date:20190412

Re: [Bioc-devel] TIMEOUTS in the submission systems

2019-04-12 Thread Shepherd, Lori

Yes we are aware. We are looking into the issue and are trying to have it 
resolve shortly.

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 Bernat Gel 
Moreno 
Sent: Friday, April 12, 2019 4:30:50 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] TIMEOUTS in the submission systems

Hi,

I assume you are already aware of it, but there's a problem with the builder 
for the new packages. It works fine in Windows but Mac and Linux cannot access 
CRAN

checking package dependencies ...Warning: unable to access index for repository 
https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'

This causes a WARNING in Malbec2 and a TIMEOUT in Celaya2.

Thanks!

Bernat


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[Bioc-devel] TIMEOUTS in the submission systems

2019-04-12 Thread Bernat Gel Moreno

Hi,

I assume you are already aware of it, but there's a problem with the builder 
for the new packages. It works fine in Windows but Mac and Linux cannot access 
CRAN

checking package dependencies ...Warning: unable to access index for repository 
https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'

This causes a WARNING in Malbec2 and a TIMEOUT in Celaya2.

Thanks!

Bernat


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Re: [Bioc-devel] New build report

2019-04-12 Thread Alina Selega

Okay, thank you very much!

On Fri, 12 Apr 2019 at 12:25, Shepherd, Lori 
wrote:

> That is not correct. The webhook was only for the package submission
> process.
>
> See the link provided on linking to Bioconductor.
>
> Other helpful github links  can be found here:
> http://bioconductor.org/developers/how-to/git/
>
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Alina Selega 
> *Sent:* Friday, April 12, 2019 12:22:40 PM
> *To:* Shepherd, Lori
> *Cc:* bioc-devel
> *Subject:* Re: [Bioc-devel] New build report
>
> Thank you for the instructions!
>
> Can I just clarify -- I was pushing changes to my Github repository that
> has a webhook set up (as per instructions from when I first submitted the
> package to Bioconductor). I thought that pushes to master branch with
> version bump should trigger package builds. Am I wrong about this?
>
> Thanks,
> Alina
>
> On Fri, 12 Apr 2019 at 12:15, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
> We are not seeing the changes pushed to the git.bioconductor server.  I am
> assuming you are referring to the RELEASE_3_8 branch since you are
> referencing 1.6.1.
>
>
> Have set up the remote upstream to point to Bioconductor,
>
> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
>
> On your repository you can check your remotes with
> git remote -v
>
> It should include something like the following:
> upstream g...@git.bioconductor.org:packages/BUMHMM.git (fetch)
> upstream g...@git.bioconductor.org:packages/BUMHMM.git (push)
>
> Make sure you pushed to the upstream remote:
>
>
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>
> and that you are working on the RELEASE_3_8 branch
>
> git fetch --all
>
> git checkout RELEASE_3_8  (or git checkout upstream RELEASE_3_8)
>
> # make your changes
>
> # commit your changes
>
> # push the changes to Bioconductor with the following:
>
> git push upstream RELEASE_3_8
>
>
>
>
> 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 Alina
> Selega 
> *Sent:* Friday, April 12, 2019 12:04:03 PM
> *To:* bioc-devel
> *Subject:* Re: [Bioc-devel] New build report
>
> Hi,
>
> Sorry, I think I must have done something wrong as the build report is not
> showing the updates to my package from 2 days ago. Could you please help me
> with this? I thought I updated the version of BUMHMM correctly (from 1.6.1
> to 1.6.2 and 1.6.3) but it is not been picked up?
>
> Thanks,
> Alina
>
> On Thu, 11 Apr 2019 at 12:47, Alina Selega  wrote:
>
> > Hi,
> >
> > I have made some minor updates to my package (BUMHMM) yesterday to fix
> the
> > warnings arising on the Windows server and pushed the changes with a
> > version bump from its current version 1.6.1. (actually, two bumps.)
> >
> > I don't see any changes in today's build report; has the build happened
> > yet?
> >
> > Thanks,
> > Alina
> >
>
> [[alternative HTML version deleted]]
>
> ___
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>
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> agent responsible for the delivery of this message to the intended
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> agent responsible for the delivery of this message to the intended
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Re: [Bioc-devel] New build report

2019-04-12 Thread Shepherd, Lori

That is not correct. The webhook was only for the package submission process.

See the link provided on linking to Bioconductor.

Other helpful github links  can be found here:
http://bioconductor.org/developers/how-to/git/

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Alina Selega 
Sent: Friday, April 12, 2019 12:22:40 PM
To: Shepherd, Lori
Cc: bioc-devel
Subject: Re: [Bioc-devel] New build report

Thank you for the instructions!

Can I just clarify -- I was pushing changes to my Github repository that has a 
webhook set up (as per instructions from when I first submitted the package to 
Bioconductor). I thought that pushes to master branch with version bump should 
trigger package builds. Am I wrong about this?

Thanks,
Alina

On Fri, 12 Apr 2019 at 12:15, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

We are not seeing the changes pushed to the git.bioconductor server.  I am 
assuming you are referring to the RELEASE_3_8 branch since you are referencing 
1.6.1.

Have set up the remote upstream to point to Bioconductor,

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

On your repository you can check your remotes with
git remote -v

It should include something like the following:
upstream g...@git.bioconductor.org:packages/BUMHMM.git (fetch)
upstream g...@git.bioconductor.org:packages/BUMHMM.git (push)

Make sure you pushed to the upstream remote:

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

and that you are working on the RELEASE_3_8 branch

git fetch --all

git checkout RELEASE_3_8  (or git checkout upstream RELEASE_3_8)

# make your changes

# commit your changes

# push the changes to Bioconductor with the following:

git push upstream RELEASE_3_8

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Alina Selega mailto:alina.sel...@gmail.com>>
Sent: Friday, April 12, 2019 12:04:03 PM
To: bioc-devel
Subject: Re: [Bioc-devel] New build report

Hi,

Sorry, I think I must have done something wrong as the build report is not
showing the updates to my package from 2 days ago. Could you please help me
with this? I thought I updated the version of BUMHMM correctly (from 1.6.1
to 1.6.2 and 1.6.3) but it is not been picked up?

Thanks,
Alina

On Thu, 11 Apr 2019 at 12:47, Alina Selega 
mailto:alina.sel...@gmail.com>> wrote:

> Hi,
>
> I have made some minor updates to my package (BUMHMM) yesterday to fix the
> warnings arising on the Windows server and pushed the changes with a
> version bump from its current version 1.6.1. (actually, two bumps.)
>
> I don't see any changes in today's build report; has the build happened
> yet?
>
> Thanks,
> Alina
>

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email message is prohibited. If you have received this message in error, please 
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Re: [Bioc-devel] New build report

2019-04-12 Thread Alina Selega

Thank you for the instructions!

Can I just clarify -- I was pushing changes to my Github repository that
has a webhook set up (as per instructions from when I first submitted the
package to Bioconductor). I thought that pushes to master branch with
version bump should trigger package builds. Am I wrong about this?

Thanks,
Alina

On Fri, 12 Apr 2019 at 12:15, Shepherd, Lori 
wrote:

> We are not seeing the changes pushed to the git.bioconductor server.  I am
> assuming you are referring to the RELEASE_3_8 branch since you are
> referencing 1.6.1.
>
>
> Have set up the remote upstream to point to Bioconductor,
>
> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
>
> On your repository you can check your remotes with
> git remote -v
>
> It should include something like the following:
> upstream g...@git.bioconductor.org:packages/BUMHMM.git (fetch)
> upstream g...@git.bioconductor.org:packages/BUMHMM.git (push)
>
> Make sure you pushed to the upstream remote:
>
>
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>
> and that you are working on the RELEASE_3_8 branch
>
> git fetch --all
>
> git checkout RELEASE_3_8  (or git checkout upstream RELEASE_3_8)
>
> # make your changes
>
> # commit your changes
>
> # push the changes to Bioconductor with the following:
>
> git push upstream RELEASE_3_8
>
>
>
>
> 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 Alina
> Selega 
> *Sent:* Friday, April 12, 2019 12:04:03 PM
> *To:* bioc-devel
> *Subject:* Re: [Bioc-devel] New build report
>
> Hi,
>
> Sorry, I think I must have done something wrong as the build report is not
> showing the updates to my package from 2 days ago. Could you please help me
> with this? I thought I updated the version of BUMHMM correctly (from 1.6.1
> to 1.6.2 and 1.6.3) but it is not been picked up?
>
> Thanks,
> Alina
>
> On Thu, 11 Apr 2019 at 12:47, Alina Selega  wrote:
>
> > Hi,
> >
> > I have made some minor updates to my package (BUMHMM) yesterday to fix
> the
> > warnings arising on the Windows server and pushed the changes with a
> > version bump from its current version 1.6.1. (actually, two bumps.)
> >
> > I don't see any changes in today's build report; has the build happened
> > yet?
> >
> > Thanks,
> > Alina
> >
>
> [[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.

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Re: [Bioc-devel] New build report

2019-04-12 Thread Shepherd, Lori

We are not seeing the changes pushed to the git.bioconductor server.  I am 
assuming you are referring to the RELEASE_3_8 branch since you are referencing 
1.6.1.

Have set up the remote upstream to point to Bioconductor,

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

On your repository you can check your remotes with
git remote -v

It should include something like the following:
upstream g...@git.bioconductor.org:packages/BUMHMM.git (fetch)
upstream g...@git.bioconductor.org:packages/BUMHMM.git (push)

Make sure you pushed to the upstream remote:

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

and that you are working on the RELEASE_3_8 branch

git fetch --all

git checkout RELEASE_3_8  (or git checkout upstream RELEASE_3_8)

# make your changes

# commit your changes

# push the changes to Bioconductor with the following:

git push upstream RELEASE_3_8

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 Alina Selega 

Sent: Friday, April 12, 2019 12:04:03 PM
To: bioc-devel
Subject: Re: [Bioc-devel] New build report

Hi,

Sorry, I think I must have done something wrong as the build report is not
showing the updates to my package from 2 days ago. Could you please help me
with this? I thought I updated the version of BUMHMM correctly (from 1.6.1
to 1.6.2 and 1.6.3) but it is not been picked up?

Thanks,
Alina

On Thu, 11 Apr 2019 at 12:47, Alina Selega  wrote:

> Hi,
>
> I have made some minor updates to my package (BUMHMM) yesterday to fix the
> warnings arising on the Windows server and pushed the changes with a
> version bump from its current version 1.6.1. (actually, two bumps.)
>
> I don't see any changes in today's build report; has the build happened
> yet?
>
> Thanks,
> Alina
>

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Re: [Bioc-devel] New build report

2019-04-12 Thread Alina Selega

Hi,

Sorry, I think I must have done something wrong as the build report is not
showing the updates to my package from 2 days ago. Could you please help me
with this? I thought I updated the version of BUMHMM correctly (from 1.6.1
to 1.6.2 and 1.6.3) but it is not been picked up?

Thanks,
Alina

On Thu, 11 Apr 2019 at 12:47, Alina Selega  wrote:

> Hi,
>
> I have made some minor updates to my package (BUMHMM) yesterday to fix the
> warnings arising on the Windows server and pushed the changes with a
> version bump from its current version 1.6.1. (actually, two bumps.)
>
> I don't see any changes in today's build report; has the build happened
> yet?
>
> Thanks,
> Alina
>

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Re: [Bioc-devel] Problem with non-portable compiler flags on package test

2019-04-12 Thread Martin Morgan

Your configure outsmarts the check system, so your options are to omit the 
flags or to live with the warning. Either solution is fine with Bioconductor.

Martin

On 4/12/19, 4:17 AM, "Bioc-devel on behalf of Jochen Knaus" 
 wrote:

Hi everybody,

for our new R package "Netboost" we have a problem about non portable 
compiler flags. Basically we support AVX in our own C++ code (using 
compiler intrinsics to use the AVX units). Of course we have a non-AVX 
code path.

For building we use autotools and configure to determine at installation 
time if the AVX unit is available and supported by the given compilers. 
If available then compilation is done with AVX, if not, then ordinary 
code path is used.

The problem is the R package test, which does see the set AVX flag in 
"Makevars" (as Makevars.in is configured to use AVX if the test is 
executed on a machine supporting AVX).

Note: due to bundled software, this is a Linux only package, so no 
support for Microsoft compilers is required (with other flag names).

Is there any way around this warning, which is a real false-positive, as 
the flag is not set in environments not suitable.

Thanks a lot for any help!

Jo


Details:

for testing we use GNU Autotools and the AX_EXT M4-macroset to determine 
the hardware and compiler support for additional features: 
https://www.gnu.org/software/autoconf-archive/ax_ext.html

configure.ac:

m4_include([m4/ax_gcc_x86_avx_xgetbv.m4])
m4_include([m4/ax_gcc_x86_cpuid.m4])
m4_include([m4/ax_check_compile_flag.m4])
m4_include([m4/ax_ext.m4])

# Probe CPU and compilers
AX_EXT

src/Makevars.in:

PKG_CXXFLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"` @SIMD_FLAGS@

Running R CMD CHECK with --as-cran, we get the warning:

http://bioconductor.org/spb_reports/netboost_buildreport_20190412033232.html

* checking compilation flags used ... WARNING Compilation used the 
following non-portable flag(s): -Wno-deprecated -maes -mavx -mavx2 -mfma 
-mmmx -msse -msse3 -msse4.1 -msse4.2 -mssse3

(Basically we only need -mavx and optionally FMA, but AX_EXT sets all).

-- 
Jochen Knaus
Institute of Biometry and Statistics
Faculty of Medicine and Medical Center - University of Freiburg
Office: IMBI library
Postal address: Stefan-Meier-Str. 26, D-79104 Freiburg
Phone: +49/761/203-5528
Mail: j...@imbi.uni-freiburg.de
Homepage: http://www.imbi.uni-freiburg.de


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[Bioc-devel] Problem with non-portable compiler flags on package test

2019-04-12 Thread Jochen Knaus

Hi everybody,

for our new R package "Netboost" we have a problem about non portable 
compiler flags. Basically we support AVX in our own C++ code (using 
compiler intrinsics to use the AVX units). Of course we have a non-AVX 
code path.

For building we use autotools and configure to determine at installation 
time if the AVX unit is available and supported by the given compilers. 
If available then compilation is done with AVX, if not, then ordinary 
code path is used.

The problem is the R package test, which does see the set AVX flag in 
"Makevars" (as Makevars.in is configured to use AVX if the test is 
executed on a machine supporting AVX).

Note: due to bundled software, this is a Linux only package, so no 
support for Microsoft compilers is required (with other flag names).

Is there any way around this warning, which is a real false-positive, as 
the flag is not set in environments not suitable.

Thanks a lot for any help!

Jo


Details:

for testing we use GNU Autotools and the AX_EXT M4-macroset to determine 
the hardware and compiler support for additional features: 
https://www.gnu.org/software/autoconf-archive/ax_ext.html

configure.ac:

m4_include([m4/ax_gcc_x86_avx_xgetbv.m4])
m4_include([m4/ax_gcc_x86_cpuid.m4])
m4_include([m4/ax_check_compile_flag.m4])
m4_include([m4/ax_ext.m4])

# Probe CPU and compilers
AX_EXT

src/Makevars.in:

PKG_CXXFLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"` @SIMD_FLAGS@

Running R CMD CHECK with --as-cran, we get the warning:

http://bioconductor.org/spb_reports/netboost_buildreport_20190412033232.html

* checking compilation flags used ... WARNING Compilation used the 
following non-portable flag(s): -Wno-deprecated -maes -mavx -mavx2 -mfma 
-mmmx -msse -msse3 -msse4.1 -msse4.2 -mssse3

(Basically we only need -mavx and optionally FMA, but AX_EXT sets all).

-- 
Jochen Knaus
Institute of Biometry and Statistics
Faculty of Medicine and Medical Center - University of Freiburg
Office: IMBI library
Postal address: Stefan-Meier-Str. 26, D-79104 Freiburg
Phone: +49/761/203-5528
Mail: j...@imbi.uni-freiburg.de
Homepage: http://www.imbi.uni-freiburg.de


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Re: [Bioc-devel] loading database package changes random number

2019-04-12 Thread Steffi Grote

Hi Martin and Herve,

thanks for the quick responses and the clarification.
It's not an issue now that I know this happens, and can just load DelayedArray 
outside of the function.

Best,
Steffi

> On April 12, 2019 at 1:10 AM Martin Morgan  wrote:
> 
> 
> That easy strategy wouldn't work, for instance two successive calls to 
> MulticoreParam() would get the same port assigned, rather than the contract 
> of a 'random' port in a specific range; the port can be assigned by the 
> manager.port= argument if the user wants to avoid random assignment. I could 
> maintain a separate random number stream in BiocParallel for what amounts to 
> a pretty trivial and probably dubious strategy [choosing random ports in 
> hopes that one is not in use], but that starts to sound like a more 
> substantial feature.
> 
> Martin
> 
> On 4/11/19, 7:06 PM, "Pages, Herve"  wrote:
> 
> Hi Steffi,
> 
> Any code that gets called between your calls to set.seed() and runif() 
> could potentially use the random number generator. So the sequence 
> set.seed(123); runif(1) is only guaranteed to be deterministic if no 
> other code is called in between, or if the code called in between does 
> not use the random number generator (but if that code is not under your 
> control it could do anything).
> 
> @Martin: I'll look at your suggestion for DelayedArray. An easy 
> workaround would be to avoid changing the RNG state in BiocParallel by 
> having .snowPort() make a copy of .Random.seed (if it exists) before 
> calling runif() and restoring it on exit.
> 
> H.
> 
> On 4/11/19 15:25, Martin Morgan wrote:
> > This is actually from a dependency DelayedArray which, on load, calls 
> DelayedArray::setAutoBPPARAM, which calls BiocParallel::MulticoreParam(), 
> which uses the random number generator to select a random port for connection.
> >
> > A different approach would be for DelayedArray to respect the user's 
> configuration and use bpparam(), or perhaps look at the class of bpparam() 
> and tell the user they should, e.g., BiocParallel::register(SerialParam()) if 
> that's appropriate, or use registered("MulticoreParam") or 
> registered("SerialParam") if available (they are by default) rather than 
> creating an ad-hoc instance.
> >
> > Martin
> >
> > On 4/11/19, 10:17 AM, "Bioc-devel on behalf of Steffi Grote" 
>  wrote:
> >
> >  Hi all,
> >  I found out that example code for my package GOfuncR yields a 
> different result the first time it's executed, despite setting a seed. All 
> the following executions are identical.
> >  It turned out that loading the database package 'Homo.sapiens' 
> changed the random numbers:
> >  
> >  set.seed(123)
> >  runif(1)
> >  # [1] 0.2875775
> >  
> >  set.seed(123)
> >  suppressWarnings(suppressMessages(require(Homo.sapiens)))
> >  runif(1)
> >  # [1] 0.7883051
> >  
> >  set.seed(123)
> >  runif(1)
> >  # [1] 0.2875775
> >  
> >  Is that known or expected behaviour?
> >  Should I not load a package inside a function that later uses 
> random numbers?
> >  
> >  Thanks in advance,
> >  Steffi
> >  
> >  ___
> >  Bioc-devel@r-project.org mailing list
> >  
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=8XXamcpEeef966i7IGk_3aE9GMJodKAzXwWW4fL_hrI=KoHGLM0HbP4whRZLG4ol66_q1qkg9E0LjFHObDqgNuo=
> >  
> 
> -- 
> 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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