[Bioc-devel] Software package dependency >=5Mb in size

[Shraddha Pai]

Hi,
Our software package relies on a Java jar file that is 11Mb in size and
there is a good chance we cannot make the file size smaller. The jar file
is used to run our algorithm so none of the vignettes can run without it
and a separate download would be tedious for users.

Is there still a way to submit our package to BioC? It would be great to
increase community adoption of our package via the BioC system.

Thanks,Shraddha

-- 
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter

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Re: [Bioc-devel] Problems with MACPET package

[Ioannis Vardaxis]

I have been trying to push the updates on RELEASE_3_9, but they don’t seem to 
get updated. They are only updated on GitHub.

Best,
Ioannis

17. jul. 2019 kl. 12:50 skrev Martin Morgan 
mailto:mtmorgan.b...@gmail.com>>:

Bioc devel prepares for the next release of bioc, using the version of R that 
will be closest to that in use at the time of the release.

The version of R that will be in use at the time of the next bioc release will 
be R-3.6.*.

You should be using R-3.6 for bioc-devel.

This is summarized at http://bioconductor.org/developers/how-to/useDevel/ ; if 
there are improvments to the wording there please feel free to provide a pull 
request on 
https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/how-to/useDevel.md

'RELEASE_3_10' as a branch does not exist because there has not yet been a 
release 3.10; the 'master' branch is the location where devel builds from.

Martin

On 7/17/19, 5:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis" 
mailto:bioc-devel-boun...@r-project.org> on 
behalf of ioannis.varda...@ntnu.no> wrote:

   My seesionInfo:
   sessionInfo()
   R Under development (unstable) (2019-07-11 r76823)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS Mojave 10.14.5

   And
   BiocManager::install("stringdist")
   Bioconductor version 3.10 (BiocManager 1.30.4), R Under development 
(unstable) (2019-07-11 r76823)
   Installing package(s) 'stringdist'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Package which is only available in source form, and may need compilation of 
C/C++/Fortran: ‘stringdist’
   Do you want to attempt to install these from sources? (Yes/no/cancel) Yes


   Also, I cannot push to RELEASE_3_10 because I get error:

   $git checkout RELEASE_3_10
   error: pathspec 'RELEASE_3_10' did not match any file(s) known to git


   Shouldn’t I use the R devel version?

   Best,
   Ioannis


   15. jul. 2019 kl. 09:53 skrev Ioannis Vardaxis 
mailto:ioannis.varda...@ntnu.no>>:

   My seesionInfo:
   sessionInfo()
   R Under development (unstable) (2019-07-11 r76823)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS Mojave 10.14.5

   And
   BiocManager::install("stringdist")
   Bioconductor version 3.10 (BiocManager 1.30.4), R Under development 
(unstable) (2019-07-11 r76823)
   Installing package(s) 'stringdist'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Package which is only available in source form, and may need compilation of 
C/C++/Fortran: ‘stringdist’
   Do you want to attempt to install these from sources? (Yes/no/cancel) Yes


   Also, I cannot such to RELEASE_3_10 because I get error:

   $git checkout RELEASE_3_10
   error: pathspec 'RELEASE_3_10' did not match any file(s) known to git



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Re: [Bioc-devel] Problems with MACPET package

[Shepherd, Lori]

Your package is building clean on the RELEASE_3_9 branch.  What are you 
updating?

This is clean:

http://bioconductor.org/checkResults/release/bioc-LATEST/MACPET/



The branch that is failing and that needs to be updated is the current 
Bioconductor devel (3.10) branch.  That branch is the "master" branch on 
git.bioconductor.org

http://bioconductor.org/checkResults/devel/bioc-LATEST/MACPET/



You would follow the steps provided here:

http://bioconductor.org/developers/how-to/git/push-to-github-bioc/


Please check that the remotes are set up correctly and show the results of  
(Step 2)


git remote -v



Assuming you have your remotes set up correctly and you have merged with 
Bioconductor Please then try (Step 6)


git push upstream master



Please show any ERRORs or outputs you receive so we can better assist.


I see you made at least one push to the master branch on Jun 25.

Bioconductor will only recognize and propagate the package if there has been a 
valid version bump.  For devel,  Please make sure you commit any changes with 
an increase from 1.5.0  (current) to 1.5.1 or the Bioconductor package/pages 
will not be updated.


Thank you,

Cheers,


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 Ioannis 
Vardaxis 
Sent: Monday, July 29, 2019 10:56:23 AM
To: Martin Morgan 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Problems with MACPET package

I have been trying to push the updates on RELEASE_3_9, but they don’t seem to 
get updated. They are only updated on GitHub.

Best,
Ioannis

17. jul. 2019 kl. 12:50 skrev Martin Morgan 
mailto:mtmorgan.b...@gmail.com>>:

Bioc devel prepares for the next release of bioc, using the version of R that 
will be closest to that in use at the time of the release.

The version of R that will be in use at the time of the next bioc release will 
be R-3.6.*.

You should be using R-3.6 for bioc-devel.

This is summarized at http://bioconductor.org/developers/how-to/useDevel/ ; if 
there are improvments to the wording there please feel free to provide a pull 
request on 
https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/how-to/useDevel.md

'RELEASE_3_10' as a branch does not exist because there has not yet been a 
release 3.10; the 'master' branch is the location where devel builds from.

Martin

On 7/17/19, 5:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis" 
mailto:bioc-devel-boun...@r-project.org> on 
behalf of ioannis.varda...@ntnu.no> wrote:

   My seesionInfo:
   sessionInfo()
   R Under development (unstable) (2019-07-11 r76823)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS Mojave 10.14.5

   And
   BiocManager::install("stringdist")
   Bioconductor version 3.10 (BiocManager 1.30.4), R Under development 
(unstable) (2019-07-11 r76823)
   Installing package(s) 'stringdist'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Package which is only available in source form, and may need compilation of 
C/C++/Fortran: ‘stringdist’
   Do you want to attempt to install these from sources? (Yes/no/cancel) Yes


   Also, I cannot push to RELEASE_3_10 because I get error:

   $git checkout RELEASE_3_10
   error: pathspec 'RELEASE_3_10' did not match any file(s) known to git


   Shouldn’t I use the R devel version?

   Best,
   Ioannis


   15. jul. 2019 kl. 09:53 skrev Ioannis Vardaxis 
mailto:ioannis.varda...@ntnu.no>>:

   My seesionInfo:
   sessionInfo()
   R Under development (unstable) (2019-07-11 r76823)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS Mojave 10.14.5

   And
   BiocManager::install("stringdist")
   Bioconductor version 3.10 (BiocManager 1.30.4), R Under development 
(unstable) (2019-07-11 r76823)
   Installing package(s) 'stringdist'
   Warning: unable to access index for repository 
https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
cannot open URL 
'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository 
https:/

[Bioc-devel] "In Bioconductor since" date wrong

[Neumann, Steffen]

Hi,

The package pages seem to have lost memory 
when a package was introduced:

http://bioconductor.org/packages/3.7/bioc/html/xcms.html 
http://bioconductor.org/packages/3.8/bioc/html/xcms.html
In Bioconductor since   BioC 1.6 (R-2.1) or earlier (> 13.5 years)

but now it has reset to:

http://bioconductor.org/packages/3.9/bioc/html/xcms.html
http://bioconductor.org/packages/3.10/bioc/html/xcms.html
http://bioconductor.org/packages/devel/bioc/html/xcms.html
In Bioconductor since   BioC 3.9 (R-3.6) (< 6 months)

Not that it really matters, but in case you revisit 
how these pages are generated at some stage ...

Yours,
Steffen

-- 

Current bits of interest:

* NFDI4Chem needs your insights! 
  See https://doi.org/10.1002/anie.201907260 in Angewandte Chemie (Intl. Ed.)
  and the survey https://www.soscisurvey.de/NFDI4Chem/

* European RFMF-Metabomeeting 2020
  Toulouse, France, January 22-24 2020
  https://rfmf-mpf-2020.sciencesconf.org

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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Re: [Bioc-devel] "In Bioconductor since" date wrong

[Robert M. Flight]

Can confirm this is affecting other package pages too. See this on my own
package as well. 3.8 shows 7 years, and then 3.9 and 3.10 show < 6 months.

http://bioconductor.org/packages/3.10/bioc/html/categoryCompare.html

Cheers,

-Robert

Robert M Flight, PhD
Bioinformatics Research Associate
Puller of Rabbits from Hats
Research Parasite
Resource Center for Stable Isotope Resolved Metabolomics
Manager, Systems Biology and Omics Integration Journal Club
Markey Cancer Center
CC434 Roach Building
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io
ORCID: http://orcid.org/-0001-8141-7788
EM rfligh...@gmail.com
PH 502-509-1827 <(502)%20509-1827>

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. - Ronald Fisher

On Mon, Jul 29, 2019 at 11:43 AM Neumann, Steffen 
wrote:

> Hi,
>
> The package pages seem to have lost memory
> when a package was introduced:
>
> http://bioconductor.org/packages/3.7/bioc/html/xcms.html
> http://bioconductor.org/packages/3.8/bioc/html/xcms.html
> In Bioconductor since   BioC 1.6 (R-2.1) or earlier (> 13.5 years)
>
> but now it has reset to:
>
> http://bioconductor.org/packages/3.9/bioc/html/xcms.html
> http://bioconductor.org/packages/3.10/bioc/html/xcms.html
> http://bioconductor.org/packages/devel/bioc/html/xcms.html
> In Bioconductor since   BioC 3.9 (R-3.6) (< 6 months)
>
> Not that it really matters, but in case you revisit
> how these pages are generated at some stage ...
>
> Yours,
> Steffen
>
> --
>
> Current bits of interest:
>
> * NFDI4Chem needs your insights!
>   See https://doi.org/10.1002/anie.201907260 in Angewandte Chemie (Intl.
> Ed.)
>   and the survey https://www.soscisurvey.de/NFDI4Chem/
>
> * European RFMF-Metabomeeting 2020
>   Toulouse, France, January 22-24 2020
>   https://rfmf-mpf-2020.sciencesconf.org
>
> ---
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] HiCBricks build error

[Koustav Pal]

Hi, 

My package HiCBricks is producing build errors on malbec1 and merida1, but 
build has passed on tokay1. The corresponding build on travis-ci has also 
passed. I can also confirm that the last commits on travis is the same as that 
on the bioconductor build machines. 

Herein, is the build logs from the malbec1. travis-ci vignette building also 
completes successfully. 

> * checking for file ‘HiCBricks/DESCRIPTION’ ... OK
> * preparing ‘HiCBricks’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘IntroductionToHiCBricks.rmd’ using rmarkdown
> Loading required package: curl
> Loading required package: rhdf5
> Loading required package: R6
> Loading required package: grid
> HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
>   #000: H5Dio.c line 199 in H5Dread(): can't read data
> major: Dataset
> minor: Read failed
>   #001: H5Dio.c line 601 in H5D__read(): can't read data
> major: Dataset
> minor: Read failed
>   #002: H5Dchunk.c line 2259 in H5D__chunk_read(): unable to read raw data 
> chunk
> major: Low-level I/O
> minor: Read failed
>   #003: H5Dchunk.c line 3624 in H5D__chunk_lock(): data pipeline read failed
> major: Dataset
> minor: Filter operation failed
>   #004: H5Z.c line 1301 in H5Z_pipeline(): required filter 'deflate' is not 
> registered
> major: Data filters
> minor: Read failed
>   #005: H5PLint.c line 270 in H5PL_load(): search in path table failed
> major: Plugin for dynamically loaded library
> minor: Can't get value
>   #006: H5PLpath.c line 604 in H5PL__find_plugin_in_path_table(): search in 
> path /usr/local/hdf5/lib/plugin encountered an error
> major: Plugin for dynamically loaded library
> minor: Can't get value
>   #007: H5PLpath.c line 656 in H5PL__find_plugin_in_path(): can't open 
> directory: /usr/local/hdf5/lib/plugin
> major: Plugin for dynamically loaded library
> minor: Can't open directory or file
> Quitting from lines 286-289 (IntroductionToHiCBricks.rmd) 
> Error: processing vignette 'IntroductionToHiCBricks.rmd' failed with 
> diagnostics:
> Unable to read dataset.
> Not all required filters available.
> Missing filters: deflate
> --- failed re-building ‘IntroductionToHiCBricks.rmd’
> 
> SUMMARY: processing the following file failed:
>   ‘IntroductionToHiCBricks.rmd’
> 
> Error: Vignette re-building failed.
> Execution halted 

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu




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Re: [Bioc-devel] "In Bioconductor since" date wrong

[Shepherd, Lori]

Just to verify -   The badge at the top is correct but the information in the 
details section at the bottom is showing the incorrect  "in Bioconductor since" 
time.


I will investigate how this section determines the value and make sure it is 
consistent with the badge as this information seems correct.



Cheers,



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 Neumann, 
Steffen 
Sent: Monday, July 29, 2019 11:43:02 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] "In Bioconductor since" date wrong

Hi,

The package pages seem to have lost memory
when a package was introduced:

http://bioconductor.org/packages/3.7/bioc/html/xcms.html
http://bioconductor.org/packages/3.8/bioc/html/xcms.html
In Bioconductor sinceBioC 1.6 (R-2.1) or earlier (> 13.5 years)

but now it has reset to:

http://bioconductor.org/packages/3.9/bioc/html/xcms.html
http://bioconductor.org/packages/3.10/bioc/html/xcms.html
http://bioconductor.org/packages/devel/bioc/html/xcms.html
In Bioconductor sinceBioC 3.9 (R-3.6) (< 6 months)

Not that it really matters, but in case you revisit
how these pages are generated at some stage ...

Yours,
Steffen

--

Current bits of interest:

* NFDI4Chem needs your insights!
  See https://doi.org/10.1002/anie.201907260 in Angewandte Chemie (Intl. Ed.)
  and the survey https://www.soscisurvey.de/NFDI4Chem/

* European RFMF-Metabomeeting 2020
  Toulouse, France, January 22-24 2020
  https://rfmf-mpf-2020.sciencesconf.org

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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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 
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Re: [Bioc-devel] "In Bioconductor since" date wrong

[Robert M. Flight]

Yes, the badge appears to be correct, but value in the details is incorrect.

Robert

On Mon, Jul 29, 2019, 12:13 PM Shepherd, Lori 
wrote:

> Just to verify -   The badge at the top is correct but the information in
> the details section at the bottom is showing the incorrect  "in
> Bioconductor since" time.
>
>
> I will investigate how this section determines the value and make sure it
> is consistent with the badge as this information seems correct.
>
>
>
> Cheers,
>
>
>
> 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 Neumann,
> Steffen 
> Sent: Monday, July 29, 2019 11:43:02 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] "In Bioconductor since" date wrong
>
> Hi,
>
> The package pages seem to have lost memory
> when a package was introduced:
>
> http://bioconductor.org/packages/3.7/bioc/html/xcms.html
> http://bioconductor.org/packages/3.8/bioc/html/xcms.html
> In Bioconductor sinceBioC 1.6 (R-2.1) or earlier (> 13.5 years)
>
> but now it has reset to:
>
> http://bioconductor.org/packages/3.9/bioc/html/xcms.html
> http://bioconductor.org/packages/3.10/bioc/html/xcms.html
> http://bioconductor.org/packages/devel/bioc/html/xcms.html
> In Bioconductor sinceBioC 3.9 (R-3.6) (< 6 months)
>
> Not that it really matters, but in case you revisit
> how these pages are generated at some stage ...
>
> Yours,
> Steffen
>
> --
>
> Current bits of interest:
>
> * NFDI4Chem needs your insights!
>   See https://doi.org/10.1002/anie.201907260 in Angewandte Chemie (Intl.
> Ed.)
>   and the survey https://www.soscisurvey.de/NFDI4Chem/
>
> * European RFMF-Metabomeeting 2020
>   Toulouse, France, January 22-24 2020
>   https://rfmf-mpf-2020.sciencesconf.org
>
> ---
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
>
> ___
> 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]]
>
> ___
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>

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Re: [Bioc-devel] tokay1 C++14 compiler

[Kasper Daniel Hansen]

My understanding - and I could be wrong - is that Stan compiles a model, so
the compiler needs to be available at run time and not just at build time.

On Thu, Jul 25, 2019 at 4:02 PM Simo Kitanovski 
wrote:

> Thanks!
>
> I will try to revise the code to avoid CXX14 if this is that case.
>
> Best
>
>
> On 25.07.19 11:52 nachm., Martin Morgan wrote:
> > Windows (and macOS) CRAN packages are installed as binaries (as
> experienced by the typical user), so don't need compilation-- Rstan is
> built by CRAN through whatever magic / agreement.
> >
> > The paragraph at the very end of
> >
> >
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-C_002b_002b14-code
> >
> > suggests
> >
> > Note that g++ 4.9.x (as used for R on Windows at the time of writing)
> has only partial C++14 support, and the flag to obtain that support is not
> included in the default Windows build of R
> >
> > so my understanding of this is that CXX14 is not supported on Windows.
> The options are either to revise your code to avoid CXX14 or to anticipate
> that your package will be 'Unsupported on Windows' (thereby losing 1/2 your
> user base).
> >
> > The expert on this (Hervé) will not be back for several days.
> >
> > Martin
> >
> > On 7/25/19, 6:33 PM, "Bioc-devel on behalf of Kasper Daniel Hansen" <
> bioc-devel-boun...@r-project.org on behalf of kasperdanielhan...@gmail.com>
> wrote:
> >
> >  What's weird here is that you supposedly depend on rstan which also
> >  requires a C++14. How can the build system have that package
> installed
> >  without having a compliant compiler?
> >
> >
> >  On Thu, Jul 25, 2019 at 12:05 PM Simo Kitanovski <
> simo.kitanov...@uni-due.de>
> >  wrote:
> >
> >  > Hello Bioconductor community,
> >  >
> >  > I maintain the Bioconductor package genphen which depends on
> rstan for
> >  > MCMC sampling. To build the package one needs a C++14 compiler.
> >  >
> >  > I have no problem building the package on malbec1 and merida1,
> but not
> >  > on tokay1. Any idea of what might have gone wrong on this server
> and how
> >  > to use C++14? I have submitted a new package (IgGeneUsage) which
> also
> >  > uses rstan and have the same problem (see build report below).
> >  >
> >  > BTW: why do we see this under the C++14 compiler box for tokay1:
> >  > Compiler version (' --version' output):
> >  > '--version' is not recognized as an internal or external command,
> >  > operable program or batch file.
> >  >
> >  > Any ideas?
> >  >
> >  > Best
> >  >
> >  > ===
> >  >
> >  >   R CMD BUILD
> >  >
> >  > ===
> >  > * checking for file 'IgGeneUsage/DESCRIPTION' ... OK
> >  > * preparing 'IgGeneUsage':
> >  > * checking DESCRIPTION meta-information ... OK
> >  > * cleaning src
> >  > * installing the package to build vignettes
> >  >---
> >  > * installing *source* package 'IgGeneUsage' ...
> >  > ** using staged installation
> >  > ** libs
> >  > Error in .shlib_internal(args) :
> >  >C++14 standard requested but CXX14 is not defined
> >  > * removing
> >  >
> >  >
> 'C:/Users/pkgbuild/AppData/Local/Temp/RtmpUDyHnY/Rinst315c22dc5ac/IgGeneUsage'
> >  >---
> >  > ERROR: package installation failed
> >  >
> >  > ___
> >  > Bioc-devel@r-project.org mailing list
> >  > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >  >
> >
> >
> >  --
> >  Best,
> >  Kasper
> >
> >   [[alternative HTML version deleted]]
> >
> >  ___
> >  Bioc-devel@r-project.org mailing list
> >  https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>


-- 
Best,
Kasper

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Re: [Bioc-devel] tokay1 C++14 compiler

[Simo Kitanovski]

Surprisingly, if I design the package such that the stan models are 
compiled only at run-time I get no issues -> all servers build the 
package correctly. 
(https://github.com/Bioconductor/Contributions/issues/1187)

On the other hand, if I follow the rstan instructions on how to design 
an R package that depends on rstan, based on which the stan models are 
compiled only once during the build, then I get the previously mentioned 
failure only on the windows-based server.

BTW: Recent updates from stan community suggest that the new rstan 
version 2.20 will reduce the model compilation time from ~35sec to 
~7sec, which makes the decision of sticking with the run-time 
compilation setup not so bad.

On 29.07.19 8:37 nachm., Kasper Daniel Hansen wrote:
> My understanding - and I could be wrong - is that Stan compiles a 
> model, so the compiler needs to be available at run time and not just 
> at build time.
>
> On Thu, Jul 25, 2019 at 4:02 PM Simo Kitanovski 
> mailto:simo.kitanov...@uni-due.de>> wrote:
>
> Thanks!
>
> I will try to revise the code to avoid CXX14 if this is that case.
>
> Best
>
>
> On 25.07.19 11:52 nachm., Martin Morgan wrote:
> > Windows (and macOS) CRAN packages are installed as binaries (as
> experienced by the typical user), so don't need compilation--
> Rstan is built by CRAN through whatever magic / agreement.
> >
> > The paragraph at the very end of
> >
> >
> 
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-C_002b_002b14-code
> >
> > suggests
> >
> > Note that g++ 4.9.x (as used for R on Windows at the time of
> writing) has only partial C++14 support, and the flag to obtain
> that support is not included in the default Windows build of R
> >
> > so my understanding of this is that CXX14 is not supported on
> Windows. The options are either to revise your code to avoid CXX14
> or to anticipate that your package will be 'Unsupported on
> Windows' (thereby losing 1/2 your user base).
> >
> > The expert on this (Hervé) will not be back for several days.
> >
> > Martin
> >
> > On 7/25/19, 6:33 PM, "Bioc-devel on behalf of Kasper Daniel
> Hansen"   on behalf of
> kasperdanielhan...@gmail.com
> > wrote:
> >
> >      What's weird here is that you supposedly depend on rstan
> which also
> >      requires a C++14. How can the build system have that
> package installed
> >      without having a compliant compiler?
> >
> >
> >      On Thu, Jul 25, 2019 at 12:05 PM Simo Kitanovski
> mailto:simo.kitanov...@uni-due.de>>
> >      wrote:
> >
> >      > Hello Bioconductor community,
> >      >
> >      > I maintain the Bioconductor package genphen which depends
> on rstan for
> >      > MCMC sampling. To build the package one needs a C++14
> compiler.
> >      >
> >      > I have no problem building the package on malbec1 and
> merida1, but not
> >      > on tokay1. Any idea of what might have gone wrong on this
> server and how
> >      > to use C++14? I have submitted a new package
> (IgGeneUsage) which also
> >      > uses rstan and have the same problem (see build report
> below).
> >      >
> >      > BTW: why do we see this under the C++14 compiler box for
> tokay1:
> >      > Compiler version (' --version' output):
> >      > '--version' is not recognized as an internal or external
> command,
> >      > operable program or batch file.
> >      >
> >      > Any ideas?
> >      >
> >      > Best
> >      >
> >      > ===
> >      >
> >      >   R CMD BUILD
> >      >
> >      > ===
> >      > * checking for file 'IgGeneUsage/DESCRIPTION' ... OK
> >      > * preparing 'IgGeneUsage':
> >      > * checking DESCRIPTION meta-information ... OK
> >      > * cleaning src
> >      > * installing the package to build vignettes
> >      >        ---
> >      > * installing *source* package 'IgGeneUsage' ...
> >      > ** using staged installation
> >      > ** libs
> >      > Error in .shlib_internal(args) :
> >      >    C++14 standard requested but CXX14 is not defined
> >      > * removing
> >      >
> >      >
> 
> 'C:/Users/pkgbuild/AppData/Local/Temp/RtmpUDyHnY/Rinst315c22dc5ac/IgGeneUsage'
> >      >        ---
> >      > ERROR: package installation failed
> >      >
> >      > ___
> >      > Bioc-devel@r-project.org
>  mailing list
> >      > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >      >
> >
>

Re: [Bioc-devel] HiCBricks build error

[Koustav Pal]

Hi Bioconductor team, can you please help with this issue? 


Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu



> On 29 Jul 2019, at 17:45, Koustav Pal  wrote:
> 
> Hi, 
> 
> My package HiCBricks is producing build errors on malbec1 and merida1, but 
> build has passed on tokay1. The corresponding build on travis-ci has also 
> passed. I can also confirm that the last commits on travis is the same as 
> that on the bioconductor build machines. 
> 
> Herein, is the build logs from the malbec1. travis-ci vignette building also 
> completes successfully. 
> 
>> * checking for file ‘HiCBricks/DESCRIPTION’ ... OK
>> * preparing ‘HiCBricks’:
>> * checking DESCRIPTION meta-information ... OK
>> * installing the package to build vignettes
>> * creating vignettes ... ERROR
>> --- re-building ‘IntroductionToHiCBricks.rmd’ using rmarkdown
>> Loading required package: curl
>> Loading required package: rhdf5
>> Loading required package: R6
>> Loading required package: grid
>> HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
>>  #000: H5Dio.c line 199 in H5Dread(): can't read data
>>major: Dataset
>>minor: Read failed
>>  #001: H5Dio.c line 601 in H5D__read(): can't read data
>>major: Dataset
>>minor: Read failed
>>  #002: H5Dchunk.c line 2259 in H5D__chunk_read(): unable to read raw data 
>> chunk
>>major: Low-level I/O
>>minor: Read failed
>>  #003: H5Dchunk.c line 3624 in H5D__chunk_lock(): data pipeline read failed
>>major: Dataset
>>minor: Filter operation failed
>>  #004: H5Z.c line 1301 in H5Z_pipeline(): required filter 'deflate' is not 
>> registered
>>major: Data filters
>>minor: Read failed
>>  #005: H5PLint.c line 270 in H5PL_load(): search in path table failed
>>major: Plugin for dynamically loaded library
>>minor: Can't get value
>>  #006: H5PLpath.c line 604 in H5PL__find_plugin_in_path_table(): search in 
>> path /usr/local/hdf5/lib/plugin encountered an error
>>major: Plugin for dynamically loaded library
>>minor: Can't get value
>>  #007: H5PLpath.c line 656 in H5PL__find_plugin_in_path(): can't open 
>> directory: /usr/local/hdf5/lib/plugin
>>major: Plugin for dynamically loaded library
>>minor: Can't open directory or file
>> Quitting from lines 286-289 (IntroductionToHiCBricks.rmd) 
>> Error: processing vignette 'IntroductionToHiCBricks.rmd' failed with 
>> diagnostics:
>> Unable to read dataset.
>> Not all required filters available.
>> Missing filters: deflate
>> --- failed re-building ‘IntroductionToHiCBricks.rmd’
>> 
>> SUMMARY: processing the following file failed:
>>  ‘IntroductionToHiCBricks.rmd’
>> 
>> Error: Vignette re-building failed.
>> Execution halted 
> 
> Koustav Pal, PhD
> Post-Doctoral Fellow in Genome Architecture,
> Computational Genomics Group,
> IFOM - The FIRC Institute of Molecular Oncology,
> Via Adamello 16,
> 20139 Milano, Italy.
> Phone: +393441130157
> E-mail: koustav@ifom.eu
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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[Bioc-devel] Using my own genome for CAGER

[Jaehyun Lee]

Hello,

My name is Jaehyun Lee, an undergraduate student at Carnegie Mellon
University conducting developmental biology research. I am currently trying
to run CAGEr using bam files from the CAGE experiment and from my own
reference genome. However, the specific genome that I need is not available
in BSgenome. Is there a way of using CAGEr without using a genome from
BSgenome or is there a way to upload my genome to BSgenome?

Thank you,

Jae
Jaehyun Lee
Candidate for Bachelor of Science in Biological Sciences
Carnegie Mellon University, Class of 2020
jaehy...@andrew.cmu.edu I 508.523.0203

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Re: [Bioc-devel] Using my own genome for CAGER

[James W. MacDonald]

This list is intended for questions about package development. The correct
forum for usage questions is at support.bioconductor.org. Please repost
your question over there.

Best,

Jim



On Mon, Jul 29, 2019 at 4:32 PM Jaehyun Lee  wrote:

> Hello,
>
> My name is Jaehyun Lee, an undergraduate student at Carnegie Mellon
> University conducting developmental biology research. I am currently trying
> to run CAGEr using bam files from the CAGE experiment and from my own
> reference genome. However, the specific genome that I need is not available
> in BSgenome. Is there a way of using CAGEr without using a genome from
> BSgenome or is there a way to upload my genome to BSgenome?
>
> Thank you,
>
> Jae
> Jaehyun Lee
> Candidate for Bachelor of Science in Biological Sciences
> Carnegie Mellon University, Class of 2020
> jaehy...@andrew.cmu.edu I 508.523.0203
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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Re: [Bioc-devel] Software package dependency >=5Mb in size

[Martin Morgan]

This conversation has moved to the community-bioc slack, where the 
recommendation is to use BiocFileCache to manage the download. Martin

On 7/29/19, 10:42 AM, "Bioc-devel on behalf of Shraddha Pai" 
 
wrote:

Hi,
Our software package relies on a Java jar file that is 11Mb in size and
there is a good chance we cannot make the file size smaller. The jar file
is used to run our algorithm so none of the vignettes can run without it
and a separate download would be tedious for users.

Is there still a way to submit our package to BioC? It would be great to
increase community adoption of our package via the BioC system.

Thanks,Shraddha

-- 
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter

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