Re: [Bioc-devel] "convert" graphics error for new submission

[Vincent Carey]

Maybe an antivirus issue?

On Thu, Apr 5, 2018 at 8:30 PM, Vincent Carey 
wrote:

> No, I did not do anything for this.
>
> On Thu, Apr 5, 2018 at 5:03 PM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
>> It seems like this has 'gone away', was that something you did, or...?
>>
>>
>>
>> On 04/02/2018 04:34 PM, Vincent Carey wrote:
>>
>>> for two host-types I am seeing an error that I do not know how to address
>>>
>>> Loading required package: ontologyIndex
>>> sh: line 1: 76907 Abort trap: 6   'convert'
>>> 'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim
>>> 'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null
>>> sh: line 1: 76914 Abort trap: 6   'convert'
>>> 'BiocOncoTK_files/figure-html/dopogmock-1.png' -trim
>>> 'BiocOncoTK_files/figure-html/dopogmock-1.png' > /dev/null
>>> Quitting from lines 351-363 (BiocOncoTK.Rmd)
>>> Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
>>>
>>> [[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.
>>
>
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] "convert" graphics error for new submission

[Vincent Carey]

No, I did not do anything for this.

On Thu, Apr 5, 2018 at 5:03 PM, Martin Morgan  wrote:

> It seems like this has 'gone away', was that something you did, or...?
>
>
>
> On 04/02/2018 04:34 PM, Vincent Carey wrote:
>
>> for two host-types I am seeing an error that I do not know how to address
>>
>> Loading required package: ontologyIndex
>> sh: line 1: 76907 Abort trap: 6   'convert'
>> 'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim
>> 'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null
>> sh: line 1: 76914 Abort trap: 6   'convert'
>> 'BiocOncoTK_files/figure-html/dopogmock-1.png' -trim
>> 'BiocOncoTK_files/figure-html/dopogmock-1.png' > /dev/null
>> Quitting from lines 351-363 (BiocOncoTK.Rmd)
>> Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
>>
>> [[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.
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Big Changes for RCy3 v2.0.0

[Alex Pico]

Dear maintainers,

The RCy3 package will be undergoing a major transformation in this upcoming 
version bump to 2.0. The details are itemized in our NEWS and we even made a 
wiki page to help folks through the upgrade process for existing scripts.

https://www.bioconductor.org/packages/3.7/bioc/news/RCy3/NEWS 


https://github.com/cytoscape/RCy3/wiki/Upgrading-Existing-Scripts 
 

The fundamental change is that CytoscapeConnection and CytoscapeWindow classes 
are no longer used. These were pervasive arguments throughout the package in 
prior versions, so practically every function signature has changed. However, 
this change simplifies functions and in 99% of cases the old arg can simply be 
deleted.

Some summary stats regarding the changes:
 * 54 new functions (244 total)
 * Other than function signatures, 
* 44 functions are otherwise unchanged
* 37 functions have been annotated as deprecated
* 69 functions have been renamed to match updated docs
* 38 functions have been annotated as defunct

Going forward, this realignment will help us maintain the package in sync with 
changes to critical upstream resources such as Cytoscape’s CyREST API. It will 
also greatly simply script writing for users.

If you have functions and vignettes that depend on RCy3, please don’t hesitate 
to contact me for help with upgrading to 2.0.
 - Alex


Alexander Pico, PhD
NRNB Executive Director
Bioinformatics Assoc. Director
Gladstone Institutes
http://nrnb.org
http://gladstoneinstitutes.org



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] "convert" graphics error for new submission

[Martin Morgan]

It seems like this has 'gone away', was that something you did, or...?


On 04/02/2018 04:34 PM, Vincent Carey wrote:

for two host-types I am seeing an error that I do not know how to address

Loading required package: ontologyIndex
sh: line 1: 76907 Abort trap: 6   'convert'
'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim
'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null
sh: line 1: 76914 Abort trap: 6   'convert'
'BiocOncoTK_files/figure-html/dopogmock-1.png' -trim
'BiocOncoTK_files/figure-html/dopogmock-1.png' > /dev/null
Quitting from lines 351-363 (BiocOncoTK.Rmd)
Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:

[[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...{{dropped:2}}

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Update data in data package, pcxnData

[Shepherd, Lori]

We are taking care of this on our end. Sorry for the confusion.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Sokratis Kariotis 
Sent: Thursday, April 5, 2018 8:02:14 AM
To: Shepherd, Lori
Cc: Turaga, Nitesh; bioc-devel
Subject: Re: [Bioc-devel] Update data in data package, pcxnData

Hey all,

The issues remain the same in both packages:

https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/malbec1-buildsrc.html

https://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html

Regards,
Sokratis

On 30 March 2018 at 18:53, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

I believe this should clear up in a few days.  Because of the circular 
dependencies, it will require a few passes through the build system.


For example:


First pass:

The pcxnData package has a force install, so it will get installed even if it 
fails the build and check. The pcxn package will also fail its first pass 
through.


Second pass:

the pcxn package will find the newly installed version of the pcxnData package 
and pass.  The pcxnData package will still fail


Third pass:

pcxnData will find the newly built software package and pass as will the linux 
version of the software package.


Forth pass:

May be needed for the mac and windows versions to find the new data package.



The last update to the software package was on March 27 - which probably missed 
being pulled for the March 28th report so probably included for the March 29th 
build report

March 29th  - both fail (but there was a force install behind the scenes)

March 30th -  data package fails, but the linux version of the software package 
built and propagated

http://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html


My guess is that by Sunday's or Monday's build reports everything will be okay.

I will keep an eye on this to make sure its the case and please let us know if 
you still are seeing issues next week.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Sokratis Kariotis 
mailto:s.kario...@sheffield.ac.uk>>
Sent: Thursday, March 29, 2018 6:49:47 AM
To: Turaga, Nitesh
Cc: Shepherd, Lori; bioc-devel
Subject: Re: [Bioc-devel] Update data in data package, pcxnData

Hey all,

The packages' changes went through to the 3_6 branch, but since pcxn and 
pcxnData depend on each other, there are errors when they get built as they see 
the old version of the other package. In the current example: 
https://www.bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html
 , the pathCor_pathprint_v1.2.3_unadjusted_frame file is now located in the new 
pcxnData package but during build the old pcxnData is being used and the error 
occurs since the file is not there. I have checked both packages locally and 
they work when both are in their updated form. How can we bypass this? Thanks.

Cheers,
Sokratis

On 27 March 2018 at 14:02, Sokratis Kariotis 
mailto:s.kario...@sheffield.ac.uk>> wrote:
Hey all,

Thanks for the advice. I managed to fix the problem of no permissions! My 
windows machine, after an update, changed the paths to my github keys and had 
to reposition them.  I have now succesfully pushed in both master and 
RELEASE_3_6 branches.

Cheers,
Sokratis

On 26 March 2018 at 15:47, Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi Sokratis,

Your key(s) on file is

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf

ssh-rsa 
B3NzaC1yc2EDAQABAAACAQDdEiGtAz6nXBAaGbUCLQFMWYE9mKRtKf+20GTGAt83aM7uMpIH9fiHIFpe+5ghm3+68fKVTuprG2PYosiy3Nvk79/WZ02IZuYGfFHXEIhsa1aIVMNsofvOrwBhFezbv

[Bioc-devel] Update of miRBaseVersions.db annotation package

[Stefan Haunsberger]

Hi everyone,

I would like to update the miRBaseVersions.db annotation package in devel
version.
It now contains the most recent miRBase release version 22, from the 12th
of March 2018, for mature miRNAs as well as precursor miRNAs.

It can be downloaded from the following google drive repository:
https://drive.google.com/file/d/1J7CFiJut-0ODDePa7oO1IY7L4JycLyX7/view?usp=sharing

The most recently developed version is also available on GitHub:
https://github.com/StefanHaunsberger/mirbaseversions.db

Thanks,

Stefan

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] BioC 3.7: build failing on Mac (merida2) because Cairo not available

[Ramon Diaz-Uriarte]

Dear Lori,

Thanks for the update.


Best,

R.


On Thu, 05-April-2018, at 14:48:09, Shepherd, Lori 
 wrote:
> It doesn't look like the CAIRO mac binary is available yet for R 3.5  - as 
> soon as it becomes available we will update our systems.  For now you can 
> ignore this ERROR.
>
>
>
> 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 Ramon 
> Diaz-Uriarte 
> Sent: Wednesday, April 4, 2018 11:20:27 AM
> To: bioc-devel@
> Cc: ramon.d...@iib.uam.es
> Subject: [Bioc-devel] BioC 3.7: build failing on Mac (merida2) because Cairo 
> not available
>
> Dear All,
>
> A package I maintain (ADaCGH2) is giving an error during  build
> (http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/merida2-buildsrc.html)
> because Cairo is not available. A quick look at other packages that depend
> on Cairo shows the same problem there.
>
> What should we do?
>
>
> Best,
>
>
> R.


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] vignette problems

[campos]

Thanks!

another question, is there any way to check if the changes that I have 
done pass the checks for all PC like on the webpage? I do not have mac 
or windows so I feel like I have to wait to the next day to check if my 
changes worked out.

Thank you very much,

Rafael


On 05.04.2018 14:29, Shepherd, Lori wrote:
>
> In order for changes to be propagated a version bump in the 
> DESCRIPTION file is needed.� Please bump the version in the 
> DESCRIPTION file to 2.7.2.
>
>
>
>
> 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 
> campos 
> *Sent:* Thursday, April 5, 2018 7:45:57 AM
> *To:* Morgan, Martin; bioc-devel
> *Subject:* Re: [Bioc-devel] vignette problems
> Hey Martin,
>
> I pushed new changes since last friday but in
> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/ says that
> the last change date was friday. Any idea what is the problem?
>
> I have tried to fix the problems with memory and all you told me.
>
> Best,
>
> Rafael
>
>
> On 03.04.2018 17:06, Martin Morgan wrote:
> > Please use 'reply all' so that the mailing list remains engaged.
> >
> > Check out the release schedule
> >
> > http://bioconductor.org/developers/release-schedule/
> >
> > in particular
> >
> > Wednesday April 25
> >
> > - Deadline for packages passing ��R CMD build�� and ��R CMD check��
> > without errors or warnings.
> >
> > so you still have time to get your package in order.
> >
> > Using the same techniques as before, I still see valgrind problems,
> > the first being
> >
> > > hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
> > sizeFactors=sizeFactors, maxIters=10)
> > ==24916== Invalid write of size 4
> > ==24916==��� at 0x4BA93FD7:
> > TransitionMatrix::updateAuxiliaries(double**, double***, double*,
> > int*, int, int**, int, double, int) (TransitionMatrix.cpp:292)
> > ==24916==��� by 0x4BA77934: HMM::updateSampleAux(double***, int*, int,
> > double**, double**, double**, double***, double*, int*, int*, int*,
> > int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int)
> > (HMM.cpp:771)
> > ==24916==��� by 0x4BA7896D: HMM::BaumWelch[abi:cxx11](double***, int*,
> > int, int, int**, int*, int*, int*, int, int, int**, double***,
> > SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)
> > ==24916==��� by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
> > ==24916==��� by 0x4F2992D: R_doDotCall (dotcode.c:692)
> > ==24916==��� by 0x4F339D5: do_dotcall (dotcode.c:1252)
> > ==24916==��� by 0x4F81BA6: bcEval (eval.c:6771)
> > ==24916==��� by 0x4F6E963: Rf_eval (eval.c:624)
> > ==24916==��� by 0x4F71188: R_execClosure (eval.c:1764)
> > ==24916==��� by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
> > ==24916==��� by 0x4F6F18B: Rf_eval (eval.c:747)
> > ==24916==��� by 0x4F74B12: do_set (eval.c:2774)
> > ==24916==� Address 0x2e73a294 is 4 bytes inside a block of size 5 
> alloc'd
> > ==24916==��� at 0x4C2DB8F: malloc (in
> > /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> > ==24916==��� by 0x4BA93FA6:
> > TransitionMatrix::updateAuxiliaries(double**, double***, double*,
> > int*, int, int**, int, double, int) (TransitionMatrix.cpp:289)
> > ==24916==��� by 0x4BA77934: HMM::updateSampleAux(double***, int*, int,
> > double**, double**, double**, double***, double*, int*, int*, int*,
> > int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int)
> > (HMM.cpp:771)
> > ==24916==��� by 0x4BA7896D: HMM::BaumWelch[abi:cxx11](double***, int*,
> > int, int, int**, int*, int*, int*, int, int, int**, double***,
> > SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)
> > ==24916==��� by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
> > ==24916==��� by 0x4F2992D: R_doDotCall (dotcode.c:692)
> > ==24916==��� by 0x4F339D5: do_dotcall (dotcode.c:1252)
> > ==24916==��� by 0x4F81BA6: bcEval (eval.c:6771)
> > ==24916==��� by 0x4F6E963: Rf_eval (eval.c:624)
> > ==24916==��� by 0x4F71188: R_execClosure (eval.c:1764)
> > ==24916==��� by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
> > ==24916==��� by 0x4F6F18B: Rf_eval (eval.c:747)
> > ==24916==
> >
> > This seems to be the exact same code as in the problem that you fixed
> > at another location. Actually, I would guess that all of these
> >
> > grep --color -nH -e ")\*ncores+1" *
> > HMM.cpp:784:��� int *myStateBuckets = 
> (int*)malloc(sizeof(int)*ncores+1);
> > MultivariateGaussian.cpp:295:��� int *myDimBuckets =
> > (int*)malloc(sizeof(int)*ncores+1);
> > MultivariateGaussian.cpp:475:��� int *myDimBuckets =
> > (int*)malloc(sizeof(int)*ncores+1);
> > TransitionMatrix.cpp:132:��� int *myStateBuckets =
> > (int*)malloc(sizeof(int)*ncores+1);
> > TransitionMatrix.cpp:289:��� int *myStateBuckets =
> > (int*)malloc(sizeof(int)*ncores+1);
> >
> > are the same problem. Also, usually code that has been copy/past

Re: [Bioc-devel] BioC 3.7: build failing on Mac (merida2) because Cairo not available

[Shepherd, Lori]

It doesn't look like the CAIRO mac binary is available yet for R 3.5  - as soon 
as it becomes available we will update our systems.  For now you can ignore 
this ERROR.



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 Ramon 
Diaz-Uriarte 
Sent: Wednesday, April 4, 2018 11:20:27 AM
To: bioc-devel@
Cc: ramon.d...@iib.uam.es
Subject: [Bioc-devel] BioC 3.7: build failing on Mac (merida2) because Cairo 
not available

Dear All,

A package I maintain (ADaCGH2) is giving an error during  build
(http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/merida2-buildsrc.html)
because Cairo is not available. A quick look at other packages that depend
on Cairo shows the same problem there.

What should we do?


Best,


R.

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut�noma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

___
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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] vignette problems

[Shepherd, Lori]

In order for changes to be propagated a version bump in the DESCRIPTION file is 
needed.  Please bump the version in the DESCRIPTION file to 2.7.2.




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 campos 

Sent: Thursday, April 5, 2018 7:45:57 AM
To: Morgan, Martin; bioc-devel
Subject: Re: [Bioc-devel] vignette problems

Hey Martin,

I pushed new changes since last friday but in
https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/ says that
the last change date was friday. Any idea what is the problem?

I have tried to fix the problems with memory and all you told me.

Best,

Rafael


On 03.04.2018 17:06, Martin Morgan wrote:
> Please use 'reply all' so that the mailing list remains engaged.
>
> Check out the release schedule
>
> http://bioconductor.org/developers/release-schedule/
>
> in particular
>
> Wednesday April 25
>
> - Deadline for packages passing ��R CMD build�� and ��R CMD check��
> without errors or warnings.
>
> so you still have time to get your package in order.
>
> Using the same techniques as before, I still see valgrind problems,
> the first being
>
> > hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
> sizeFactors=sizeFactors, maxIters=10)
> ==24916== Invalid write of size 4
> ==24916==at 0x4BA93FD7:
> TransitionMatrix::updateAuxiliaries(double**, double***, double*,
> int*, int, int**, int, double, int) (TransitionMatrix.cpp:292)
> ==24916==by 0x4BA77934: HMM::updateSampleAux(double***, int*, int,
> double**, double**, double**, double***, double*, int*, int*, int*,
> int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int)
> (HMM.cpp:771)
> ==24916==by 0x4BA7896D: HMM::BaumWelch[abi:cxx11](double***, int*,
> int, int, int**, int*, int*, int*, int, int, int**, double***,
> SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)
> ==24916==by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
> ==24916==by 0x4F2992D: R_doDotCall (dotcode.c:692)
> ==24916==by 0x4F339D5: do_dotcall (dotcode.c:1252)
> ==24916==by 0x4F81BA6: bcEval (eval.c:6771)
> ==24916==by 0x4F6E963: Rf_eval (eval.c:624)
> ==24916==by 0x4F71188: R_execClosure (eval.c:1764)
> ==24916==by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
> ==24916==by 0x4F6F18B: Rf_eval (eval.c:747)
> ==24916==by 0x4F74B12: do_set (eval.c:2774)
> ==24916==  Address 0x2e73a294 is 4 bytes inside a block of size 5 alloc'd
> ==24916==at 0x4C2DB8F: malloc (in
> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==24916==by 0x4BA93FA6:
> TransitionMatrix::updateAuxiliaries(double**, double***, double*,
> int*, int, int**, int, double, int) (TransitionMatrix.cpp:289)
> ==24916==by 0x4BA77934: HMM::updateSampleAux(double***, int*, int,
> double**, double**, double**, double***, double*, int*, int*, int*,
> int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int)
> (HMM.cpp:771)
> ==24916==by 0x4BA7896D: HMM::BaumWelch[abi:cxx11](double***, int*,
> int, int, int**, int*, int*, int*, int, int, int**, double***,
> SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)
> ==24916==by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
> ==24916==by 0x4F2992D: R_doDotCall (dotcode.c:692)
> ==24916==by 0x4F339D5: do_dotcall (dotcode.c:1252)
> ==24916==by 0x4F81BA6: bcEval (eval.c:6771)
> ==24916==by 0x4F6E963: Rf_eval (eval.c:624)
> ==24916==by 0x4F71188: R_execClosure (eval.c:1764)
> ==24916==by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
> ==24916==by 0x4F6F18B: Rf_eval (eval.c:747)
> ==24916==
>
> This seems to be the exact same code as in the problem that you fixed
> at another location. Actually, I would guess that all of these
>
> grep --color -nH -e ")\*ncores+1" *
> HMM.cpp:784:int *myStateBuckets = (int*)malloc(sizeof(int)*ncores+1);
> MultivariateGaussian.cpp:295:int *myDimBuckets =
> (int*)malloc(sizeof(int)*ncores+1);
> MultivariateGaussian.cpp:475:int *myDimBuckets =
> (int*)malloc(sizeof(int)*ncores+1);
> TransitionMatrix.cpp:132:int *myStateBuckets =
> (int*)malloc(sizeof(int)*ncores+1);
> TransitionMatrix.cpp:289:int *myStateBuckets =
> (int*)malloc(sizeof(int)*ncores+1);
>
> are the same problem. Also, usually code that has been copy/pasted
> like this can instead be refactored to  a single function call, so a
> bug can be fixed in one place.
>
> I still see a number of compiler warnings, the first of which is
>
> STAN master$ R CMD INSTALL .
> Bioconductor version 3.7 (BiocInstaller 1.29.5), ?biocLite for help
> * installing to library
> '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.7'
> * installing *source* package 'STAN' ...
> ** libs
> g++  -I"/home/mtmorgan/bin/R-3-5-branch/include" -DNDEBUG
> -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O0 -Wall -pedantic
> -c HMM.cpp -o HMM.o
> HMM.cpp: In member

Re: [Bioc-devel] Update data in data package, pcxnData

[Sokratis Kariotis]

Hey all,

The issues remain the same in both packages:

https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/malbec1-buildsrc.html

https://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html

Regards,
Sokratis

On 30 March 2018 at 18:53, Shepherd, Lori 
wrote:

> I believe this should clear up in a few days.  Because of the circular
> dependencies, it will require a few passes through the build system.
>
>
> For example:
>
>
> First pass:
>
> The pcxnData package has a force install, so it will get installed even
> if it fails the build and check. The pcxn package will also fail its first
> pass through.
>
>
> Second pass:
>
> the pcxn package will find the newly installed version of the pcxnData
> package and pass.  The pcxnData package will still fail
>
>
> Third pass:
>
> pcxnData will find the newly built software package and pass as will the
> linux version of the software package.
>
>
> Forth pass:
>
> May be needed for the mac and windows versions to find the new data
> package.
>
>
>
> The last update to the software package was on March 27 - which probably
> missed being pulled for the March 28th report so probably included for the
> March 29th build report
>
> March 29th  - both fail (but there was a force install behind the scenes)
>
> March 30th -  data package fails, but the linux version of the software
> package built and propagated
>
> http://bioconductor.org/checkResults/3.6/bioc-LATEST/
> pcxn/malbec1-buildsrc.html
>
>
> My guess is that by Sunday's or Monday's build reports everything will be
> okay.
>
> I will keep an eye on this to make sure its the case and please let us
> know if you still are seeing issues next week.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis 
> *Sent:* Thursday, March 29, 2018 6:49:47 AM
> *To:* Turaga, Nitesh
> *Cc:* Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>
> Hey all,
>
> The packages' changes went through to the 3_6 branch, but since pcxn and
> pcxnData depend on each other, there are errors when they get built as they
> see the old version of the other package. In the current example:
> https://www.bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-
> buildsrc.html , the pathCor_pathprint_v1.2.3_unadjusted_frame file is now
> located in the new pcxnData package but during build the old pcxnData is
> being used and the error occurs since the file is not there. I have checked
> both packages locally and they work when both are in their updated form.
> How can we bypass this? Thanks.
>
> Cheers,
> Sokratis
>
> On 27 March 2018 at 14:02, Sokratis Kariotis 
> wrote:
>
> Hey all,
>
> Thanks for the advice. I managed to fix the problem of no permissions! My
> windows machine, after an update, changed the paths to my github keys and
> had to reposition them.  I have now succesfully pushed in both master and
> RELEASE_3_6 branches.
>
> Cheers,
> Sokratis
>
> On 26 March 2018 at 15:47, Turaga, Nitesh 
> wrote:
>
> Hi Sokratis,
>
> Your key(s) on file is
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp
> +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0
> Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL
> xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZ
> j/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNW
> cEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+Q
> V5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6n
> FfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+
> rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80T
> a0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJ
> Yw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkB
> CHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2
> CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0
> UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR
> 2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8
> cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf
>
> ssh-rsa B3NzaC1yc2EDAQABAAACAQDdEiGtAz6nXBAaGbUCLQFMWYE9mKRt
> Kf+20GTGAt83aM7uMpIH9fiHIFpe+5ghm3+68fKVTuprG2PYosiy3Nvk79/W
> Z02IZuYGfFHXEIhsa1aIVMNsofvOrwBhFezbvoZ3b9oPakFbQFiAtjPkN6h4
> drr+iQq4to4jc5wvYw07uqIEEG8nZfiB+QWa5s+rplTS3zJZzr7xpEDT/7ZH
> pKVduZUg34tzaN4+vONgofgOthUMWArO3oO69wPwAdoAUACRmXT02xknrcWZ
> m4UtuhzT98FHLznSowZMLG3jm8vKgsgbH8UGGtz478UZW5xE4qS5LHiKJbcZ
> FBCLFABUjCajuYF3z+bZF0cxbT9d+25kpp/p89lvljsvlE7vbxdqFmeobGSQ
> 6ftDq5btdEHfD2rc++iWEZgmOGjcHtDxUem3nNGCOYtDkPAIKES5oCCtlD9s
> BL5gLFHTkl3KyxNdIsH9j0iNFdJmEHy

Re: [Bioc-devel] vignette problems

[campos]

Hey Martin,

I pushed new changes since last friday but in 
https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/ says that 
the last change date was friday. Any idea what is the problem?


I have tried to fix the problems with memory and all you told me.

Best,

Rafael


On 03.04.2018 17:06, Martin Morgan wrote:

Please use 'reply all' so that the mailing list remains engaged.

Check out the release schedule

http://bioconductor.org/developers/release-schedule/

in particular

Wednesday April 25

- Deadline for packages passing ‘‘R CMD build’’ and ‘‘R CMD check’’ 
without errors or warnings.


so you still have time to get your package in order.

Using the same techniques as before, I still see valgrind problems, 
the first being


> hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog, 
sizeFactors=sizeFactors, maxIters=10)

==24916== Invalid write of size 4
==24916==    at 0x4BA93FD7: 
TransitionMatrix::updateAuxiliaries(double**, double***, double*, 
int*, int, int**, int, double, int) (TransitionMatrix.cpp:292)
==24916==    by 0x4BA77934: HMM::updateSampleAux(double***, int*, int, 
double**, double**, double**, double***, double*, int*, int*, int*, 
int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int) 
(HMM.cpp:771)
==24916==    by 0x4BA7896D: HMM::BaumWelch[abi:cxx11](double***, int*, 
int, int, int**, int*, int*, int*, int, int, int**, double***, 
SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)

==24916==    by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
==24916==    by 0x4F2992D: R_doDotCall (dotcode.c:692)
==24916==    by 0x4F339D5: do_dotcall (dotcode.c:1252)
==24916==    by 0x4F81BA6: bcEval (eval.c:6771)
==24916==    by 0x4F6E963: Rf_eval (eval.c:624)
==24916==    by 0x4F71188: R_execClosure (eval.c:1764)
==24916==    by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
==24916==    by 0x4F6F18B: Rf_eval (eval.c:747)
==24916==    by 0x4F74B12: do_set (eval.c:2774)
==24916==  Address 0x2e73a294 is 4 bytes inside a block of size 5 alloc'd
==24916==    at 0x4C2DB8F: malloc (in 
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==24916==    by 0x4BA93FA6: 
TransitionMatrix::updateAuxiliaries(double**, double***, double*, 
int*, int, int**, int, double, int) (TransitionMatrix.cpp:289)
==24916==    by 0x4BA77934: HMM::updateSampleAux(double***, int*, int, 
double**, double**, double**, double***, double*, int*, int*, int*, 
int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int) 
(HMM.cpp:771)
==24916==    by 0x4BA7896D: HMM::BaumWelch[abi:cxx11](double***, int*, 
int, int, int**, int*, int*, int*, int, int, int**, double***, 
SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)

==24916==    by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
==24916==    by 0x4F2992D: R_doDotCall (dotcode.c:692)
==24916==    by 0x4F339D5: do_dotcall (dotcode.c:1252)
==24916==    by 0x4F81BA6: bcEval (eval.c:6771)
==24916==    by 0x4F6E963: Rf_eval (eval.c:624)
==24916==    by 0x4F71188: R_execClosure (eval.c:1764)
==24916==    by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
==24916==    by 0x4F6F18B: Rf_eval (eval.c:747)
==24916==

This seems to be the exact same code as in the problem that you fixed 
at another location. Actually, I would guess that all of these


grep --color -nH -e ")\*ncores+1" *
HMM.cpp:784:    int *myStateBuckets = (int*)malloc(sizeof(int)*ncores+1);
MultivariateGaussian.cpp:295:    int *myDimBuckets = 
(int*)malloc(sizeof(int)*ncores+1);
MultivariateGaussian.cpp:475:    int *myDimBuckets = 
(int*)malloc(sizeof(int)*ncores+1);
TransitionMatrix.cpp:132:    int *myStateBuckets = 
(int*)malloc(sizeof(int)*ncores+1);
TransitionMatrix.cpp:289:    int *myStateBuckets = 
(int*)malloc(sizeof(int)*ncores+1);


are the same problem. Also, usually code that has been copy/pasted 
like this can instead be refactored to  a single function call, so a 
bug can be fixed in one place.


I still see a number of compiler warnings, the first of which is

STAN master$ R CMD INSTALL .
Bioconductor version 3.7 (BiocInstaller 1.29.5), ?biocLite for help
* installing to library 
'/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.7'

* installing *source* package 'STAN' ...
** libs
g++  -I"/home/mtmorgan/bin/R-3-5-branch/include" -DNDEBUG 
-I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O0 -Wall -pedantic 
-c HMM.cpp -o HMM.o
HMM.cpp: In member function ‘virtual void 
HMM::calcEmissionProbs(double***, double**, int*, int, int**, int*, 
int*, int**, int, int, int*)’:

HMM.cpp:112:15: warning: unused variable ‘j’ [-Wunused-variable]
 int i,j,t,k;
   ^
It really pays to clean these up; most are harmless, but they obscure 
the more important warnings.


Martin


On 04/03/2018 09:58 AM, campos wrote:

Hi Martin,

when I run now valgrind seems that there are no problems. I pushed 
yesterday the changes, was I still on time for the new release? We 
want to publish the changes and it would be really helpful if the 
package is running on Bioconductor.


Than

Re: [Bioc-devel] Why my package has not been uploaded on bioc devel build list?

[Shepherd, Lori]

Please wait and see if it is on today's build report.  Depending on when it was 
added to the manifest it might have not made it over in time to build on the 
previous report.


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 Minoo Ashtiani 

Sent: Thursday, April 5, 2018 2:10:30 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Why my package has not been uploaded on bioc devel build 
list?

Hello,

I supposed that my new package called "IMMAN" be included in the next nigthly 
'devel' build on Wednesday. However, I did not find it on the list. I wanted to 
know whether there is problem with my package or not.


Bests,

Minoo

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel