >
>> >
>> > Yours Sincerely,
>> >
>> > Jianhong Ou
>> >
>> > Email: jianhong...@duke.edu
>> > Bioinformatician II
>> > Department of Cell Biology
>> > Duke University School of Medicine
>> > Durham, NC, 27710
>> >
>> > Confidentiality Notice:\ This e-mail message, including 
>> ...{{dropped:12}}
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w=
>> >
>>  --
>> Hervé Pagès
>>  Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>  E-mail: hpa...@fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:(206) 667-1319
>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi Stefano,

Thank you for your share.

Jianhong.

From: Stefano de Pretis 
Date: Friday, April 17, 2020 at 3:18 PM
To: "Jianhong Ou, Ph.D." 
Cc: "bioc-devel@r-project.org" 
Subject: Re: [Bioc-devel] Got timeout for machv2 BUILD

HI,

We solved a similar issue for the INSPEcT package avoiding the parallelization 
in the computation of examples and vignettes. In our case it caused the timeout 
in the Windows environment.

Best,
Stefano

Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. 
mailto:jianhong...@duke.edu>> ha scritto:
Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.
________
From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu<mailto:jianhong...@duke.edu>
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] How to speed up GRange comparision

[Jianhong Ou, Ph.D.]

Oh, I forget that. Thank you for reminder. 
Then how about:

distance(query, narrow(subject, start=2, end=-2)) == 0

?


On 1/29/20, 12:40 PM, "Pages, Herve"  wrote:

On 1/29/20 08:04, Jianhong Ou, Ph.D. wrote:
> Try
> dist=distance(query, subject)
> dist==0
> ?

Please be aware that dist==0 does NOT mean that 2 ranges overlap. It 
means that they overlap OR are **adjacent**:

 > distance(GRanges("chr1:1-20"), GRanges("chr1:21-25"))
[1] 0

H.

> 
> On 1/29/20, 10:50 AM, "Bioc-devel on behalf of web working" 
 wrote:
> 
>  Hello,
>  
>  I have two big GRanges objects and want to search for an overlap of  
the
>  first range of query with the first range of subject. Then take the
>  second range of query and compare it with the second range of subject
>  and so on. Here an example of my problem:
>  
>  # GRanges objects
>  query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10,
>  22)), id=1:4)
>  subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2,
>  21)), id=1:4)
>  
>  # The 2 overlaps at the first position should not be counted, because
>  these ranges are at different rows.
>  countOverlaps(query, subject)
>  
>  # Approach 1 (bad style. I have simplified it to understand)
>  dat <- as.data.frame(findOverlaps(query, subject))
>  indexDat <- apply(dat, 1, function(x) x[1]==x[2])
>  indexBool <- dat[indexDat,1]
>  out <- rep(FALSE, length(query))
>  out[indexBool] <- TRUE
>  as.numeric(out)
>  
>  # Approach 2 (bad style and takes too long)
>  out <- vector("numeric", 4)
>  for(i in seq_along(query)) out[i] <- (overlapsAny(query[i], 
subject[i]))
>  out
>  
>  # Approach 3 (wrong results)
>  as.numeric(overlapsAny(query, subject))
>  as.numeric(overlapsAny(split(query, 1:4), split(subject, 1:4)))
>  
>  
>  Maybe someone has an idea to speed this up?
>  
>  
>  Best,
>  
>  Tobias
>  
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319


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Re: [Bioc-devel] How to speed up GRange comparision

[Jianhong Ou, Ph.D.]

Try 
dist=distance(query, subject)
dist==0
?

On 1/29/20, 10:50 AM, "Bioc-devel on behalf of web working" 
 wrote:

Hello,

I have two big GRanges objects and want to search for an overlap of  the 
first range of query with the first range of subject. Then take the 
second range of query and compare it with the second range of subject 
and so on. Here an example of my problem:

# GRanges objects
query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10, 
22)), id=1:4)
subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2, 
21)), id=1:4)

# The 2 overlaps at the first position should not be counted, because 
these ranges are at different rows.
countOverlaps(query, subject)

# Approach 1 (bad style. I have simplified it to understand)
dat <- as.data.frame(findOverlaps(query, subject))
indexDat <- apply(dat, 1, function(x) x[1]==x[2])
indexBool <- dat[indexDat,1]
out <- rep(FALSE, length(query))
out[indexBool] <- TRUE
as.numeric(out)

# Approach 2 (bad style and takes too long)
out <- vector("numeric", 4)
for(i in seq_along(query)) out[i] <- (overlapsAny(query[i], subject[i]))
out

# Approach 3 (wrong results)
as.numeric(overlapsAny(query, subject))
as.numeric(overlapsAny(split(query, 1:4), split(subject, 1:4)))


Maybe someone has an idea to speed this up?


Best,

Tobias

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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

It looks like for arch'x64', there is no package org.Hs.eg.db.

Following is the whole error message:

** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
trackViewer-package 22.44   0.07   24.88
viewTracks  13.97   0.02   14.84
parseWIG12.81   0.00   12.94
browseTracks12.04   0.00   12.69
geneModelFromTxdb7.30   0.319.28
viewGene 5.15   0.115.26
** running examples for arch 'x64' ... ERROR
Running examples in 'trackViewer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackViewer-package
> ### Title: Minimal designed plotting tool for genomic data
> ### Aliases: trackViewer trackViewer-package
> 
> ### ** Examples
> 
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(org.Hs.eg.db)
Error in library(org.Hs.eg.db) : 
  there is no package called 'org.Hs.eg.db'
Execution halted



On 6/14/19, 9:31 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with 
no issues.   Let's wait and see if it clears up on todays build report.  If not 
we will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets
    
    Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong 
Ou, Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with no 
issues.   Let's wait and see if it clears up on todays build report.  If not we 
will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

____
From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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[Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

[Jianhong Ou, Ph.D.]

 unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(1, "lines"))
  grid.text("5'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(1, 
"lines"))
} else {
  grid.lines(x=c(convertUnit(unit(3, "lines"), "npc", valueOnly = TRUE), 1 - 
convertUnit(unit(1, "lines"), "npc", valueOnly = TRUE)),
 y=unit(1.5, "lines"), gp=gpar(col = "blue", lwd = 1.5, xpd=NA),
 arrow=arrow(length = unit(0.1, "inches"), angle = 15, ends = 
"first"))
  grid.text("5'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(1, "lines"))
  grid.text("3'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(1, 
"lines"))
}
popViewport()
popViewport()
  grid.text(label = paste(motif.match$motif, " Motif Scan for ", 
motif.match$snpid, sep=""),
y=unit(1, "npc") - unit(1.5, "lines"),
gp=gpar(cex.main=cex.main, fontface="bold"))

You may want to double check if I understand your parameters correctly. And add 
grid as a Import package.

Jianhong.

From: "Shin, Sunyoung" 
Date: Sunday, April 28, 2019 at 3:55 PM
To: "Jianhong Ou, Ph.D." , "bioc-devel@r-project.org" 

Subject: Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

Hello Jianhong,

Thank you very much for the quick response. I dropped all par commands, and 
used layout() instead of par(mfrow=c(4,1)). But, I still get the same error 
message. I put the updated code below. Do you have some suggestions on 
debugging?

* creating vignettes ... ERROR

--- re-building ‘atsnp-vignette.rmd’ using rmarkdown

Quitting from lines 292-294 (atsnp-vignette.rmd)

Error: processing vignette 'atsnp-vignette.rmd' failed with diagnostics:

invalid graphics state

--- failed re-building ‘atsnp-vignette.rmd’
plot.new()
  layout(matrix(c(1,2,3,4), 4, 1, byrow = TRUE))
  plotMotifLogo(pcm2pfm(ref_aug_pwm), "Best match to the reference genome", 
yaxis=FALSE, xaxis=FALSE, xlab="", ylab="PWM", ...)
if(motif.match$ref_strand=='+') {
arrows((min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17, 
max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17, length = 0.1, 
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
  mtext("5'", 1, adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), 
padj=1, col="blue", cex=1)
  mtext("3'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), 
padj=1, col="blue", cex=1)
} else {
arrows(max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17, 
(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17, length = 0.1, 
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
  mtext("5'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), 
padj=1, col="blue", cex=1)
  mtext("3'", 1, adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), 
padj=1, col="blue", cex=1)
}
plotMotifLogo(pcm2pfm(ref_aug_match_pwm), font="mono,Courier", yaxis=FALSE, 
xlab="", ylab=paste("(", motif.match$ref_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0, 
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
  if(motif.match$ref_strand=="+")   {
  mtext("5'", 1,  adj=0, padj=1, col="blue", cex=1)
  mtext("3'", 1,  adj=1, padj=1, col="blue", cex=1)
} else {
  mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
  mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
  }
plotMotifLogo(pcm2pfm(snp_aug_match_pwm), "Best match to the SNP genome", 
font="mono,Courier", yaxis=FALSE, xlab="", ylab=paste("(", 
motif.match$snp_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0, 
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif

Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

[Jianhong Ou, Ph.D.]

Hi Sunyong,

plotMotifLogo does not compatible with par now. Please use grid to plot the 
multiple panels in one canvas. I am working on this but it takes time.

Jianhong.

On 4/23/19, 12:47 AM, "Bioc-devel on behalf of Shin, Sunyoung" 
 
wrote:

Dear all,

I got an error message: invalid graphics state as below from BUILD report 
for atSNP 0.99.23 
(https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_packages_3.9_bioc_html_atSNP.html=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8=PbqNdXfVMLxlePSjrHOEN8-tkQLva8Pg6UAfB4VOTUw=lESpOegy3zU7jKZUfxiUhG5mSg7qotzhof_KHZmVEB8=).
 This occurs on every platform: malbec2, tokay2, and celaya2. Running  
devtools::check()  on my local computer does not produce the error. I would 
appreciate it if anyone can help debugging.

* creating vignettes ... ERROR

--- re-building ‘atsnp-vignette.rmd’ using rmarkdown
Quitting from lines 292-294 (atsnp-vignette.rmd)
Error: processing vignette 'atsnp-vignette.rmd' failed with diagnostics:
invalid graphics state
--- failed re-building ‘atsnp-vignette.rmd’

SUMMARY: processing the following file failed:
  ‘atsnp-vignette.rmd’

Error: Vignette re-building failed.
Execution halted

The graphing function which makes the error is plotMotifMatch(match.seq,  
motif.lib = motif_library). Below is the part of the code that is needed  to be 
fixed, I think.

{
  par(mfrow=c(4,1), oma=c(1,1,4,1))
  plot.new()
  par(mar=c(1.5, 3, 4, 2))
  plotMotifLogo(pcm2pfm(ref_aug_pwm), "Best match to the reference genome", 
yaxis=FALSE, xaxis=FALSE, xlab="", ylab="PWM", ...)
if(motif.match$ref_strand=='+') {
arrows((min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17, 
max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17, length = 0.1, 
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
  mtext("5'", 1, 
adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), padj=1, 
col="blue", cex=1)
  mtext("3'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), 
padj=1, col="blue", cex=1)
} else {
arrows(max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17, 
(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17, length = 0.1, 
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
  mtext("5'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), 
padj=1, col="blue", cex=1)
  mtext("3'", 1, 
adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), padj=1, 
col="blue", cex=1)
}
  par(mar = c(4, 3, 1.5, 2))
plotMotifLogo(pcm2pfm(ref_aug_match_pwm), font="mono,Courier", yaxis=FALSE, 
xlab="", ylab=paste("(", motif.match$ref_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0, 
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
  if(motif.match$ref_strand=="+")   {
  mtext("5'", 1,  adj=0, padj=1, col="blue", cex=1)
  mtext("3'", 1,  adj=1, padj=1, col="blue", cex=1)
} else {
  mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
  mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
  }
par(mar=c(1.5, 3, 4, 2))
plotMotifLogo(pcm2pfm(snp_aug_match_pwm), "Best match to the SNP genome", 
font="mono,Courier", yaxis=FALSE, xlab="", ylab=paste("(", 
motif.match$snp_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0, 
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0, 
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
  if(motif.match$snp_strand=="+")   {
  mtext("5'", 1,  adj=0, padj=1, col="blue", cex=1)
  mtext("3'", 1,  adj=1, padj=1, col="blue", cex=1)
} else {
  mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
  mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
  }
par(mar=c(4, 3, 1.5, 2))
plotMotifLogo(pcm2pfm(snp_aug_pwm), yaxis=FALSE, xaxis=FALSE, xlab="", 
ylab="PWM", ...)
if(motif.match$snp_strand=='+') {
arrows((min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), -0.17, 
max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm), -0.17, length = 0.1, 
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
  mtext("5'", 1, 

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

[Jianhong Ou, Ph.D.]

Thank you all very much.

Jianhong.

On 11/2/18, 3:03 PM, "Obenchain, Valerie"  
wrote:

Hi Jianhong,

Ghostscript is already installed on the builders.

On the Nov 1 build report for Bioc 3.9, motifStack is clean on tokay2 
(Windows) but failed on malbec2 (Linux). There were other packages that 
depended on grImports with similar errors on Linux - dagLogo and 
motifbreakR.

I went on the Linux builder to investigate and was able to build and 
check motifStack with no problem. I also saw the build results for today 
(Nov 2) and motifStack is clean so I'm not sure what happened in the 
previous day's builds.

The build report for today, Nov 2, should post within the next hour and 
motifStack should be green.

Valerie






On 11/2/18 6:05 AM, Jianhong Ou, Ph.D. wrote:
> My package motifStack import grImport which is depend on ghostscript.
> 
> Jianhong.
> 
> From: Kasper Daniel Hansen 
> Date: Friday, November 2, 2018 at 8:55 AM
> To: "Jianhong Ou, Ph.D." 
> Cc: bioc-devel 
> Subject: Re: [Bioc-devel] Ask help to install gs tokay2 build/check
> 
> Perhaps explain why
    > 
> On Fri, Nov 2, 2018 at 8:19 AM Jianhong Ou, Ph.D. 
mailto:jianhong...@duke.edu>> wrote:
> Hi,
> 
> Is it possible to install ghostscript in tokay2 for development package 
build?
> 
> Yours Sincerely,
> 
> Jianhong Ou
> 
> Email: 
jianhong...@duke.edu<mailto:jianhong...@duke.edu><mailto:jianhong...@duke.edu<mailto:jianhong...@duke.edu>>
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
> 
> Confidentiality Notice:
> This e-mail message, including any attachments, is for the sole use of 
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Re: [Bioc-devel] Ask help to install gs tokay2 build/check

[Jianhong Ou, Ph.D.]

My package motifStack import grImport which is depend on ghostscript.

Jianhong.

From: Kasper Daniel Hansen 
Date: Friday, November 2, 2018 at 8:55 AM
To: "Jianhong Ou, Ph.D." 
Cc: bioc-devel 
Subject: Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Perhaps explain why

On Fri, Nov 2, 2018 at 8:19 AM Jianhong Ou, Ph.D. 
mailto:jianhong...@duke.edu>> wrote:
Hi,

Is it possible to install ghostscript in tokay2 for development package build?

Yours Sincerely,

Jianhong Ou

Email: 
jianhong...@duke.edu<mailto:jianhong...@duke.edu><mailto:jianhong...@duke.edu<mailto:jianhong...@duke.edu>>
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] Ask help to install gs tokay2 build/check

[Jianhong Ou, Ph.D.]

Hi,

Is it possible to install ghostscript in tokay2 for development package build?

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:
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Re: [Bioc-devel] Have trouble in push to master branch

[Jianhong Ou, Ph.D.]

Thank you Nitesh,

It works now.

Jianhong.

On 10/11/18, 1:53 PM, "Turaga, Nitesh"  wrote:

Please try now. 

> On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie)  
wrote:
> 
> Nitesh,
> 
> I encountered the same issue with CRISPRseek package. Could you please 
help? Thanks!
> 
> To git.bioconductor.org:packages/CRISPRseek.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/CRISPRseek.git'
> 
> Best regards,
> 
> Julie
> 
> On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" 
 
wrote:
> 
>Hi Jianhong,
> 
> 
> 
>I’m looking into it now. 
> 
> 
    > 
>Nitesh 
> 
> 
> 
>> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D.  
wrote:
> 
>> 
> 
>> Hi,
> 
>> 
> 
>> I am trying to fix bug in my package. However, I got declined message:
> 
>> 
> 
>> 
> 
>> git push upstream master
> 
>> 
> 
>> Counting objects: 38, done.
> 
>> 
> 
>> Delta compression using up to 8 threads.
> 
>> 
> 
>> Compressing objects: 100% (26/26), done.
> 
>> 
> 
>> Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.
> 
>> 
> 
>> Total 38 (delta 30), reused 16 (delta 12)
> 
>> 
> 
>> remote: Traceback (most recent call last):
> 
>> 
> 
>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 
104, in 
> 
>> 
> 
>> remote: hooks_dict = read_bioc_conf(conf)
> 
>> 
> 
>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 
60, in read_bioc_conf
> 
>> 
> 
>> remote: for hook in d[package]:
> 
>> 
> 
>> remote: KeyError: 'Package: NADfinder'
> 
>> 
> 
>> To 
https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org=DwIGaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=ldl4cdibkRktwLiyZ6niwklGYISVFGeXm27fs_BVZbo=X0WooCCk3_DxndJDvyJOOlMSACg6AVEER4VTQcjlcEw=:packages/NADfinder.git
> 
>> 
> 
>> ! [remote rejected] master -> master (pre-receive hook declined)
> 
>> 
> 
>> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/NADfinder.git'
> 
>> 
> 
>> How could I fix this? Thank you for your help.
> 
>> 
> 
>> Yours Sincerely,
> 
>> 
> 
>> Jianhong Ou
> 
>> 
> 
>> Email: jianhong...@duke.edu<mailto:jianhong...@duke.edu>
> 
>> Bioinformatician II
> 
>> Department of Cell Biology
> 
>> Duke University School of Medicine
> 
>> Durham, NC, 27710
> 
>> 
> 
>> Confidentiality Notice:
> 
>> This e-mail message, including any attachments, is for the sole use of 
the intended recipient(s) and may contain confidential, proprietary and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender immediately and destroy or permanently delete all copies of 
the original message.
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[Bioc-devel] Have trouble in push to master branch

[Jianhong Ou, Ph.D.]

Hi,

I am trying to fix bug in my package. However, I got declined message:


git push upstream master

Counting objects: 38, done.

Delta compression using up to 8 threads.

Compressing objects: 100% (26/26), done.

Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.

Total 38 (delta 30), reused 16 (delta 12)

remote: Traceback (most recent call last):

remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 104, in 


remote: hooks_dict = read_bioc_conf(conf)

remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 60, in 
read_bioc_conf

remote: for hook in d[package]:

remote: KeyError: 'Package: NADfinder'

To git.bioconductor.org:packages/NADfinder.git

 ! [remote rejected] master -> master (pre-receive hook declined)

error: failed to push some refs to 
'g...@git.bioconductor.org:packages/NADfinder.git'

How could I fix this? Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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