Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

[Levi Waldron]

Nice example of a reproducible bug report and rapid bug-fix!

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Re: [Bioc-devel] Important Bioconductor Release Deadlines

[Levi Waldron]

Anatoly, delaying dependency on R 4.4 until October would mean 6 months of 
Bioconductor release requiring an old release of R for users. Bioconductor 
developers developing against r-devel means that users get a new Bioconductor 
release that works immediately on the new R. And I think a main purpose of a 6 
month devel and release cycle is to provide a comfortable period for everyone 
to work out new features and bugs and to resolve downstream consequences that 
may arise.  Delaying the Bioconductor release by a week or something might 
actually encourage a habit of last-week bug fixes that should be discouraged . 
I really can’t see any way around requiring developers to test against r-devel 
without sacrificing timeliness and reliability for users. There are also Docker 
and GitHub Actions options that don’t require installing r-devel to test 
against it.

I think many HPC clusters now support Singularity, which is a more reliable and 
easier way to run packages with a compatible version of R. Installing from 
GitHub on an old version of R has no guarantees of being tested or working 
correctly even if it installs without error, and I see as a sacrifice of 
software reliability for convenience that can be avoided with Singularity or 
regular R updates.

Henrik, if Bioconductor releases weren’t tied to R releases, how could 
Bioconductor test them? I guess like CRAN where as long as a package says it 
depends on R >= 2.0 then you’re free to try installing on 2.0 even though the 
combination has never been tested? Maybe I worry too much about such testing 
since CRAN seems OK anyways, as far as we know?

From: Bioc-devel  on behalf of Anatoly 
Sorokin 
Sent: Thursday, April 4, 2024 10:28:47 PM
To: Kern, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Important Bioconductor Release Deadlines

Hi all,

I'm sorry for the complaint, but do you really think it is wise to make the
new release dependent on the R version which has not released yet?

I have a lot of R-related projects going on apart from maintaining the
Bioconductor package and I'm not comfortable installing the unreleased
version of R on my machine and spending time debugging it in the case of
possible problems.

At the same time, I have an error, possibly caused by a new version of
GO.db package, which BioNAR is dependent upon and I can not fix it
until the R 4.4 release on the 24th of April when I would have less than a
day to fix the possible problem and fit into R CMD build and R CMD check by
the Friday April 26th. Don't you think this is a rather tight time frame?


Sorry once again, for the complaint.

Cheers,
Anatoly

On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:

> Import update:  The Bioconductor Release will be May 1 following the
> release of R 4.4 on April 24.
>
> The Bioconductor 3.18 branch will be frozen Monday April 15th. After that
> date, no changes will be permitted ever on that branch.
>
> The deadline for devel Bioconductor 3.19 for packages to pass R CMD build
> and R CMD check is Friday April 26th. While you will still be able to make
> commits past this date, This ensures any changes pushed to
> git.bioconductor.org are reflected in at least one build report before
> the devel branch will be copied to a release 3.19 branch.
>
> Cheers,
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> 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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>
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Re: [Bioc-devel] benchdamic TIMEOUT in merida1 and kunpeng2

[Levi Waldron]

It looks to me like benchdamic doesn't actually use the HMP16SData package,
but a repackaged example dataset placed in the data/ directory. I do notice
that the vignette takes very long to run, especially the chunks below. My
guess is that you are seeing differences in speed or number of available
cores on the build machines, one of which can't build the vignette within
the 10-minute time limit (e.g. it takes more than 10 minutes to build on my
laptop). Can you reduce the number of rows or columns in your example
dataset, or reduce permutations, to speed up the computation while still
demonstrating how the package should be used?

```{r runMocks}
bpparam <- BiocParallel::SerialParam()
# Random grouping each time
Stool_16S_mockDA <- runMocks(
mocks = my_mocks,
method_list = my_methods,
object = ps_stool_16S,
weights = zinbweights,
verbose = FALSE,
BPPARAM = bpparam)
```

```{r runSplits}
# Set the parallel framework
# Remember that ANCOMBC based methods are compatible only with SerialParam()
bpparam <- BiocParallel::SerialParam()

# Make sure the subject ID variable is a factor
phyloseq::sample_data(ps_plaque_16S)[, "RSID"] <- as.factor(
phyloseq::sample_data(ps_plaque_16S)[["RSID"]])

Plaque_16S_splitsDA <- runSplits(
split_list = my_splits,
method_list = my_methods_noWeights,
normalization_list = my_normalizations,
object = ps_plaque_16S,
min_counts = 0, min_samples = 2,
verbose = TRUE,
BPPARAM = bpparam)
```

(returns lots of "Warning: Computed variance-covariance matrix problem: not
a positive definite matrix (and positive semidefiniteness is not
checked); returning
NA matrixboundary (singular) fit: see help('isSingular')" warnings)


-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

Book a meeting with me
<https://outlook.office365.com/owa/calendar/leviwald...@cuny907.onmicrosoft.com/bookings/>

Join the microbiome Virtual International Forum: https://microbiome-vif.org

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[Bioc-devel] converting old Rnw vignettes to Rmd + BiocStyle

[Levi Waldron]

Bioconductor has many (>800) Rnw PDF vignettes that would be more
user-friendly if converted to using Rmd+BiocStyle. I've identified a couple
students who are willing to work on this, and have started a Trello board
to organize the work:
https://trello.com/b/nJHqzR1j/bioconductor-vignettes-rnw-rmd-project. I
have a couple questions for bioc-devel:

1. I've only started moving vignettes from pre-triage to "core team
maintained", "community-contributed low priority" (less downloaded
packages), and "community-contributed high priority" (highly downloaded
packages). Please use comments on Trello to note any packages you'd like to
see added to the lower or high-priority list, including your own. If you
want to do a bunch of triage, I can add you to the Trello board. Before
starting work on any community-contributed package, we will contact the
maintainer to confirm whether they will accept a pull request that updates
their vignette.
2. Anyone have experience with the many Rnw -> Rmd converters that a Google
search turns up? I see Mike Love and Laurent Gatto are responsible for one
of them (https://gist.github.com/lgatto/d9d0e3afcc0a4417e5084e5ca46a4d9e),
would you still recommend it? I expect there to be some manual cleanup in
addition to adding BiocStyle markup, but the less the better.
3. If you or anyone you know wants to help out, let me know, I'll be
organizing a little group to work on this together.

-Levi

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

Join the microbiome Virtual International Forum: https://microbiome-vif.org

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[Bioc-devel] Developing requirements for API + web-based *Hubs

[Levi Waldron]

Anyone interested in helping formulate requirements for an API + web-based
(Experiment/Annotation)Hub submission system, we're setting a time to meet
next week at
https://doodle.com/poll/uu5ikxqun78twzzr?utm_source=poll_medium=link.


-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

Join the *Microbiome Virtual International Forum*:
https://microbiome-vif.org

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Re: [Bioc-devel] BioC2022 Seattle July 27-29 hybrid conference organizing committee

[Levi Waldron]

Correction, I'd like to invite any interested members of the **community**
to get involved! Feel free to get in touch with me with any questions. This
is a great way to get to know other passionate Bioconductor users and
developers while providing a great service to the community.

On Thu, Dec 16, 2021 at 1:53 PM Levi Waldron 
wrote:

> I'd like to invite any interested members of the committee to get involved
> in organizing BioC2022, planned to be in a hybrid format in Seattle
> July 27-29, 2022. There is lots to be done, including sponsorship and
> funding, outreach, website, workshop technical organization, program
> development, code of conduct communication and enforcement, and local
> organization.  Please fill out this form if you'd like to get involved:
> https://forms.gle/cbjHww7uHJFRzwVx5
>
>

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[Bioc-devel] BioC2022 Seattle July 27-29 hybrid conference organizing committee

[Levi Waldron]

I'd like to invite any interested members of the committee to get involved
in organizing BioC2022, planned to be in a hybrid format in Seattle
July 27-29, 2022. There is lots to be done, including sponsorship and
funding, outreach, website, workshop technical organization, program
development, code of conduct communication and enforcement, and local
organization.  Please fill out this form if you'd like to get involved:
https://forms.gle/cbjHww7uHJFRzwVx5

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[Bioc-devel] NCBI taxonomy annotation

[Levi Waldron]

Does anyone else do mapping between NCBI taxids, names, and ranks? We do
this in curatedMetagenomicData and soon other packages, currently using
external files that lack provenance and versioning, so Ludwig Geistlinger
was looking for Bioconductor annotation resources. The closest he found was
in GenomeInfoDbData <https://bioconductor.org/packages/GenomeInfoDbData> but
this has only genus and species, and some quirks like Bacteria being listed
as a genus:

> library(GenomeInfoDbData)
> data(specData)
> head(specData)
  tax_idgenus species
1  1  all
2  1 root
3  2 Bacteria
4  6 Azorhizobium
5  7 Azorhizobium caulinodans
6  9 Buchnera  aphidicola
> dim(specData)
[1] 2521271   3
> subset(specData, c(genus == "Escherichia" & species == "coli"))$tax_id
[1] 562

Any thoughts from the GenomeInfoDbData maintainer ("Bioconductor Maintainer
") about a pull request either to a) update
specData to add additional columns for all taxonomic levels, or b) creating
a new object? Or, another approach altogether? See
https://github.com/waldronlab/curatedMetagenomicData/issues/245.

--

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

Join the microbiome Virtual International Forum: https://microbiome-vif.org

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Re: [Bioc-devel] BioC2021 abstract/syllabus submissions

[Levi Waldron]

This deadline is extended by one week, until March 16. Submit a talk,
digital poster, Birds-of-a-feather session, or a syllabus for a software
demo or long workshop at BioC2021 on Aug 4-6! We can confirm that the
conference will be virtual. https://bioc2021.bioconductor.org/submissions/.

On Thu, Feb 18, 2021 at 4:52 PM Levi Waldron 
wrote:

> Submit an abstract for a talk, digital poster, or Birds-of-a-feather
> session, or a syllabus for a software demo or long workshop at BioC2021 on
> Aug 4-6! The conference will most likely again be virtual this year.
> https://bioc2021.bioconductor.org/submissions/
>
> --
>
> Levi Waldron
>
> Associate Professor
>
> Department of Epidemiology and Biostatistics
>
> CUNY Graduate School of Public Health and Health Policy
>
> Institute for Implementation Science in Population Health
>
> 55 W 125th St, New York NY 10035
>
> https://waldronlab.io
>


-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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[Bioc-devel] BioC2021 abstract/syllabus submissions

[Levi Waldron]

Submit an abstract for a talk, digital poster, or Birds-of-a-feather
session, or a syllabus for a software demo or long workshop at BioC2021 on
Aug 4-6! The conference will most likely again be virtual this year.
https://bioc2021.bioconductor.org/submissions/

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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Re: [Bioc-devel] Recent change in MultiAssayExperiment for inferred MAE-level colData

[Levi Waldron]

Hi Dario and Andrea, I don't think you'll have to do anything - it was
meant to be a feature that shouldn't have affected your use cases
of not specifying the sampleMap.  I've opened an issue at
https://github.com/waldronlab/MultiAssayExperiment/issues/291.

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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[Bioc-devel] BioC2021 organizing committee

[Levi Waldron]

I want to welcome all the new Bioconductor 3.12 contributors, and invite
new and existing contributors to take part in organizing the BioC2021
conference. It will be a hybrid conference online and, pandemic permitting,
in Seattle next August 4-6. The conference organizing committee meets
monthly until next spring, when the frequency of meetings increases with
the approaching conference. If you're interested in getting more involved
with the project and in expanding your Bioconductor network, it is a good
way to contribute.  There is work to be done on sponsorship, communication,
program development, technical development of various platforms, Code of
Conduct enforcement, and local organizing in Seattle. If you are interested
in getting involved, fill out this short survey with your contact
information and interests: https://forms.gle/Hb6WYxBzUJfqkq2D6

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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Re: [Bioc-devel] Request package deprecation

[Levi Waldron]

Gives me some nostalgia because I think simpleaffy was the first
Bioconductor package I used!

Il gio 27 ago 2020, 1:46 PM Shepherd, Lori 
ha scritto:

> Thank you for letting us know.  I will begin the deprecation process for
> the package. Thank you for your contributions.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of Crispin
> Miller 
> Sent: Thursday, August 27, 2020 5:27 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Request package deprecation
>
> Hi there,
> I’ve moved email address since creation of this package but I would like
> to request deprecation and End of Life for the package: simpleaffy
> It’s been superseded and is out of date.
> Best wishes,
> Crispin Miller
>
>
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>
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Re: [Bioc-devel] bioconductor_docker updates

[Levi Waldron]

Thanks Nitesh! Very much appreciated. I was wondering, is there a way to
inspect the version from _within_ the image, i.e., that could supplement a
sessionInfo() command?

On Mon, Aug 3, 2020 at 6:30 PM Turaga, Nitesh 
wrote:

> Hello Bioconductor Community,
>
> A quick update about the latest developments on the Bioconductor Docker
> images.
>
> We have updated the ‘devel’ image to inherit from the latest
> ‘rocker/rstudio:4.0.2’ image. This means that the
> `bioconductor/Bioconductor_docker:devel` image, which is now available will
> be running on,
>
>
>   1.  Ubuntu 20.04
>   2.  R version 4.0.2
>   3.  Bioconductor version 3.12.
>
> One major update to the system requirements was the installation of the
> ‘libglpk-dev’ which seemed to have caused issues installing the ‘igraph’
> package. The version number of this image which can be queried through the
> docker command is going to be 3.12.13.
>
> If you pull the updates from dockerhub using,
>
>   docker pull bioconductor/Bioconductor_docker:devel
>
> And check the version number using, (the result is going to be 3.12.13.
>
>docker inspect --format '{{ index .Config.Labels.version}}'
> bioconductor/bioconductor_docker:devel
>
>
> NOTE: The release image stayed exactly the same but with the addition of
> the `libglpk-dev` package. The RELEASE_3_11 image did not get updated to
> Ubuntu 20.04. It is still based on Ubuntu 18.04. The devel image now works
> on a different version of Ubuntu (20.04) as compared to the build system
> (18.04. The support for the 18.04 image on rocker is no longer available.
>
> The inspect label command for  RELEASE_3_11 (given below) should produce
> the new version number 3.11.11. Do not forget to pull. This is a bug fix
> with regards to the igraph package’s missing dependency.
>
> docker inspect --format '{{ index .Config.Labels.version}}'
> bioconductor/bioconductor_docker:RELEASE_3_11
>
>
> If you have any further questions, please reply to this thread.
>
> Best regards,
>
> Nitesh Turaga
> Bioconductor Core Team
>
>
> 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
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-- 

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Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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[Bioc-devel] Fwd: [cbioportal] Installation cBioPortalData error

[Levi Waldron]

FYI, rtracklayer not installing on OSX (
http://bioconductor.org/checkResults/release/bioc-LATEST/rtracklayer/) may
be causing issues like the one below. (I've recommended to this user to
install the binary for the time being)

-- Forwarded message -
From: de Leeuw, Renee 
Date: Mon, Jun 1, 2020 at 8:02 PM
Subject: Re: [cbioportal] Installation cBioPortalData error
To: mohammed imran Khan , Levi Waldron <
lwaldron.resea...@gmail.com>
Cc: JJ Gao , Marcel Ramos ,
cbiopor...@googlegroups.com 


Hi,

Thank you for your quick responses. Unfortunately this did not resolve my
issue, I still got the same error.

This is the output re: Bioconductor and R versions:

> BiocManager::version()
[1] ‘3.11’
> BiocManager::valid()
[1] TRUE
> BiocManager::install()
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)

As for the error and session info, see here:

Error: package or namespace load failed for ‘cBioPortalData’ in
loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]]):
 there is no package called ‘rtracklayer’
>
>
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
 methods   base

other attached packages:
 [1] MultiAssayExperiment_1.14.0 SummarizedExperiment_1.18.1
DelayedArray_0.14.0 matrixStats_0.56.0  Biobase_2.48.0
 GenomicRanges_1.40.0
 [7] GenomeInfoDb_1.24.0 IRanges_2.22.2
 S4Vectors_0.26.1BiocGenerics_0.34.0 AnVIL_1.0.3
  dplyr_1.0.0

loaded via a namespace (and not attached):
 [1] httr_1.4.1bit64_0.9-7   jsonlite_1.6.1
   splines_4.0.0 assertthat_0.2.1  askpass_1.1

 [7] BiocManager_1.30.10   BiocFileCache_1.12.0  blob_1.2.1
   GenomeInfoDbData_1.2.3RTCGAToolbox_2.18.0   progress_1.2.2

[13] yaml_2.2.1pillar_1.4.4  RSQLite_2.2.0
lattice_0.20-41   glue_1.4.1limma_3.44.1

[19] digest_0.6.25 XVector_0.28.0swirl_2.4.5
Matrix_1.2-18 XML_3.99-0.3  pkgconfig_2.0.3

[25] biomaRt_2.44.0zlibbioc_1.34.0   purrr_0.3.4
RCircos_1.2.1 rapiclient_0.1.3  openssl_1.4.1

[31] tibble_3.0.1  generics_0.0.2ellipsis_0.3.1
   survival_3.1-12   RJSONIO_1.3-1.4   magrittr_1.5

[37] crayon_1.3.4  memoise_1.1.0 xml2_1.3.2
   prettyunits_1.1.1 tools_4.0.0
data.table_1.12.8
[43] hms_0.5.3 formatR_1.7   lifecycle_0.2.0
stringr_1.4.0 Biostrings_2.56.0
AnnotationDbi_1.50.0
[49] lambda.r_1.2.4compiler_4.0.0rlang_0.4.6
futile.logger_1.4.3   grid_4.0.0
 GenomicDataCommons_1.12.0
[55] RCurl_1.98-1.2rstudioapi_0.11   rappdirs_0.3.1
   bitops_1.0-6  testthat_2.3.2DBI_1.1.0

[61] curl_4.3  R6_2.4.1  bit_1.1-15.2
   futile.options_1.0.1  readr_1.3.1   stringi_1.4.6

[67] RaggedExperiment_1.12.0   Rcpp_1.0.4.6  vctrs_0.3.0
dbplyr_1.4.4  tidyselect_1.1.0


Hope this helps and thanks for helping me troubleshoot!

Renée
--
*From:* mohammed imran Khan 
*Sent:* Sunday, May 31, 2020 8:37 PM
*To:* Levi Waldron 
*Cc:* JJ Gao ; Marcel Ramos ;
cbiopor...@googlegroups.com ; de Leeuw, Renee <
rdele...@uic.edu>
*Subject:* Re: [cbioportal] Installation cBioPortalData error

Please install the missing package using this script hopefully it will
resolve your problem.

install.packages("rtracklayer")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

if (!requireNamespace("cBioPortalData", quietly = TRUE))
BiocManager::install("cBioPortalData")

library(cBioPortalData)

if you still have a problem run this script to see if you have required
packages to work in R session.

sessionInfo()


Best regards--
*Mohammed Imran **Khan*, PhD
*imrankhanbioi...@gmail.com *
*mkhan...@uwo.ca *
*Postdoctoral Associate (PDA)*
*Department of Otolaryngology-Head & Neck Surgery,*
*Western University, London, ON, Canada*
*https://www.researchgate.net/profile/Mohammed_Khan41
<https://www.researchgate.net/profile/Mohammed_Khan41>*
https://scholar.google.com/citations?hl=en=K3hnREYJ


On Sun, May 31, 2020 at 9:1

Re: [Bioc-devel] How to add an experiment to an empty MultiAssayExperiment file ?

[Levi Waldron]

Thanks for the question and report Charles. I've expanded on the issue at
https://github.com/waldronlab/MultiAssayExperiment/issues/274.

On Fri, Apr 17, 2020 at 5:08 AM Charles Plessy 
wrote:

> Dear all,
>
> in the CAGEr pakcage, our main class, CAGEexp is a wrapper on the
> MultiAssayExperiment class.  In a typical workflow, we first create a
> MultiAssayExperiment object with no experiment in, and then add the
> experiments one by one as the analysis proceeds.
>
> As the checks in MultiAssayExperiment get tighter and tighter, I am
> struggling to find the appropriate way to add experiments.  Therefore,
> the package is in a painful cycle of fixes followed by build failures
> each time MultiAssayExperiment gets stricter.
>
> To solve this once for all, my questions are:
>
> 1) I have a MultiAssayExperiment object with no experiments in, and a
> SummarizedExperiment object that I want to add as experiment.  I also
> made sure that `rownames(colData(object)) == colnames(value)`.  How
> can I add this SummarizedExperiment to the MultiAssayExperiemnt? I have
> tried `object[["myExp"]] <- value` and `object <- c(object, myExp=value)`
> but both of them fail.
>
> 2) If I want to update an experiment (for instance because I added a
> new assay in a SummarizedExperiment, on which I applied a normalisation
> method), what is the most appropriate way ?
>
> Have a nice day,
>
> Charles
>
> --
> Charles Plessy
> Akano, Uruma, Okinawa, Japan
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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[Bioc-devel] BioC2019 Code of Conduct violation response

[Levi Waldron]

Dear developers, for your information, the Bioconductor Code of Conduct
committee's response to a violation reported at BioC2019 has been posted at
https://bioc2019.bioconductor.org/code_of_conduct.

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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Re: [Bioc-devel] Bioc2020 - Deadline for workshops/talk/poster TOMORROW

[Levi Waldron]

Let's say 11:59 pm in the time zone of your choice :) In practice, the
Google Forms will get closed to further submissions sometime on March 4
when it is no longer March 3 anywhere.

On Mon, Mar 2, 2020 at 2:58 PM Simina Boca  wrote:

> Is the deadline 11:59 pm tomorrow or another time?
>
> Thanks!
> Cheers,
> Simina
>
> On Mon, Mar 2, 2020, 8:08 AM Shepherd, Lori  >
> wrote:
>
> > Reminder: TOMORROW March 3rd is the last day to submit proposals for
> > Bioc2020 workshops/talks/posters!
> > http://bioc2020.bioconductor.org/call-for-abstracts
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > 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
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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Re: [Bioc-devel] Use of SummerisedExperiments or MultiAssayExperiments of many many Dataframes/ nested List objects

[Levi Waldron]

Krutik, what's the link to your package submission issue on GitHub? I feel
I would need a little more information on the package to give my opinion or
advice. It is true that SummarizedExperiment and MultiAssayExperiment are
designed primarily for experimental data rather than for differential
expression output.  But my first impression is that it will be important
for you to directly support output from DESeq2, edgeR, and limma, since
those are where most Bioconductor users get differential expression output
from.

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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[Bioc-devel] BioC2020 - mark your calendars!

[Levi Waldron]

BioC2020 will be held Wed July 29 - Fri July 31 in Boston, at Simmons
University and Harvard Medical School. The website is up at
https://bioc2020.bioconductor.org and will be undergoing frequent updates.
Stay tuned for the announcement of invited speakers, registration and
accommodations, calls for talk/poster abstracts, workshop proposals, and
scholarship applications. There is a #bioc2020 channel on the community-bioc
Slack team <https://bioc-community.herokuapp.com/> where you can discuss or
ask questions. Announcements will also be made by the @Bioconductor
organization on Twitter <https://twitter.com/bioconductor> using the
#bioc2020 hashtag. Some key dates:
Mark the date!
Jan 9 Registration Opens
Jan 15 Call for abstracts/applications for talks, early posters,
scholarships, workshops
March 3 Deadline for proposals for talks, workshops, early posters, and
travel scholarships
March 24 Notification of decision
July 1 Deadline for late posters and for Birds of a Feather meetings
July 10 Notification of decision for late posters
July 10 Last day of early registration (2x fees)
July 29-31 BioC2020 Meeting, Boston

-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

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Re: [Bioc-devel] Bioconductor 3.10 is released!!

[Levi Waldron]

Indeed, it's amazing. Thank you, Lori and core team.

Il gio 31 ott 2019, 1:11 PM Sean Davis  ha scritto:

> Huge kudos to the team for another successful release.
>
> Sean
>
> On Wed, Oct 30, 2019 at 4:54 PM Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
> > Thanks to all developers and community members for contributing to the
> > project!
> >
> > Please see the full release announcement:
> >
> >https://www.bioconductor.org/news/bioc_3_10_release/
> >
> > The Bioconductor Team
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > 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
> >
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>
> [[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] Bioc2019 NYC registration nearly full

[Levi Waldron]

Bioc2019 NYC registration has been very strong and we will likely have to
close registration soon. If you are planning to present, have made travel
plans, or otherwise have your heart set on it but haven't registered, I
highly recommend doing so in the next couple days. Early registration ends
May 24 but may even be closed before then.

http://bioc2019.bioconductor.org/registration

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Re: [Bioc-devel] package named spdeq causes error

[Levi Waldron]

Looking further up the list of error messages, there is a long dependency
chain ending with a missing system dependency (see below):
   * anamiR -> agricolae -> spdep -> sf -> system dependency libgdal-dev

You should be able to fix it with `apt install libgdal-dev` if you're on
Debian/Ubuntu. BTW, I figured this out on a Docker+Singularity container
and scripts I've been working on to try to make almost all of Bioconductor
installable, to make it easier to run release+devel side by side, and to
smooth the edges for people who don't feel like learning the million flags
Docker has or where their package and home directories go every time they
restart :). I'll add libgal-dev. It's early but see
https://github.com/waldronlab/bioconductor_devel if you want to try, and I
really welcome feedback on documentation or functionality.

Dependency error chain:

* installing *source* package ‘sf’ ...

** package ‘sf’ successfully unpacked and MD5 sums checked

configure: CC: gcc

configure: CXX: g++ -std=gnu++11

*checking for gdal-config... no*

*no*

*configure: error: gdal-config not found or not executable.*

*ERROR: configuration failed for package ‘sf’*

* removing ‘/usr/local/lib/R/host-site-library/sf’

* installing *source* package ‘minfi’ ...

** R

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (minfi)

* installing *source* package ‘klaR’ ...

** package ‘klaR’ successfully unpacked and MD5 sums checked

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

* DONE (klaR)

*ERROR: dependency ‘sf’ is not available for package ‘spdep’*

** removing ‘/usr/local/lib/R/host-site-library/spdep’*

* installing *source* package ‘methylumi’ ...

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (methylumi)

*ERROR: dependency ‘spdep’ is not available for package ‘agricolae’*

* removing ‘/usr/local/lib/R/host-site-library/agricolae’

* installing *source* package ‘lumi’ ...

** R

** data

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (lumi)

ERROR: dependency ‘agricolae’ is not available for package ‘anamiR’

* removing ‘/usr/local/lib/R/host-site-library/anamiR’


The downloaded source packages are in

‘/tmp/RtmpOjPTFv/downloaded_packages’

Warning messages:

1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘sf’ had non-zero exit status

2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘spdep’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘agricolae’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :

  installation of package ‘anamiR’ had non-zero exit status

> *


On Thu, Feb 21, 2019 at 11:00 PM Dario Strbenac 
wrote:

> Good day,
>
> I don't, but your software package imports agricolae which imports spdep.
> spdep is available from CRAN, so it's strange that the Bioconductor build
> server running Linux has not been able to install it.
>
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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[Bioc-devel] BioC2019 talk/workshop/scholarship submission deadline MARCH 15

[Levi Waldron]

The deadline to submit a syllabus proposing a workshop, an abstract for a
talk or poster, or a travel scholarship application to BioC2019 in New York
City is fast approaching on March 15. Will be again producing a workshop
booklet from accepted workshops (see the BioC2018 workshop booklet
<https://bioconductor.github.io/BiocWorkshops/> for example).
https://bioc2019.bioconductor.org/call-for-abstracts

Registration <https://bioc2019.bioconductor.org/registration> is open, and
we've identified nearby hotels to recommend at a range of affordable prices
(see travel and accommodations
<https://bioc2019.bioconductor.org/travel-accommodations>). This year is
also associated with an added one-day symposium in honor of Robert
Gentleman's 60th birthday
<https://bioc2019.bioconductor.org/schedule-gentleman-day>, providing a
chance to meet and hear from founders of R and Bioconductor.
Apologies for cross-posting (https://support.bioconductor.org/p/118159/)
but I want to make sure no one misses this deadline accidentally.

-- 
Levi Waldron
https://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health

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Re: [Bioc-devel] return value of BiocManager::install()

[Levi Waldron]

BTW I just noticed the alternative approach of searching through the
warnings, used at
https://github.com/Bioconductor/bioc_docker/blob/5be6d37ded4f97995640cbb3a7d201165234b1e4/src/core/install.R.in#L42
:

if (!is.null(warnings()))
{
w <- capture.output(warnings())
if (length(grep("is not available|had non-zero exit status", w)))
quit("no", 1L)
}


On Tue, Jan 22, 2019 at 10:19 AM Levi Waldron 
wrote:

> I opened an issue on BiocManager (
> https://github.com/Bioconductor/BiocManager/issues/39) somewhat related
> to Sean's recent post, about what BiocManager::install() should return, and
> it occurs to me that I should mention it here too for feedback:
>
> > Having `BiocManager::install()` return the "pkgs" argument is not
> especially useful. Could it instead return success/error codes? Otherwise,
> how can you tell in a script whether the requested packages were installed
> successfully or not?
>
> The most basic return value I can think of would be like `require()`, TRUE
> if successful and FALSE if unsuccessful. More sophisticated behavior could
> give different error codes for different failures, although I don't know
> how difficult that would be to implement. This came up from wanting to test
> a Docker container for ability to install many different packages within
> it, and doing this by making a (hacked and specific to my purpose of
> installing/testing one package at a time) wrapper around
> `BiocManager::install()` that uses require() to test whether the
> installation was successful. That said, the workaround was not that
> difficult and it's probably not a priority for too many other users if
> you're hesitant to change the return value of BiocManager::install().
>
> installcheck <- function(x){
>   if (x %in% installed.packages())
> return(TRUE)
>   BiocManager::install(x, ask=FALSE, update=FALSE)
>   res <- require(x, character.only = TRUE)
>   detach(paste0("package:", x), unload=TRUE, character.only = TRUE)
>   return(res)
> }
>
>
>

-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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[Bioc-devel] return value of BiocManager::install()

[Levi Waldron]

I opened an issue on BiocManager (
https://github.com/Bioconductor/BiocManager/issues/39) somewhat related to
Sean's recent post, about what BiocManager::install() should return, and it
occurs to me that I should mention it here too for feedback:

> Having `BiocManager::install()` return the "pkgs" argument is not
especially useful. Could it instead return success/error codes? Otherwise,
how can you tell in a script whether the requested packages were installed
successfully or not?

The most basic return value I can think of would be like `require()`, TRUE
if successful and FALSE if unsuccessful. More sophisticated behavior could
give different error codes for different failures, although I don't know
how difficult that would be to implement. This came up from wanting to test
a Docker container for ability to install many different packages within
it, and doing this by making a (hacked and specific to my purpose of
installing/testing one package at a time) wrapper around
`BiocManager::install()` that uses require() to test whether the
installation was successful. That said, the workaround was not that
difficult and it's probably not a priority for too many other users if
you're hesitant to change the return value of BiocManager::install().

installcheck <- function(x){
  if (x %in% installed.packages())
return(TRUE)
  BiocManager::install(x, ask=FALSE, update=FALSE)
  res <- require(x, character.only = TRUE)
  detach(paste0("package:", x), unload=TRUE, character.only = TRUE)
  return(res)
}

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Re: [Bioc-devel] No curatedMetagenomicData build triggered

[Levi Waldron]

Thanks Val. Indeed, the release version built yesterday, but there still
hasn't been a build on devel since Thursday.

On Sat, Nov 3, 2018 at 10:12 PM Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Levi,
>
> We've had one experimental data build since the release, posted on Nov
> 1. Data experiment packages build on Tues, Thurs and Sun. Release should
> continue to follow this schedule.
>
> The devel builds are taking a very long time to complete and overlapping
> each other which means less dependable builds. Please see this post:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014281.html
>
> Valerie
>
> On 11/3/18 7:08 AM, Levi Waldron wrote:
> > I remember now (I think) that experimental data packages are built on
> > Wednesday and *Saturday* nights - in which case I’ll just check again
> > tomorrow morning.
> >
> > On Sat, Nov 3, 2018 at 8:59 AM Levi Waldron  >
> > wrote:
> >
> >> curatedMetagenomicData hasn't built yet on the new release or devel. I
> >> believe this was originally because the required ExperimentHub database
> >> update occurred after the last curatedMetagenomicData version bump, but
> >> since I bumped the version on Thursday it still hasn't built. Can you
> >> advise?
> >>
>
>
>
> 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.
>


-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] No curatedMetagenomicData build triggered

[Levi Waldron]

I remember now (I think) that experimental data packages are built on
Wednesday and *Saturday* nights - in which case I’ll just check again
tomorrow morning.

On Sat, Nov 3, 2018 at 8:59 AM Levi Waldron 
wrote:

> curatedMetagenomicData hasn't built yet on the new release or devel. I
> believe this was originally because the required ExperimentHub database
> update occurred after the last curatedMetagenomicData version bump, but
> since I bumped the version on Thursday it still hasn't built. Can you
> advise?
>
-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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[Bioc-devel] No curatedMetagenomicData build triggered

[Levi Waldron]

curatedMetagenomicData hasn't built yet on the new release or devel. I
believe this was originally because the required ExperimentHub database
update occurred after the last curatedMetagenomicData version bump, but
since I bumped the version on Thursday it still hasn't built. Can you
advise?

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[Bioc-devel] BioC2019 June 24-27 in New York City

[Levi Waldron]

Mark your calendars for the BioC2019 Bioconductor annual conference in
Manhattan, New York City (Twitter: #BioC2019
<https://twitter.com/search?q=%23BioC2019=tyah>). *Developer Day is
June 24* at NYU Langone Medical Center, the *User Conference is June 25-26*
at The Rockefeller University, and there will be a special
one-time-only *"Robert
Gentleman Symposium" hosting Robert Gentleman with current and former
colleagues on June 27 *(additional small registration fee will apply),
including other founders of R and Bioconductor.

In addition to the developer and scientific programme, BioC2019 will
provide the most comprehensive and intensive set of Bioconductor workshops
you can find, from the creators of the software. See the BioC2018 workshops
for reference: http://bioc2018.bioconductor.org

More details and the conference website, including calls for workshops,
talks, and posters, to come soon.
-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health

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Re: [Bioc-devel] Why bioconductor?

[Levi Waldron]

On Wed, Oct 10, 2018 at 3:25 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> As far as Levi’s comment about PEP8. It’s possible to design something
> similar with Jim Hester’s “lintr” package, which purely defines a style
> guide for code.
>
> https://github.com/jimhester/lintr


As I understand lintr it allows you to specify and perform syntax checks,
but you still have to write the style guide (as opposed e.g. to Swagger UI
for defining APIs)? On this thread, a couple more examples of pieces of
acquired knowledge that are non-obvious to newcomers:

   - Key elements of the "Bioconductor family tree" of core classes
   including: Annotated -> Vector -> (IRanges, GRanges, SummarizedExperiment,
   RangedSummarizedExperiment)
   - conventions like: core Bioconductor classes have constructors of the
   same name as the class
   - constructors can be called with no arguments

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Re: [Bioc-devel] Why bioconductor?

[Levi Waldron]

A related comment came up in a conversation I recently had with a potential
Bioconductor developer I met recently, who commented that even as an
experienced Python or CRAN developer, it is difficult to orient oneself to
the Bioconductor "style" and infrastructure for developers. He gave the
example of wishing there were something like
https://www.python.org/dev/peps/pep-0008/ available. One specific that we
discussed was how to orient oneself to the hierarchy of Bioconductor S4
classes and how to choose classes to develop from, something that
http://bioconductor.org/developers/how-to/commonMethodsAndClasses/ falls
short on because it only gives the biological contexts of some important
classes.


On Wed, Oct 10, 2018 at 11:52 AM Ludwig Geistlinger <
ludwig.geistlin...@sph.cuny.edu> wrote:

> While this might be obvious to most of us, it seems to be less clear to
> others.
>
> In particular, those who worked out their first package and wonder what's
> the difference between having a package available on Github, CRAN, or
> Bioconductor.
>
>
> I wonder whether it would be helpful for the Bioc webpage to pick up on
> the benefits of submitting to CRAN by Hadley
>
>
> http://r-pkgs.had.co.nz/release.html
>
>
> and several considerations with respect to Bioconductor
>
>
> https://bioinformatics.stackexchange.com/questions/639/why-bioconductor
>
>
> (Maybe FAQ?)
>
>
>  Just a thought.
>
>
> [[alternative HTML version deleted]]
>
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>


-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] Updating information on Bioconductor site

[Levi Waldron]

John, is your new version number reflected on the devel version of the
package landing page and the build report? After you push a new version
number to master, it will propagate the next day after overnight
building/testing.

AFAIK, there are only a few explanations for why git pushes do not show up
on the package landing page (have I missed any?):

1. You didn't actually push to the relevant branch at git.bioconductor.org
(e.g. you pushed to GitHub only, or pushed to master but checked the
release landing page)

2. You didn't bump the version number

3. There was an error in the package build

4. You haven't waited until the next day for software packages, or for the
twice a week builds of experimental data packages

5. Occasionally, there is a problem with the build systems that affects
many packages

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[Bioc-devel] Bioc2019 planning committee

[Levi Waldron]

Hi all,

I'm organizing a planning committee for Bioc2019 in New York City (at NYU
and Rockefeller University), June 24-26. There is lots to be done including
peer review of proposed talks, workshops, and posters, developing the
programme, adapting the web site (e.g. see http://bioc2018.bioconductor.org/),
seeking sponsorship, promoting the conference, and creating next year's
workshop booklet (e.g. see https://bioconductor.github.io/BiocWorkshops/).
If you like to take part, let me know, and I will include you in a kick-off
planning meeting within the next couple weeks.

Sincerely,
Levi

-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health

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Re: [Bioc-devel] Change the citation of my Bioconductor R package "BUScorrect"

[Levi Waldron]

And don't forget to bump your version number, and to check that the new
version number is reflected at the bioc-devel landing page. You will have
to do a separate commit to the release branch if you want to add the
citation to release before the next release cycle (I assume this is an
allowable change to the release branch):

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


On Tue, Sep 4, 2018 at 9:05 AM Martin Morgan 
wrote:

> Have you pushed your changes to
> g...@git.bioconductor.org:packages/BUScorrect and waited for a successful
> nightly build
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/BUScorrect/
>
> ?
>
> On 09/03/2018 07:10 AM, Xiangyu Luo wrote:
> > Dear All,
> >
> > The citation information of my "BUScorrect" R package is shown as an R
> > package version (e.g., xxx, xxx, R package version 0.99.10.), but I want
> it
> > to be my original paper (e.g., xxx, xxx, JournalName).
> >
> > I tried to manually insert the "CITATION" file in the "inst" folder, as
> > described in
> >
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files
> .
> > It works if the package is installed locally. However, when the package
> is
> > installed from the Bioconductor platform, the citation is still the R
> > package version.  I am wondering how to change the citation on
> Bioconductor?
> >
> > Many thanks for your great help!
> >
> > Xiangyu
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> ___
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>


-- 
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] Handling larger data in vignette

[Levi Waldron]

There are also weekly "long test" builds with a 6h timeout:

https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012326.html

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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

[Levi Waldron]

On Fri, Jul 20, 2018 at 10:26 AM Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> I think it's a Mac thing, and it's decided to install binary (tgz), and
> the annotation packages are source (tar.gz).
>
> Have you set options(pkgType = "both") ?
>

Thanks Martin, and sorry for the slow reply. You're right, I don't see the
same behavior on GNU/Linux (not sure about Windows). But options(pkgType =
"both") does not alter this behavior.

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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

[Levi Waldron]

I think the problem I was actually having was that
BiocManager::install("githubuser/repo")
will not install annotation or experimental data packages that are among
the repo's dependencies. It is the same
for devtools::install_github("githubuser/repo", repos =
BiocManager::repositories(), dependencies = TRUE). Here is a minimal
example from github.com/lwaldron/nothing, which depends on one software,
one annotation, and one experimental data package - the software package
will be installed, but the annotation and data packages are not available:

> remove.packages(c("TCGAutils", "mirbase.db", "curatedTCGAData"))
Removing packages from
‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
(as ‘lib’ is unspecified)
> BiocManager::install("lwaldron/nothing")
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing github package(s) 'lwaldron/nothing'
Downloading GitHub repo lwaldron/nothing@master
Skipping 3 packages not available: curatedTCGAData, GenomeInfoDbData,
mirbase.db
Installing 1 packages: TCGAutils
ERROR: dependencies *‘mirbase.db’, ‘curatedTCGAData’* are not available for
package ‘nothing’


On Mon, Jul 9, 2018 at 12:48 PM Levi Waldron 
wrote:

> Thanks Pariksheet and Martin! It seems that in fact both of these
> approaches work, e.g. (I made a simpler test case to figure this out):
>
> devtools::install_github("lwaldron/nothing", repos =
> BiocManager::repositories(), dependencies = TRUE)
> remove.packages(c("nothing", "ABCp2"))
> BiocManager::install("lwaldron/nothing", dependencies = TRUE)
>
> It's the dependencies of the Remotes: in Bioconductor/BiocWorkshops that
> get skipped, but at this point it seems like trying to do dependency
> management through GitHub and asking for trouble. I think the thing to do
> is to copy all the dependencies of the Remotes: directly into the
> DESCRIPTION file to streamline installation.
>


-- 
Levi Waldron
http://www.waldronlab.io
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

[Levi Waldron]

Thanks Pariksheet and Martin! It seems that in fact both of these
approaches work, e.g. (I made a simpler test case to figure this out):

devtools::install_github("lwaldron/nothing", repos =
BiocManager::repositories(), dependencies = TRUE)
remove.packages(c("nothing", "ABCp2"))
BiocManager::install("lwaldron/nothing", dependencies = TRUE)

It's the dependencies of the Remotes: in Bioconductor/BiocWorkshops that
get skipped, but at this point it seems like trying to do dependency
management through GitHub and asking for trouble. I think the thing to do
is to copy all the dependencies of the Remotes: directly into the
DESCRIPTION file to streamline installation.

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[Bioc-devel] BiocManager to install Depends/Imports/Suggests

[Levi Waldron]

It would be useful to be able to use BiocManager to install
the Depends/Imports/Suggests of a source package not on Bioconductor, e.g.:

BiocManager::install("Bioconductor/BiocWorkshops")  #works but only if all
Depends/Imports are already installed

or:

BiocManager::install_deps("Bioconductor/BiocWorkshops")  #to avoid any
change to BiocManager::install()
BiocManager::install("Bioconductor/BiocWorkshops")  #recommends the above
if not all deps are available

Also from a local package, e.g.:

BiocManager::install("mypackage_0.1.tar.gz")  # or,
BiocManager::install("mypackage")

BiocManager::install_deps("mypackage_0.1.tar.gz")  # or,
BiocManager::install_deps("mypackage")

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Re: [Bioc-devel] BiocStickers license

[Levi Waldron]

I see no need to require attribution, which doesn't seem practical anyways
if printing a sticker design.

On Thu, Jun 14, 2018 at 1:10 PM Laurent Gatto  wrote:

>
> For those that have BiocStickers, what are your toughts on license and
> requiring attributions, as they seem to limit reuse possibilities.
>
> See
>
>  https://github.com/Bioconductor/BiocStickers/issues/54
>
> for details.
>
> Best wishes,
>
> Laurent
>
> ___
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>


-- 
Levi Waldron
http://www.waldronlab.io
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] Missed deadline

[Levi Waldron]

ONE more note that Gabe reminded me of! As soon as your package is accepted
into bioc-devel, it will be accessible via
https://bioconductor.org/packages/mypackage/. Once it enters the release
branch, that URL will instead point to the release page.

On Tue, Apr 3, 2018 at 11:56 AM, Gabe Becker <becker.g...@gene.com> wrote:

> Indeed, and to be a bit more explicit about Levi's point, you *can*
> publish your package to bioconductor any time after the deadline, it will
> simply go to the development repo for ~6 months, which, as he points out,
> may not be a bad thing if it's not ready yet.
>
> On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron <lwaldron.resea...@gmail.com>
> wrote:
>
>> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon <roonysga...@gmail.com>
>> wrote:
>>
>> > Have I missed the deadline for the latest release? I have created a
>> > package, that runs great but there are a number of errors still from R
>> CMD
>> > check that I am sorting out.
>> >
>> > This is my first R package so I'm not sure if development is far enough
>> > along, although I suspect it might be.
>> >
>>
>> IMHO, when you're not sure a package is mature enough, and especially for
>> a
>> first package, it's actually better to miss the release deadline and allow
>> bioc-devel users test your package for 6 months before entering the
>> release
>> cycle. Making significant bug fixes and other changes becomes more
>> complicated and more of a pain for you and your users once you are in the
>> release...
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>>
>>
>
>
> --
> Gabriel Becker, Ph.D
> Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] Missed deadline

[Levi Waldron]

On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
wrote:

> Have I missed the deadline for the latest release? I have created a
> package, that runs great but there are a number of errors still from R CMD
> check that I am sorting out.
>
> This is my first R package so I'm not sure if development is far enough
> along, although I suspect it might be.
>

IMHO, when you're not sure a package is mature enough, and especially for a
first package, it's actually better to miss the release deadline and allow
bioc-devel users test your package for 6 months before entering the release
cycle. Making significant bug fixes and other changes becomes more
complicated and more of a pain for you and your users once you are in the
release...

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Re: [Bioc-devel] "extra" unit tests

[Levi Waldron]

Thanks Pete! Didn't know about those.

On Oct 24, 2017 11:17 PM, "Peter Hickey" <peter.hic...@gmail.com> wrote:

> A partial answer if you are using the 'testthat' framework: you can use
> `testthat::skip_on_bioc()` to specify that a test should be skipped if it
> is running on the BioC build machines. The test will otherwise be run
> (e.g., during local development). There are some other `testthat::skip*()`
> functions that may also be useful.
> Cheers,
> Pete
>
> On Wed, 25 Oct 2017 at 12:47 Levi Waldron <lwaldron.resea...@gmail.com>
> wrote:
>
>> Any thoughts about how to implement optional or "extra" unit tests, that
>> are too resource intensive to be part of the Bioconductor daily builds,
>> but
>> that should be run once in a while, say with major updates?
>>
>> [[alternative HTML version deleted]]
>>
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>>
>

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[Bioc-devel] MultiAssayExperiment compared to SummarizedExperiment (was: Why should Bioconductor developers re-use core classes?)

[Levi Waldron]

On Wed, Oct 18, 2017 at 8:00 PM, Dario Strbenac <dstr7...@uni.sydney.edu.au>
wrote:

> Good day,
>
> It might be useful to readers to have a comparison table (ticks and
> crosses) in the MultiAssayExperiment vignette that compares the features
> available in it to those available in SummarizedExperiment, to allow
> quicker decision making.
>

Good point, this is worth adding. I think the decision can probably be made
on one consideration: if it makes sense to represent all your assays by a
single set of rownames or row ranges, and a single set of colnames, then
you should use SummarizedExperiment. If your assays don't "match up" in
this way, then MultiAssayExperiment. Of course, the ExperimentList elements
of a MultiAssayExperiment can be SummarizedExperiments...


-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

[Levi Waldron]

Thanks for all your thoughts Joey, and I hope I didn't come across as
critical of phyloseq in particular. In fact, the couple packages I created
as a post-doc (doppelgangR and ffpe) did exactly the same thing, but unlike
phyloseq have never been used enough for it to make much difference :).
This comparison with phyloseq and metagenomeSeq is just one that I have
personal experience with because I use both packages and it was something
of a revelation to me when I realized that MRExperiment and all other
eSet-derived classes would "just work" as elements of a
MultiAssayExperiment. My motivation in making these slides was mainly to
share my own very recent revelations and try to make life better for new
package developers and their users.  A couple comments below:


On Wed, Oct 18, 2017 at 11:36 PM, Paul Joseph McMurdie 
wrote:

>
> - Hopefully it is obvious from my description, and also what I imagine to
> be Levi's motivation for making the slide deck, but somehow new eager
> developers are missing out on this great infrastructure and it isn't
> because they want to re-implement core stuff. I sure didn't! I simply
> didn't know what was there or best practices for BioC. *A "beginner's
> guide to BioC package development"* would have been at the top of my list
> of things to read back then.
>

I think this is still not abundantly clear from
http://bioconductor.org/developers/ and I'm not sure how much it factors
into the package review process. Would it be helpful to have a short
questionnaire for creators of new packages that includes some things not
part of R CMD BiocCheck, or CHECK, like - what new classes do you define,
and what is the purpose of defining them?


> - It isn't that I didn't read other established packages. I did. However,
> a lot of core BioC tools had gene-expression specific names even for data
> classes that were not intrinsically gene expression (e.g. it's actually a
> matrix, or related tables) -- and I'm happy many of these now use more
> general names like "experiment" or "row". The old names signaled to me
> "this isn't for you". And I naively, ignorantly, accepted that at mostly
> face value.
>
> - Conversely, sometimes not-inheriting methods is a feature, because it
> protects users from doing something that is great and appropriate for one
> domain (gene expression) but totally irrational in another (microbiome).
> I'm not saying my original implementation made great nuanced decisions
> about this -- it has many trappings of a new developer -- but I did have
> some pretty naive users in mind with phyloseq, for whom navigating legacy
> methods and method names from other domain(s) was expected to be a hurdle.
> Curious to hear thoughts on this.
>

Something you did well in phyloseq was define methods for all common user
operations, and if you had inherited from eSet, you probably still would've
wanted to do this - except that more of your methods would've been just
wrappers for inappropriately named eSet methods, and your average user
wouldn't have known the difference. Because of your use of methods and not
direct slot access by users, I think you could still change the underlying
data model without it being noticeable to basic users, even if it expanded
the number of methods actually available. Thankfully, SummarizedExperiment
I think now avoids these "this isn't for you" signals.


> - There actually *still isn't core support for evolutionary trees in BioC* (as
> mentioned by Joe Paulson and Ben Callahan in other threads). One of
> phyloseq's key contributions was to leverage the fantastic representation
> of trees implemented in the CRAN package "ape" in order to support analysis
> techniques popular among microbiome researchers that require a phylogenetic
> tree. The integration in the phyloseq-class and ape is necessarily pretty
> deep, including certain row operations. Users also needed a familiar and
> simple R interface to manipulate that composite object despite the complex
> hierarchical relationship among rows. Correct me if I'm wrong, but I think
> there is still no core BioC support for representing tree-like or
> bio-taxonomy-like hierarchy among rows in a SummarizedExperiment, or
> equivalent; and consequently certain row operations may have to be modified
> more deeply than usual if we were to re-implement phyloseq "the right way".
> I'd love to hear thoughts on this.
>

AFAIK you're right, and I don't know the solution, although I hope it can
be built on SummarizedExperiment. Looking forward to talking more about
this.


> Even though phyloseq is at the receiving end, I think the criticism is
> fair, and I want current and future new BioC contributors to not re-make my
> mistakes circa 2011-12. I'm happy to help if I can.
>
> Cheers, and thanks for the interesting, collegial thread.
>
> Joey
>

Thanks Joey, and I do want to say also that I think phyloseq is responsible
for making Bioconductor a viable and already superior choice for

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

[Levi Waldron]

>
> On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson 
> wrote:
>
>> I think the main reason for reusing/subclassing core classes that users
>> can
>> appreciate is that it makes it much easier for users to integrate multiple
>> packages into a single workflow. Only the most basic of pipelines uses
>> just
>> a single Bioconductor package. For instance, an "edgeR" pipeline obviously
>> uses the edgeR package, but it likely also uses several other packages,
>> like sva, RUV, variancePartition, etc. The more these different packages
>> operate on the same core data structures, the less work the user has to do
>> to use them together. And to bring that back around to an incentive for
>> developers, making your package interoperate with other packages more
>> easily means that users will be more likely to use your package.
>>
>
My impression is that the interoperability argument may already be more
widely appreciated, because in the pipeline example you can have several
packages operating on the same data class. It seems less obvious when you
are doing something different that requires defining a new class, why you
should extend an existing class to meet your needs. Although I guess your
point extends to interoperability with other packages providing methods for
the parent class, and the ability to use coercion methods defined for the
parent class, which I didn't mention...

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:

https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf

But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for ExpressionSet but for
everything else derived from eSet? The coercion function seems to work fine
on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from))
 seems to work regardless of the storage mode}:

> library(Biobase)> library(SummarizedExperiment)> example("NChannelSet-class", 
> echo=FALSE)> class(obj)[1] "NChannelSet"
attr(,"package")
[1] "Biobase"> is(obj, "eSet")[1] TRUE

> storageMode(obj)[1] "lockedEnvironment"

> makeSummarizedExperimentFromExpressionSet(obj) class:
RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData annotation
protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
colnames(3): A B C colData names(3): ChannelRData ChannelGData ChannelRAndG

> as(obj, "RangedSummarizedExperiment")

Error in as(obj, "RangedSummarizedExperiment") :
  no method or default for coercing “NChannelSet” to
“RangedSummarizedExperiment”

>

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès  wrote:

> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>

Thank you Hervé!


> The current behavior of the SummarizedExperiment() constructor
> when called on a ExpressionSet object doesn't make much sense to
> me. I'd rather have it consistent with what the coercion does.
> Will fix it.
>

Thank you, again.

A couple more questions while I'm at it, that may expose the limitations in
my understanding of inheritance and project history... 1) Why have some
developers chosen to extend eSet instead of ExpressionSet (definition
),
and 2) why are these coercion methods developed for ExpressionSet rather
than eSet? Wouldn't an eSet coercion method be preferable because it would
cover ExpressionSet as well as all the classes that extend eSet?

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:

> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `SummarizedExperiment`, it does not really coerce it to
> SummarizedExperiment, eg. `fData` and `pData` are not accordingly
> transferred to colData and rowData.
>

Right, I had forgotten about that - this isn't a coercion but a
construction, which should be obvious from the use of a constructor
function. This behavior is intuitive if you remember that
SummarizedExperiment(assays, ...) is a constructor that accepts as assays
any object or list of objects supporting square bracket matrix-like
subsetting. Sorry for my brain hiccup there.


> While I can understand that this is by design of `SummarizedExperiment`, I
> really wonder whether there are use cases where somebody would like to put
> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
> would like to coerce it that way.
>
> Furthermore, if you would indeed like to have several `ExpressionSet`s in
> a `SummarizedExperiment`, haven't you already arrived at a scenario where
> use of `MultiAssayExperiment` is indicated?
>

I think the behavior of the constructor SummarizedExperiment() here is
correct and expected, the issue here is that we're actually looking for
coercion methods.

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

Thanks Martin! I see the RangedSummarizedExperiment coercion method works
when there are no mappable ranges (for example curatedMetagenomicData
ExpressionSet objects), although the rowRanges is a GRangesList of empty
elements. It might be worth also having a SummarizedExperiment coercion
method it it's not a problematic or big job. And now I suppose I can ask
the question I *really* wanted to know, which is why can't I coerce an
object that extends eSet? I can still use the SummarizedExperiment()
constructor, but for example:

> library(metagenomeSeq)> data(mouseData)> class(mouseData)[1] "MRexperiment"
attr(,"package")
[1] "metagenomeSeq"> is(mouseData, "ExpressionSet")[1] FALSE>
is(mouseData, "eSet")[1] TRUE

> SummarizedExperiment(mouseData)class: SummarizedExperiment
dim: 10172 139
metadata(0):
assays(1): ''
rownames(10172): Prevotellaceae:1 Lachnospiraceae:1 ... Bryantella:103
  Parabacteroides:956
rowData names(0):
colnames(139): PM1:20080107 PM1:20080108 ... PM9:20080225 PM9:20080303
colData names(0):

> as(mouseData, "RangedSummarizedExperiment") Error in as(mouseData,
"RangedSummarizedExperiment") : no method or default for coercing
“MRexperiment” to “RangedSummarizedExperiment” > as(mouseData,
"SummarizedExperiment") Error in as(mouseData, "SummarizedExperiment") : no
method or default for coercing “MRexperiment” to
“SummarizedExperiment” > as(mouseData,
"ExpressionSet") Error in updateOldESet(from, "ExpressionSet") : no slot of
name "pData" for this object of class "AnnotatedDataFrame" >




On Mon, Sep 11, 2017 at 6:58 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 09/10/2017 08:38 PM, Levi Waldron wrote:
>
>> I just dug up this old thread because I realized we still don't have a
>> coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
>>
>
> try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
> ?makeSummarizedExperimentFromExpressionSet
>
> do have SummarizedExperiment(sample.ExpressionSet), could the coercion
>> method also be added easily?
>>
>> library(Biobase) > library(SummarizedExperiment) >
>>>
>> example("ExpressionSet")
>>
>> SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment
>>>
>> dim: 500 26
>> metadata(0):
>> assays(1): ''
>> rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
>> rowData names(0):
>> colnames(26): A B ... Y Z
>> colData names(0):> as(sample.ExpressionSet,
>> "SummarizedExperiment")Error in as(sample.ExpressionSet,
>> "SummarizedExperiment") :
>>no method or default for coercing “ExpressionSet” to
>> “SummarizedExperiment”
>>
>> sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)
>>>
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.3 LTS
>>
>> Matrix products: default
>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8
>>   [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
>> LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>> LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4parallel  stats graphics  grDevices utils
>> datasets  methods   base
>>
>> other attached packages:
>> [1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
>> matrixStats_0.52.2
>> [4] GenomicRanges_1.29.6   GenomeInfoDb_1.13.4
>> IRanges_2.11.7
>> [7] S4Vectors_0.15.5   Biobase_2.37.2
>> BiocGenerics_0.23.0
>>
>> loaded via a namespace (and not attached):
>>   [1] lattice_0.20-35 bitops_1.0-6grid_3.4.0
>>   [4] zlibbioc_1.23.0 XVector_0.17.0  Matrix_1.2-11
>>   [7] tools_3.4.0 RCurl_1.95-4.8  compiler_3.4.0
>> [10] GenomeInfoDbData_0.99.1
>>
>>
>>>
>> On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès <hpa...@fhcrc.org> wrote:
>>
>> Hi,
>>>
>>> On 09/20/2014 11:14 AM, Martin Morgan wrote:
>>>
>>> On 09/20/2014 10:43 AM, Sean Davis wrote:
>>>>
>>>> Hi, Vince.
>>>>>
>>>>> Looks like a good start.  I'd probably pull all the assays from
>>>>> ExpressionSet into SummarizedExperiment as the default, avoiding data
>&g

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

me that we might want something like this in
>>>> GenomicRanges
>>>> (that's where SummarizedExperiment is managed, right?) and I will add it
>>>> if there are no objections
>>>>
>>>> the arguments are currently
>>>>
>>>>   assayname = "exprs",# for naming SimpleList element
>>>>   fngetter =
>>>> function(z) rownames(exprs(z)),   # extract usable
>>>> feature names
>>>>   annDbGetter =
>>>>function(z) {
>>>>clnanno = sub(".db", "", annotation(z))
>>>>stopifnot(require(paste0(annotation(z), ".db"),
>>>> character.only=TRUE) )
>>>>get(paste0(annotation(z), ".db"))  # obtain resource for
>>>> mapping feature names to coordinates
>>>>},
>>>>   probekeytype = "PROBEID",   # chipDb field to use
>>>>   duphandler = function(z) {# action to take to process
>>>> duplicated
>>>> features
>>>>if (any(isd <- duplicated(z[,"PROBEID"])))
>>>>return(z[!isd,,drop=FALSE])
>>>>z
>>>>},
>>>>   signIsStrand = TRUE,   # verify that signs of addresses define
>>>> strand
>>>>   ucsdChrnames = TRUE# prefix 'chr' to chromosome token
>>>>
>>>>  [[alternative HTML version deleted]]
>>>>
>>>> ___
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>>>>
>>>>
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>>>
>>> ___
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>>>
>>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fhcrc.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
>
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>



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Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 <+1%20646-364-9616>
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[Bioc-devel] NEWS, inst/NEWS, NEWS.md

[Levi Waldron]

What's the currently recommended location for package NEWS?  At
https://www.bioconductor.org/developers/package-submission/ it says
inst/NEWS, and I feel like I heard somewhere that NEWS.md was supported.
But in a scan of the first page of https://github.com/bioconductor, all use
NEWS in the base package directory, and that is the only option I was able
to make show up on
https://bioconductor.org/packages/devel/data/experiment/news/curatedMetagenomicData/NEWS
when I played with it a couple months ago. Just want to get it straight.

-Levi

-- 
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http://www.waldronlab.org
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US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] experimental data packages and git-lfs

[Levi Waldron]

Thanks, Nitesh! See below:

On Thu, Sep 7, 2017 at 4:21 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Levi,
>
> I’m not sure what you mean by tracked vs checked.
>

Sorry, I meant whether there are any differences in the way software and
experimental data packages are handled by Bioconductor. It seems like from
the developer's perspective now, they are handled exactly the same, as
opposed to in the past when experimental data packages were tracked in two
separate svn repos and checked only twice a week.

On another note, I have explored your package a little on GitHub
> (waldronLab/curatedOvarianData), and I’ve noticed that the data files
> there are stored as LFS files. As long as you don’t add the .gitattributes
> file in upstream, you should be fine. You can keep the LFS tracking on
> Github and non-LFS storage on bioc-git separate.

To summarize:  No LFS support as of right now on bioc-git server, so I
> wouldn’t use any LFS commands.
>

So the way I understand this is, I can continue using LFS on GitHub, and
merging my changes upstream to git.bioconductor.org, as long as I avoid
adding the .gitattributes file upstream. I have already used LFS commands
to initiate LFS on GitHub, but these shouldn't affect git.bioconductor.org
if I avoid adding the .gitattributes file upstream.

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Re: [Bioc-devel] experimental data packages and git-lfs

[Levi Waldron]

Thank you, Nitesh.  Is there any difference at all now in how experimental
data vs. software packages are tracked and checked?

On Tue, Sep 5, 2017 at 8:40 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Levi,
>
> The external_data_store.txt file is not needed anymore.
>
> The current git.bioconductor.org server does not store files in the LFS
> mode, so you can just add a file, commit and push. But for Github, you
> might have to use LFS for such large files. I’ll look into this more and
> get back to you with a detailed reply.
>
> Best,
>
> Nitesh
>
> > On Sep 5, 2017, at 4:49 PM, Levi Waldron <lwaldron.resea...@gmail.com>
> wrote:
> >
> > Also, can I now remove external_data_store.txt?
> >
> > $ cat external_data_store.txt
> > data
> > inst/extdata
> >
> >
> > On Tue, Sep 5, 2017 at 4:38 PM, Levi Waldron <
> lwaldron.resea...@gmail.com>
> > wrote:
> >
> >> Are a couple extra commands needed at https://www.bioconductor.
> >> org/developers/how-to/git/maintain-github-bioc/ for experimental data
> >> packages? I followed the instructions here for curatedOvarianData, but
> got
> >> GitHub warnings on push:
> >>
> >> remote: warning: GH001: Large files detected. You may want to try Git
> >> Large File Storage - https://git-lfs.github.com.
> >> remote: warning: See http://git.io/iEPt8g for more information.
> >> remote: warning: File data/TCGA_eset.rda is 53.10 MB; this is larger
> than
> >> GitHub's recommended maximum file size of 50.00 MB
> >>
> >> So I followed the instructions at https://git-lfs.github.com/:
> >>
> >> git lfs track "*.rda"
> >> git add .gitattributes
> >> git commit -a
> >>
> >> Does this seem correct, and is there anything else to know for
> >> experimental data packages with large files?
> >>
> >> --
> >> Levi Waldron
> >> http://www.waldronlab.org
> >> Assistant Professor of Biostatistics CUNY School of Public Health
> >> US: +1 646-364-9616 <+1%20646-364-9616>
> >> Skype: levi.waldron
> >>
> >
> >
> >
> > --
> > Levi Waldron
> > http://www.waldronlab.org
> > Assistant Professor of Biostatistics CUNY School of Public Health
> > US: +1 646-364-9616   Skype:
> > levi.waldron
> >
> >   [[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.




-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] experimental data packages and git-lfs

[Levi Waldron]

Also, can I now remove external_data_store.txt?

$ cat external_data_store.txt
data
inst/extdata


On Tue, Sep 5, 2017 at 4:38 PM, Levi Waldron <lwaldron.resea...@gmail.com>
wrote:

> Are a couple extra commands needed at https://www.bioconductor.
> org/developers/how-to/git/maintain-github-bioc/ for experimental data
> packages? I followed the instructions here for curatedOvarianData, but got
> GitHub warnings on push:
>
> remote: warning: GH001: Large files detected. You may want to try Git
> Large File Storage - https://git-lfs.github.com.
> remote: warning: See http://git.io/iEPt8g for more information.
> remote: warning: File data/TCGA_eset.rda is 53.10 MB; this is larger than
> GitHub's recommended maximum file size of 50.00 MB
>
> So I followed the instructions at https://git-lfs.github.com/:
>
> git lfs track "*.rda"
> git add .gitattributes
> git commit -a
>
> Does this seem correct, and is there anything else to know for
> experimental data packages with large files?
>
> --
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics CUNY School of Public Health
> US: +1 646-364-9616 <+1%20646-364-9616>
>  Skype: levi.waldron
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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[Bioc-devel] experimental data packages and git-lfs

[Levi Waldron]

Are a couple extra commands needed at
https://www.bioconductor.org/developers/how-to/git/maintain-github-bioc/
for experimental data packages? I followed the instructions here for
curatedOvarianData, but got GitHub warnings on push:

remote: warning: GH001: Large files detected. You may want to try Git Large
File Storage - https://git-lfs.github.com.
remote: warning: See http://git.io/iEPt8g for more information.
remote: warning: File data/TCGA_eset.rda is 53.10 MB; this is larger than
GitHub's recommended maximum file size of 50.00 MB

So I followed the instructions at https://git-lfs.github.com/:

git lfs track "*.rda"
git add .gitattributes
git commit -a

Does this seem correct, and is there anything else to know for experimental
data packages with large files?

-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] stale data experiment package builds

[Levi Waldron]

On Tue, Jun 20, 2017 at 7:24 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> This is now fixed.
>
> Valerie
>

Thank you Val! curatedMetagenomicData is back under review now, so much
appreciated.

http://biorxiv.org/content/early/2017/06/21/103085

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Re: [Bioc-devel] ExperimentHub broken in bioc-devel?

[Levi Waldron]

Thanks Val! 2.9.4 isn't in bioc-devel yet, but I got it through Subversion
and am up and running again.

On Sat, Jun 3, 2017 at 11:26 AM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Levi,
>
> Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4.
>
> Val
>
>
> On 06/03/2017 05:55 AM, Levi Waldron wrote:
> > It works for me when I have an existing cache, but not after removing the
> > cache:
> >
> >> unlink("~/.ExperimentHub", recursive=TRUE)
> >> suppressPackageStartupMessages(library(curatedMetagenomicData))
> >> ExperimentHub()
> > updating metadata: retrieving 1 resource
> >
> > |===
> ==|
> > 100%
> > snapshotDate(): 2016-12-12
> > *Error in gzfile(file, "rb") : cannot open the connection*
> > In addition: Warning message:
> > In gzfile(file, "rb") :
> >   cannot open compressed file '/Users/lwaldron//.
> ExperimentHub/index.rds',
> > probable reason 'No such file or directory'
> >> sessionInfo()
> > R version 3.4.0 Patched (2017-06-02 r72758)
> > Platform: x86_64-apple-darwin15.6.0 (64-bit)
> > Running under: macOS Sierra 10.12.4
> >
> > Matrix products: default
> > BLAS:
> > /System/Library/Frameworks/Accelerate.framework/Versions/
> A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> > LAPACK:
> > /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] parallel  stats graphics  grDevices utils datasets  methods
> > base
> >
> > other attached packages:
> > [1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0
> >
> > loaded via a namespace (and not attached):
> >  [1] Rcpp_0.12.11  IRanges_2.11.3
> >  [3] digest_0.6.12 mime_0.5
> >  [5] R6_2.2.1  xtable_1.8-2
> >  [7] DBI_0.6-1 stats4_3.4.0
> >  [9] RSQLite_1.1-2 BiocInstaller_1.27.2
> > [11] httr_1.2.1curl_2.6
> > [13] S4Vectors_0.15.2  tools_3.4.0
> > [15] Biobase_2.37.2shiny_1.0.3
> > [17] httpuv_1.3.3  yaml_2.1.14
> > [19] compiler_3.4.0AnnotationDbi_1.39.1
> > [21] memoise_1.1.0 htmltools_0.3.6
> > [23] interactiveDisplayBase_1.15.0
> >   [[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.
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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[Bioc-devel] ExperimentHub broken in bioc-devel?

[Levi Waldron]

It works for me when I have an existing cache, but not after removing the
cache:

> unlink("~/.ExperimentHub", recursive=TRUE)
> suppressPackageStartupMessages(library(curatedMetagenomicData))
> ExperimentHub()
updating metadata: retrieving 1 resource

|=|
100%
snapshotDate(): 2016-12-12
*Error in gzfile(file, "rb") : cannot open the connection*
In addition: Warning message:
In gzfile(file, "rb") :
  cannot open compressed file '/Users/lwaldron//.ExperimentHub/index.rds',
probable reason 'No such file or directory'
> sessionInfo()
R version 3.4.0 Patched (2017-06-02 r72758)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats graphics  grDevices utils datasets  methods
base

other attached packages:
[1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11  IRanges_2.11.3
 [3] digest_0.6.12 mime_0.5
 [5] R6_2.2.1  xtable_1.8-2
 [7] DBI_0.6-1 stats4_3.4.0
 [9] RSQLite_1.1-2 BiocInstaller_1.27.2
[11] httr_1.2.1curl_2.6
[13] S4Vectors_0.15.2  tools_3.4.0
[15] Biobase_2.37.2shiny_1.0.3
[17] httpuv_1.3.3  yaml_2.1.14
[19] compiler_3.4.0AnnotationDbi_1.39.1
[21] memoise_1.1.0 htmltools_0.3.6
[23] interactiveDisplayBase_1.15.0
>

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[Bioc-devel] DataFrame errors with a Surv class column

[Levi Waldron]

Running and updated Bioc 3.5:

> library(survival)
> set.seed(1)
> cens <- sample(0:1, 100, replace=TRUE)
> time <- rnorm(100)
> df = DataFrame(time=time, cens=cens, y=Surv(time, cens))
> df[1:3, ]  #OK
DataFrame with 3 rows and 3 columns
time  cens   y.from
   
1  0.3981059 0  0.398105880367068:0
2 -0.6120264 0 -0.612026393250771:0
3  0.3411197 1  0.341119691424425:1
> df #error
DataFrame with 100 rows and 3 columns
*Error in unclass(x)[i, , drop = FALSE] : subscript out of bounds*
>

This came up after I noticed something similar in
MultiAssayExperiment::wideFormat() when trying to reshape a Surv column,
but I'm not sure it's a bug in MultiAssayExperiment:

> library(MultiAssayExperiment)
> miniACC$y <- Surv(miniACC$days_to_death, miniACC$vital_status)
> res = wideFormat(miniACC["EZH2", , ], colDataCols="y")
 Show Traceback

 Rerun with Debug
* Error in unclass(x)[i, , drop = FALSE] : subscript out of bounds *
>

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Re: [Bioc-devel] Bioconductor mirror is gone

[Levi Waldron]

Dear Maia, I believe that is part of the Git transition plan, see
https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010691.html

On Mon, Apr 17, 2017 at 10:26 PM, Maia Smith <ma...@sfu.ca> wrote:

> Hi all,
>
> My bioconductor mirror is gone -
> https://github.com/Bioconductor-mirror/timescape returns a 404 now.
> Everything else about the package seems to be fine. How do I get it back?
>
> Thanks
> Maia
>
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>
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>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
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Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

[Levi Waldron]

On Feb 22, 2017 1:42 PM, "Vincent Carey"  wrote:

might there have been an object that references the obsolete class around?


There were no objects in the environment, ie being loaded from an .RData,
if that's what you mean.

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Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

[Levi Waldron]

Thank you, Martin. I did that and went through the long tree re-installing
from source the re-starting R and trying my example again. It wasn't
successful until I tried re-installing phyloseq itself from source, and
that worked! I still don't understand why, since neither grep
vectorORfactor or vector_OR_factor matches anything in the R/ directory of
phyloseq. But, my phyloseq installation is working again.

On Tue, Feb 21, 2017 at 5:33 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 02/21/2017 03:24 PM, Levi Waldron wrote:
>
>> On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès <hpa...@fredhutch.org
>> <mailto:hpa...@fredhutch.org>> wrote:
>>
>> Hi Levi,
>>
>> Were you able to sort this out? I think we should emphasize the
>> importance of re-installing packages *from source* (i.e. with
>> biocLite(..., type="source")). This is because some of the package
>> binaries we distribute seem to be affected by this problem too.
>> We're planning to fix these binaries over the next couple of days.
>>
>>
>> Thank you, Hervé. I hadn't re-installed from source, and haven't gotten
>> around to doing a complete re-install, so I tried again with
>> `biocLite(..., type="source")`. But it still didn't fix the problem
>> re-installing `mydep$phyloseq` above with type="source". It isn't a
>> great rush, so perhaps I'll just wait until you've updated the binaries.
>>
>
> Here's an attempt to fail when the vectorORfactor class is contained in
> 'list', which I think is where the problem comes from
>
> trace(
> loadNamespace,
> quote(print(package)),
> exit=quote({
> contains <- names(getClass("list")@contains)
> if (any(grepl("vectorORfactor", contains)))
> stop("found after: ", package)
> })
> )
> library(phyloseq)
>
>
>
>>
>> Sorry for the inconvenience,
>>
>>
>> No worries!
>>
>> -Levi
>>
>>
>
> 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.
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

[Levi Waldron]

On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès  wrote:

> Hi Levi,
>
> Were you able to sort this out? I think we should emphasize the
> importance of re-installing packages *from source* (i.e. with
> biocLite(..., type="source")). This is because some of the package
> binaries we distribute seem to be affected by this problem too.
> We're planning to fix these binaries over the next couple of days.
>

Thank you, Hervé. I hadn't re-installed from source, and haven't gotten
around to doing a complete re-install, so I tried again with `biocLite(...,
type="source")`. But it still didn't fix the problem re-installing
`mydep$phyloseq` above with type="source". It isn't a great rush, so
perhaps I'll just wait until you've updated the binaries.


> Sorry for the inconvenience,
>

No worries!

-Levi

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Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

[Levi Waldron]

On Sun, Feb 19, 2017 at 2:54 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
>
> It is a variant of
>>
>> https://stat.ethz.ch/pipermail/bioc-devel/2017-February/010463.html
>>
>> and requires re-installation of one or more of your Bioconductor
>> packages that depend directly or indirectly on S4Vectors; it's easy to
>>
>
> should have been 'not easy'
>

Thanks, Martin. I reinstalled both the "installme" and "mydep" packages
below using biocLite(installme), then when that didn't work, I also tried
biocLite(mydep$phyloseq). I guess a full Bioconductor reinstall would be a
heavy-handed but effective fix?

> db = available.packages(repos=BiocInstaller::biocinstallRepos()[1])
   revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE,
   reverse=TRUE)
> mydep = tools::package_dependencies("phyloseq", db, recursive=TRUE)
> installme = mydep$phyloseq[mydep$phyloseq %in% revdeps$S4Vectors]
> mydep
$phyloseq
 [1] "BiocGenerics" "ade4" "ape"  "biomformat"
"Biostrings"
 [6] "cluster"  "data.table"   "foreach"  "ggplot2"  "igraph"

[11] "methods"  "multtest" "plyr" "reshape2" "scales"

[16] "vegan""Biobase"  "utils""graphics" "stats"

[21] "parallel" "jsonlite" "Matrix"   "rhdf5"
 "S4Vectors"
[26] "IRanges"  "XVector"  "survival" "MASS" "stats4"

[31] "zlibbioc"
> installme
[1] "Biostrings" "IRanges""XVector"
>

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[Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

[Levi Waldron]

 I am getting this error from a basic phyloseq function, which doesn't
appear in the build system's check.  Is this some strange thing wrong with
my installation? From a fresh R session:

> library(phyloseq)
> example("sample_data")

smpl_d> #
smpl_d> data(soilrep)

smpl_d> head(sample_data(soilrep))
Error in validObject(.Object) :
  invalid class “sample_data” object: superclass "vectorORfactor" not
defined in the environment of the object's class
> devtools::session_info()
Session info

 setting  value
 version  R Under development (unstable) (2017-02-10 r72157)
 system   x86_64, darwin13.4.0
 ui   RStudio (1.0.136)
 language (EN)
 collate  en_US.UTF-8
 tz   America/New_York
 date 2017-02-18

Packages

 package  * version date   source
 ade4   1.7-5   2016-12-13 CRAN (R 3.4.0)
 ape4.1 2017-02-14 CRAN (R 3.4.0)
 assertthat 0.1 2013-12-06 CRAN (R 3.4.0)
 Biobase2.35.0  2016-10-23 Bioconductor
 BiocGenerics   0.21.3  2017-01-12 Bioconductor
 biomformat 1.3.0   2016-10-23 Bioconductor
 Biostrings 2.43.4  2017-02-02 Bioconductor
 cluster2.0.5   2016-10-08 CRAN (R 3.4.0)
 codetools  0.2-15  2016-10-05 CRAN (R 3.4.0)
 colorspace 1.3-2   2016-12-14 CRAN (R 3.4.0)
 data.table 1.10.4  2017-02-01 CRAN (R 3.4.0)
 devtools   1.12.0  2016-06-24 CRAN (R 3.4.0)
 digest 0.6.12  2017-01-27 CRAN (R 3.4.0)
 foreach1.4.3   2015-10-13 CRAN (R 3.4.0)
 ggplot22.2.1   2016-12-30 CRAN (R 3.4.0)
 gtable 0.2.0   2016-02-26 CRAN (R 3.4.0)
 igraph 1.0.1   2015-06-26 CRAN (R 3.4.0)
 IRanges2.9.18  2017-02-02 Bioconductor
 iterators  1.0.8   2015-10-13 CRAN (R 3.4.0)
 jsonlite   1.2 2016-12-31 CRAN (R 3.4.0)
 lattice0.20-34 2016-09-06 CRAN (R 3.4.0)
 lazyeval   0.2.0   2016-06-12 CRAN (R 3.4.0)
 magrittr   1.5 2014-11-22 CRAN (R 3.4.0)
 MASS   7.3-45  2016-04-21 CRAN (R 3.4.0)
 Matrix 1.2-8   2017-01-20 CRAN (R 3.4.0)
 memoise1.0.0   2016-01-29 CRAN (R 3.4.0)
 mgcv   1.8-17  2017-02-08 CRAN (R 3.4.0)
 multtest   2.31.0  2016-10-23 Bioconductor
 munsell0.4.3   2016-02-13 CRAN (R 3.4.0)
 nlme   3.1-131 2017-02-06 CRAN (R 3.4.0)
 permute0.9-4   2016-09-09 CRAN (R 3.4.0)
 phyloseq * 1.19.1  2016-11-21 Bioconductor
 plyr   1.8.4   2016-06-08 CRAN (R 3.4.0)
 Rcpp   0.12.9  2017-01-14 CRAN (R 3.4.0)
 reshape2   1.4.2   2016-10-22 CRAN (R 3.4.0)
 rhdf5  2.19.0  2016-10-23 Bioconductor
 S4Vectors  0.13.15 2017-02-14 Bioconductor
 scales 0.4.1   2016-11-09 CRAN (R 3.4.0)
 stringi1.1.2   2016-10-01 CRAN (R 3.4.0)
 stringr1.1.0   2016-08-19 CRAN (R 3.4.0)
 survival   2.40-1  2016-10-30 CRAN (R 3.4.0)
 tibble 1.2 2016-08-26 CRAN (R 3.4.0)
 vegan  2.4-2   2017-01-17 CRAN (R 3.4.0)
 withr  1.0.2   2016-06-20 CRAN (R 3.4.0)
 XVector0.15.2  2017-02-02 Bioconductor
 zlibbioc   1.21.0  2016-10-23 Bioconductor
>

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Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Levi Waldron]

On Wed, Feb 1, 2017 at 12:51 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> Levi triggered the problem with install.packages("lazyeval",
> repos=biocinstallRepos(), which is an R-only command. Also, there have not
> been any changes to the logic of biocLite() in this regard, so the problem
> is likely to be in R (devel) per se. I'll try to get access to a Mac and
> investigate.


Yes, in fact, now I notice that it also happens with just
install.packages("lazyeval"), on the second invocation with the same repo
argument (although exiting and starting R again creates a new tmp directory
so gives another free invocation. Sorry for blaming it on biocLite().

-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Levi Waldron]

On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> It seems like this is a local cache of the rstudio file that describes the
> mac repository. Maybe your vanilla execution of install.packages() does not
> use the repository that BiocInstaller does. So maybe


One more note, I am doing all this from a terminal - I think the only
association with RStudio is that its mirror was my default.


-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Levi Waldron]

On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan
 wrote:
> It seems like this is a local cache of the rstudio file that describes the
> mac repository. Maybe your vanilla execution of install.packages() does not
> use the repository that BiocInstaller does. So maybe
>
> install.packages("lazyeval", repos=biocinstallRepos())
>
> fails (maybe if repeated a second time)?

Yes, you're right, it fails.

> This would sound like an RStudio
> problem. Is a work-around possible with
>
>   options(repos=c(CRAN="https://cran.r-project.org;))
>   biocinstallRepos()   # should pick up new repository
>   biocLite("lazyeval")

This works for one install, then subsequently produces the same error:

Browse[1]> file

[1] 
"/var/folders/6n/cj15_ryn3ls0jtvfhtxztq08gn/T//RtmpYdXlSZ/repos_https%3A%2F%2Fcran.r-project.org%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds"

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Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Levi Waldron]

On Sun, Jan 29, 2017 at 11:36 PM, Martin Morgan
 wrote:
>
>
> can you try to find out what file it is trying to read and what function 
> call, e.g.,
>
>   options(error=recover)
>   biocLite("lazyeval")
>
> That should get the call stack; choose readRDS and look for the 'file' 
> variable for the exact file.
>
> Martin


It is:

/var/folders/6n/cj15_ryn3ls0jtvfhtxztq08gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds


Lewis-MacBook-Air:~ lw391$ ls -l
/var/folders/6n/cj15_ryn3ls0jtvfhtxztq08gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds

-rw-r--r--  1 lw391  staff  0 Jan 29 23:49
/var/folders/6n/cj15_ryn3ls0jtvfhtxztq08gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds

I removed this file, then I could call biocLite once, but the second
time got the same error and the same file:

/var/folders/6n/cj15_ryn3ls0jtvfhtxztq08gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds

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[Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Levi Waldron]

Not sure anyone will be able to help with this, but I can no longer install
packages from bioc-devel using a current R-devel and biocLite() on my
OSX Yosemite 10.10.5. I can still install from the command line `R CMD
INSTALL` and `install.packages()`. Here is the error - the package lazyeval
is just an example of a commonly used package from CRAN so I can show that
install.packages works, but it seems to happen for all CRAN, Bioconductor,
or Github packages. I don't have any problems when using R 3.3.2 patched +
Bioc 3.4.

> biocLite("lazyeval")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development
(unstable)

  (2017-01-26 r72035).

Installing package(s) ‘lazyeval’

*Error in readRDS(dest) : error reading from connection*

Note that the problem isn't there with `install.packages()`:

> install.packages("lazyeval")  ##successful install

Following some advice from stackoverflow
 and rstudio

for
people who've had the same error in R, I tried starting from a fresh
install (and didn't see any zero-size rds files in my R library), and am
still having the problem *only* when using biocLite (not install.packages
or R CMD INSTALL).  Just to show this is a fresh installation (I have only
installed R-devel from https://r.research.att.com/, then done `> source("
https://www.bioconductor.org/biocLite.R;)`):

> dir(.libPaths())

 [1] "AnnotationDbi" "base"  "BH""Biobase"

 [5] "BiocGenerics"  "BiocInstaller" "boot"  "class"

 [9] "cluster"   "codetools" "compiler"  "datasets"

[13] "DBI"   "digest""foreign"   "graphics"

[17] "grDevices" "grid"  "IRanges"   "KernSmooth"

[21] "lattice"   "lazyeval"  "MASS"  "Matrix"

[25] "memoise"   "methods"   "mgcv"  "nlme"

[29] "nnet"  "parallel"  "plogr" "Rcpp"

[33] "rpart" "RSQLite"   "S4Vectors" "spatial"

[37] "splines"   "stats" "stats4""survival"

[41] "tcltk" "tools" "translations"  "utils"


One other strange thing I've noticed - using my primary user account I got
one good call to biocLite after the fresh install of R-devel, then all
subsequent calls produced this error. The good call installed Bioconductor
in a system directory for all users. Then starting as another user without
write access to the system package library, that user got one good call
which created a user directory library, and I could use to run
biocLite("lazyeval") locally, but then subsequent calls to biocLite failed
for that user too.

biocValid() and session info:

> biocValid()

[1] TRUE

> sessionInfo()

R Under development (unstable) (2017-01-26 r72035)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X Yosemite 10.10.5


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] BiocInstaller_1.25.3


loaded via a namespace (and not attached):

[1] compiler_3.4.0 tools_3.4.0tcltk_3.4.0

>

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Re: [Bioc-devel] hg133plus2.db

[Levi Waldron]

Well that's embarrassing, thanks Val!

On Tue, Dec 27, 2016 at 11:00 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> I think you're missing a 'u',
>
> > biocLite("hgu133plus2.db")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development
> (unstable)
>   (2016-10-22 r71581).
> Installing package(s) ‘hgu133plus2.db’
> trying URL
> 'https://bioconductor.org/packages/3.5/data/annotation/
> src/contrib/hgu133plus2.db_3.2.3.tar.gz'
> Content type 'application/x-gzip' length 2139642 bytes (2.0 MB)
> ==
> downloaded 2.0 MB
>
> Val
>
> On 12/27/2016 02:00 PM, Levi Waldron wrote:
> > I don't seem to be able to install hgu133plus2.db in bioc-devel?
> >
> >> library(BiocInstaller)
> > Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> >
> >> biocLite("hg133plus2.db")
> > BioC_mirror: https://bioconductor.org
> >
> > Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development
> (unstable)
> >
> >   (2016-10-26 r71594).
> >
> > Installing package(s) ‘hg133plus2.db’
> >
> > Warning: unable to access index for repository
> > https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
> >
> >   cannot download all files
> >
> > Warning message:
> >
> > package ‘hg133plus2.db’ is not available (for R Under development)
> >
> >> sessionInfo()
> > R Under development (unstable) (2016-10-26 r71594)
> >
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> >
> > Running under: OS X Yosemite 10.10.5
> >
> >
> > locale:
> >
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> >
> > attached base packages:
> >
> > [1] stats graphics  grDevices utils datasets  methods   base
> >
> >
> > other attached packages:
> >
> > [1] BiocInstaller_1.25.2
> >
> >
> > loaded via a namespace (and not attached):
> >
> > [1] tools_3.4.0
> >
> >
>
>
>
> 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.
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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[Bioc-devel] hg133plus2.db

[Levi Waldron]

I don't seem to be able to install hgu133plus2.db in bioc-devel?

> library(BiocInstaller)

Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help

> biocLite("hg133plus2.db")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable)

  (2016-10-26 r71594).

Installing package(s) ‘hg133plus2.db’

Warning: unable to access index for repository
https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:

  cannot download all files

Warning message:

package ‘hg133plus2.db’ is not available (for R Under development)

> sessionInfo()

R Under development (unstable) (2016-10-26 r71594)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X Yosemite 10.10.5


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] BiocInstaller_1.25.2


loaded via a namespace (and not attached):

[1] tools_3.4.0

>


-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] BioC 3.2 branch created

[Levi Waldron]

Just a small suggestion, it might be helpful to put a date on
https://www.bioconductor.org/news/bioc_3_2_release/ - currently it's not
obvious when you land on that page when the announcement was made, or that
this is the current release version.

Thanks core team for your hard work in getting another release out on
schedule!



On Tue, Oct 13, 2015 at 4:20 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:

>
> The BioC 3.2 branch is now ready.
>
> Remember, you always have access to 2 versions of your package:
> the "release" and the "devel" versions.
>
> Right now the "release" version of your package (which is not
> officially released yet but will be tomorrow if
> everything goes well) is in the 3.2 branch and accessible at:
>
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/
> 
>
> Only bug fixes and documentation improvements should go here.
>
> As always the "devel" version of your package is at:
>
>  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
>
> Similarly for experiment packages, where your package is available in
> devel at
>
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>
> The release branch of it is in:
>
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/
> 
>
>
> Normal development of your package can now resume here.
>
> Please let us know if you have any questions.
>
>
> Thanks!
>
> Dan
>
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>



-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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Re: [Bioc-devel] Package submission with library requirement

[Levi Waldron]

On Fri, Jan 23, 2015 at 1:58 PM, Dan Tenenbaum dtene...@fredhutch.org wrote:
 However, you should consider using Rlecuyer as it has no external 
 dependencies (see Levi's post to this thread). Then your package should build 
 on windows.

I think so too - it's also a standard solution in R, implemented
natively in r-core's parallel library and suggested by the snow
library.  I used it in my pensim library before transitioning to
parallel, and have tested its streams on hyperthreaded CPUs and
clusters.

-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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[Bioc-devel] post-doc position

[Levi Waldron]

A post-doctoral fellow position is available in New York, as part of the
same NCI-funded project as Martin's post below.  See
https://rfcuny.org/hr/pvn/cgi-bin/show_job.asp?pvn=REA-1776 for details, or
please don't hesitate to contact me.

On Fri, Nov 7, 2014 at 1:22 PM, Martin Morgan mtmor...@fredhutch.org
wrote:

 SYSTEMS ANALYST PROGRAMMER  III / IV

 The Bioconductor project (http://bioconductor.org) seeks an individual to
 join our software development team.

 If you're interested, or know someone who is, please visit

   https://support.bioconductor.org/p/62737/

 for more details!

 Best,

 Martin Morgan
 --
 Computational Biology / Fred Hutchinson Cancer Research Center
 1100 Fairview Ave. N.
 PO Box 19024 Seattle, WA 98109

 Location: Arnold Building M1 B861
 Phone: (206) 667-2793

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-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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[Bioc-devel] mis-spelled BiocViews term

[Levi Waldron]

PrinicpalComponent (1)
http://bioconductor.org/packages/release/BiocViews.html# - I'm reviewing
an incoming package that spells it correctly, not sure if it should change
to the mis-spelled version (hopefully not) or if it can be corrected
in SomaticSignatures and BiocViews?

-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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[Bioc-devel] daily build system behind

[Levi Waldron]

I just noticed that the daily build systems are several days behind, eg for
experimental data packages:

http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/

Snapshot Date: 2014-09-06 06:15:22 -0700 (Sat, 06 Sep 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
Last Changed Rev: 2991 / Revision: 2991
Last Changed Date: 2014-09-02 08:08:09 -0700 (Tue, 02 Sep 2014)


-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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[Bioc-devel] upgrade instructions at http://bioconductor.org/install/

[Levi Waldron]

I just noticed that there is no mention on
http://bioconductor.org/install/of how to upgrade from the previous
Bioconductor.  I think it would be
helpful to advise that it can be done with biocLite(BiocUpgrade).

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Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

[Levi Waldron]

I agree with Dan on the need to be able to save analysis done in a Shiny
Bioconductor app, allowing someone later to reload the same state, and to
inspect a session and see what was done.  Perhaps save and load buttons
should be present in the user interface of any Bioconductor Shiny app that
is not read-only.

If interactive user input can be saved (as an .RData file?), could that
file be used as input for unit tests either the usual console way or
something like an http POST?

-Levi





On Fri, Jul 26, 2013 at 5:42 PM, Michael Lawrence lawrence.mich...@gene.com
 wrote:

 An answer to both of these issues is the use of R code. It should be
 possible to drive shiny apps through the server, without the user's code
 knowing the difference. And you've already thought of recording user
 actions as R code. This would be an application of the command pattern, as
 with undo/redo stacks, except each object boils down to a
 function/expression (Tengfei and I have a CRAN package called commandr
 related to this). Someone should try to make a prototype to explore these
 issues then we can start thinking about common infrastructure.


 On Fri, Jul 26, 2013 at 12:23 PM, Dan Tenenbaum dtene...@fhcrc.org
 wrote:

  Hi everyone,
 
  There was a lot of talk about shiny at BioC2013 and it seems like a
  lot of people are using it for lots of different cool stuff.
 
  Now we are at the point where some contributors want to add shiny apps
  to Bioconductor as packages.
 
  We had some discussion internally and decided that there are a few
  issues we wanted to discuss with BioC developers as well as some of
  the shiny developers. Please feel free to share your thoughts.
 
  1) Testing shiny apps
 
  Typically, bioconductor packages have man page examples, vignettes,
  and (sometimes) unit tests, so when we build the packages every day on
  our build system, the code in all of these is evaluated and we have
  some idea of whether the package is working as it's supposed to.
 
  I'm not clear on how to do similar testing of a shiny application.
  Since launching a shiny app takes away the R console (until the app is
  closed), shiny apps should probably not be launched in example or test
  code (unless interactive() is TRUE).
 
  Do the shiny folks (or anyone else) have thoughts on testing shiny apps?
 
  2) Reproducible research
 
  Reproducible research is really important in our community, but shiny
  apps are sort of a black box as far as reproducibility is concerned.
 
  If shiny apps are read-only (that is, if they are just used to view
  an object) then this is not really a problem. But shiny has the
  ability now to change objects back in your R session, so we need to be
  able to track what is done inside the shiny app.
 
  shiny apps can return some sort of object that tells you what was done
  in the shiny session (insofar as it modifies any objects in the
  users's session) and this object can provide a way to reproduce those
  steps without the shiny app. So maybe the object would consist of
  lines of code. This means that if there is a shiny app, the package
  author must also provide ways to do the same transformations on
  objects without shiny.
 
  There are probably other approaches as well. But the end goal would be
  a scriptable, reproducible shiny session.
 
  Another thought was that a shiny app could emit some sort of state
  object, and then be restarted with that object.
 
  Not sure if the place for such infrastructure is inside shiny itself,
  or perhaps in a BioC infrastructure package.
 
  What are your thoughts?
  Dan
 
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-- 
Levi Waldron
Post-doctoral fellow
Department of Biostatistics, Harvard School of Public Health
Department of Biostatistics and Computational Biology, Dana-Farber Cancer
Institute
Building 1, room 412C
655 Huntington Avenue
Boston, Massachusetts 02115
mobile: (617) 851-6849
fax: (617) 432-5619
http://www.hsph.harvard.edu/research/levi-waldron/

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[Bioc-devel] broken links for curatedOvarianData package

[Levi Waldron]

Dear Bioconductors,

I  noticed that the NEWS from my new experimental data package
curatedOvarianData (
http://www.bioconductor.org/packages/2.12/data/experiment/html/curatedOvarianData.html)
didn't make it into the release notes.  The NEWS link from its 2.12 page is
broken, as is its Download Stats link.  The file inst/NEWS exists in the
non-data repository but not in the data repository, should I add it to the
data repository instead?

Thanks!
-Levi

-- 
Levi Waldron
Post-doctoral fellow
Department of Biostatistics, Harvard School of Public Health
Department of Biostatistics and Computational Biology, Dana-Farber Cancer
Institute
Building 1, room 412C
655 Huntington Avenue
Boston, Massachusetts 02115
mobile: (617) 851-6849
fax: (617) 432-5619
http://www.hsph.harvard.edu/research/levi-waldron/

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