[Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Thu Jun 25 20:54:14 CEST 2020


Hi Ahmed,

Just a heads up that Lori's workaround (reinstalling iheatmap from 
source on all the builders) should be considered a temporary one and 
that the fundamental problem remains. The fundamental problem being that 
the iheatmap's Windows and Mac binaries that are on CRAN are broken. And 
the reason they are broken is because they contain stale information in 
their method cache.

As a consequence, the lipidr error you were seeing a few days ago on our 
build report is back today on the devel report:

   https://bioconductor.org/checkResults/3.12/bioc-LATEST/lipidr/

Note that this time it's only on Windows and Mac. This is because 
yesterday we updated R to R 4.0.2 on the devel builders so the build 
machines automatically reinstalled all the deps from scratch. iheatmap 
is one of them and the build system picked up the Windows and Mac 
binaries from CRAN, which are broken :-/

We'll see the same problem on the release builds when we update R to R 
4.0.2 there too.

Bottom line: the only true fix is that the iheatmap authors/maintainers 
upload a new version of their package to CRAN. The only change they need 
to do is bump the version. Alternatively, they could reconsider 
depending on S4Vectors. Bioconductor moves fast and CRAN packages that 
depend on Bioconductor packages are inherently at the risk of seeing 
their binaries become stale.

Hope this helps,
H.


On 6/22/20 04:50, Shepherd, Lori wrote:
> I reinstalled iheatmap yesterday and it should be reflected in today's 
> (Mondays) report.
> 
> Cheers,
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> ------------------------------------------------------------------------
> *From:* Ahmed Mohamed <mohamed using kuicr.kyoto-u.ac.jp>
> *Sent:* Monday, June 22, 2020 2:18 AM
> *To:* Martin Morgan <mtmorgan.bioc using gmail.com>
> *Cc:* Vincent Carey <stvjc using channing.harvard.edu>; Hervé Pagès 
> <hpages using fredhutch.org>; bioc-devel <bioc-devel using r-project.org>; Shepherd, 
> Lori <Lori.Shepherd using RoswellPark.org>
> *Subject:* Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly 
> from S4Vectors)
> Excellent catch Martin.
> I was able to confirm the issue using the script below (on Bioc-Devel 
> Docker). The issue was also resolved by simply reinstalling iheatmapr. 
> It would be great if iheatmapr is reinstalled manually on the devel 
> build systems.
> 
> remove.packages(c("iheatmapr", "S4Vectors"))
> devtools::install_github("Bioconductor/S4Vectors", 
> ref="e8dffc0157f2c4779fce3c85e5ef601bb0a35d33")
> install.packages("iheatmapr")
> packageVersion("S4Vectors")
> # "0.27.0"
> packageVersion("iheatmapr")
> # "0.4.12"
> library(lipidr)
> library(iheatmapr)
> example("iheatmap")
> # Runs successfully
> 
> ## Update S4Vector
> rm(list = ls())
> rstudioapi::restartSession()
> devtools::install_github("Bioconductor/S4Vectors")
> packageVersion("S4Vectors")
> # "0.27.12"
> 
> library(iheatmapr)
> example("iheatmap")
> # Error in .wrap_in_length_one_list_like_object(value, name, x) :
> #   failed to coerce 'list(value)' to a IheatmapPlots object of length 1
> 
> ## Reinstall iheatmapr
> rm(list = ls())
> rstudioapi::restartSession()
> install.packages("iheatmapr")
> library(iheatmapr)
> example("iheatmap")
> # Runs successfully
> 
> 
> Cheers.
> Ahmed.
> 
> On Thu, 18 Jun 2020 at 00:52, Martin Morgan <mtmorgan.bioc using gmail.com 
> <mailto:mtmorgan.bioc using gmail.com>> wrote:
> 
>     You can see package versions on the build system from
> 
>     https://bioconductor.org/checkResults/devel/bioc-LATEST/index.html
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1HWo5rIWA1m5ihxjEdHQES7eiiUCH5lqvmKOON4J2Nm8lJSd6ncmMQs2-5FhUktt5pXPTp1smrU6cKa4190T7elc944QS2Ydfuvp0t0c29VorU11a-5FJwrxBfbADYAfJGX5CDQJNzcBds5IVb-5FLtdmsg7t8Ld-5FJyXp3M7L7uW2MvmMMnH8ci3Phnzvw-5FiaOi0u9G-2Dl54dBJQI5av1sYcF-2DXB-2DchvqVtJ-5FdoIbdWZgo0cQbvpDTl4qwhMSI3-2DT5j57ghQcQiG5qiGemiudrobXzA6XqKDpvteiE2tnv1JEegc1WaEKcl6RRjDDR3DXUQOSDD-2Diwfdcr-5FfKL4y8BIfVSxVcfA9foqFw5ODRUoVPtzsaS0_https-253A-252F-252Fbioconductor.org-252FcheckResults-252Fdevel-252Fbioc-2DLATEST-252Findex.html&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=HMLRRZSzTs8eBf-GQBqLOx4AlcpY2d5kNsLvFPq7SQY&e=>
> 
>     clicking on 'installed pkgs' link in the center top table. iheatmapr
>     is at version 0.4.12.
> 
>     I think what is happening is like
>     https://support.bioconductor.org/p/131689/#131695
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1CwyVIg3N8SoBBwdD-5FFZCiSutr81swQb4KYpE6AXzbu-2DD36e-5F5eSxfAEMhJSyL-2DJ7KoruFV35JklCfpumYnw-5FPV4SpILT4B7wuZtuwXsxnWJYFdapO9ukunWgWn39PwtvG1o5zkiJjv1wwLOio-2D63U40zo3qPGplTSe3XQN4LtamopYmUBwTYsEewP58hJ4qna2-2DBpptSChUQo998UFg55JhNHe8ejCjdB1IvVvZSikJx2zpcqfEQZ-2DkvLK-5FNcASuHZk8jVRxH9LtAiCXae2enWAZvaXxUDc-2D-5F0Oiov8GTnMdglDnbpl2KouhuA9-5F2xdNAvcsZwWynXeOmu0sJhz8GA_https-253A-252F-252Fsupport.bioconductor.org-252Fp-252F131689-252F-2523131695&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=3KVxHEJz2pfQnC1j0ujPEyZd4m4g6K_HYtqOooMmNKA&e=>
>     where S4Vector method has been changed but packages that use it have
>     a methods table that is cached when the package is installed.
> 
>     So there are no errors if you do a new install of packages (like on
>     CI or the docker) but not if the iheatmapr package has already been
>     installed (as I guess on the build system).
> 
>     This means that the only way to reproduce this would be to install a
>     previous version of S4Vectors, then install iheatmapr to capture the
>     old methods table, then install the current version of S4Vectors.
>     But at the end of the day the solution is (a) for iheatmapr to be
>     updated on the build systems and ideally (b) for iheatmapr to bump
>     it's version. A version bump would be trivial if it were a
>     Bioconductor package, but could be problematic for CRAN. I did bcc
>     the maintainer.
> 
>     I don't think you should work around this (e.g., by disabling the
>     example) because, at least if it were me, I'd forget to reenable
>     this and hence end up with less extensive testing of my package (and
>     the overall Bioconductor ecosystem).
> 
>     Maybe @Hervé Pagès will chime in; my diagnosis could be wrong.
> 
>     Martin
> 
>     On 6/17/20, 6:56 AM, "Bioc-devel on behalf of Ahmed Mohamed"
>     <bioc-devel-bounces using r-project.org
>     <mailto:bioc-devel-bounces using r-project.org> on behalf of
>     mohamed using kuicr.kyoto-u.ac.jp <mailto:mohamed using kuicr.kyoto-u.ac.jp>> wrote:
> 
>          Thanks Vincent.
> 
>          I would like to debug the error, but I still cannot reproduce it.
>          SessionInfo, below, shows update to date versions! My Travis
>     build also
>          works, with Bioc Devel and iheapmapr 0.4.12 (
>     https://travis-ci.org/github/ahmohamed/lipidr/jobs/696329028#L2718
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1If8yOo3b-5FxBYYwzpHg-2Dc7ZSLnTAhugHgmCjgkxTHiPbgSmK-2DeSNwegV5ae-5Fl5VcGUe0rds-2Df7dFKtbjP7jCW1gpaFTioG1RhvwHy1xdrRWcQt-2DRqbT5PGC-5FIDlLdsQe132vjO1GjpChUt-5FK8tweNVhePXGcHlTmc-5FKOfzswdP-5F0X9YEmStFcons03ZGXW-2DlRS3oObzAeqSeuMiqJwarP6pM87LZPguM8Z6aotYwPlhBqwjaFubrbVbeQWJYtOkMXvOUzTo-2D0LaJAc1fhF7z-2DZNlnVXYTGY9b7Yh-2DOQrG9rQzucF3nO4J7jl48ZhfGNTuoNbb0e7opYwWBH7qWU-2Dptw_https-253A-252F-252Ftravis-2Dci.org-252Fgithub-252Fahmohamed-252Flipidr-252Fjobs-252F696329028-2523L2718&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=i4n6aBAm0IWMm11VV0AuKf-Jq61pEHvyTEZGu9MCpHE&e=>).
>     What
>          am I missing?
> 
>          > sessionInfo()R version 4.0.0 (2020-04-24)
>          Platform: x86_64-pc-linux-gnu (64-bit)
>          Running under: Ubuntu 18.04.4 LTS
> 
>          Matrix products: default
>          BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_1oB-2DH4JrlZ3Yw2PA1QlZgPu-2D-5FXEPyS21Qc6ieR-2DurRitGqbuk0Me344f9ma39c2DI9zAMJLdWApN4WESftimsVP0KegYiLOCcT8vFiUci3sKe0rUYtsktX5YSyEJXLBEt9y9ucaujFQYeZUdyqYdVcm94SMos00SQgQ6oK-5FPBNeHCk6ZnNtnKfoPhBQJ4Od-2DurXG9Y47nMj-5FURgWBajqf9spQcOmCUi9JWW6fbiPPcK1cDYYZ-2DgiE78iwi4fNHcQSJeltQd2s7VVYdbgj8Tmu-2DUW0evWQXfkqNWY7YFjVOlbLM1qiQ7s3VPbNtiv0BlhX_http-253A-252F-252Flibopenblasp-2Dr0.2.20.so&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=xNH-mluwP2TY76rL-3yFRqVFhl2nn1F9pzfXnWtuhuo&e=>
> 
>          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=C
>           [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] parallel  stats4    stats     graphics  grDevices utils
>          datasets  methods
>          [9] base
> 
>          other attached packages:
>           [1] lipidr_2.3.0                SummarizedExperiment_1.19.5
>          DelayedArray_0.15.4
>           [4] matrixStats_0.56.0          Matrix_1.2-18
>          Biobase_2.49.0
>           [7] GenomicRanges_1.41.5        GenomeInfoDb_1.25.2
>          IRanges_2.23.10
>          [10] S4Vectors_0.27.12           BiocGenerics_0.35.4
>          iheatmapr_0.4.12
>          [13] BiocManager_1.30.10
> 
>          loaded via a namespace (and not attached):
>           [1] fastcluster_1.1.25     tidyselect_1.1.0       xfun_0.14
>           [4] purrr_0.3.4            lattice_0.20-41        colorspace_1.4-1
>           [7] vctrs_0.3.1            generics_0.0.2         htmltools_0.5.0
>          [10] yaml_2.2.1             rlang_0.4.6            pillar_1.4.4
>          [13] glue_1.4.1             RColorBrewer_1.1-2   
>       GenomeInfoDbData_1.2.3
>          [16] lifecycle_0.2.0        plyr_1.8.6             zlibbioc_1.35.0
>          [19] munsell_0.5.0          gtable_0.3.0         
>       htmlwidgets_1.5.1
>          [22] knitr_1.28             forcats_0.5.0          Rcpp_1.0.4.6
>          [25] scales_1.1.1           limma_3.45.7           jsonlite_1.6.1
>          [28] XVector_0.29.2         farver_2.0.3           ggplot2_3.3.1
>          [31] digest_0.6.25          dplyr_1.0.0            ropls_1.21.0
>          [34] grid_4.0.0             tools_4.0.0            bitops_1.0-6
>          [37] magrittr_1.5           RCurl_1.98-1.2         tibble_3.0.1
>          [40] ggdendro_0.1-20        tidyr_1.1.0            crayon_1.3.4
>          [43] pkgconfig_2.0.3        MASS_7.3-51.5          ellipsis_0.3.1
>          [46] data.table_1.12.8      rstudioapi_0.11        R6_2.4.1
>          [49] compiler_4.0.0
> 
> 
>          On Wed, 17 Jun 2020 at 20:12, Vincent Carey
>     <stvjc using channing.harvard.edu <mailto:stvjc using channing.harvard.edu>>
>          wrote:
> 
>          > I can reproduce the error, which arises from iheatmapr.  Note
>     that
>          >
>          >
>          >
>     http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec1-R-instpkgs.html
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_1rYAquRJ83K8T643flMr-5FbBScyZIdY3FrFaIgQuLbXOutf-5FgMOARcKj8K0yRn8yfyYNA-2DtBjkjHdgxgEWDc0sGvqg-5Fvwn7R55w8NVN-2DSfRM2nbUZerRc7yDry-5FzAwNTTRRb9BOD3-2D7qkauyY76VrBbr7-2DzRaACgHUYUrHfL-2DylWki8L-2D1WdP3bSpJrKBeE3v2YastiiLk6nB5sjW8KdCTE3ZjdW4l6MsePg4bvxEPVErCoRuSnNH4IU-2DJINZxMtP4J0JI-2D0eSmEkbPZVyaDzghsrg43By7CkTcO8YBMGure9h-5F5T16JTLfyjcY9787BWxCIpuE3xpyIvTEyArZTcp-2DsdcJvAOq1DrOlGZADJbFlU_http-253A-252F-252Fbioconductor.org-252FcheckResults-252Fdevel-252Fbioc-2DLATEST-252Fmalbec1-2DR-2Dinstpkgs.html&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=Cb_3DEHAUwpHBeVUgnIthK0WvM_ANNSqXIzVMwgzRVY&e=>
>          >
>          > shows that iheatmapr is 0.4.12 and on my system
>     example(iheatmap) fails
>          > with the
>          > error you showed.  In future please provide sessionInfo()
>     result when
>          > reporting a
>          > problem.
>          >
>          > on my system, example(iheatmap) dies in an unexported function
>          > main_heatmap.  iheatmapr is an ropensci
>          > package that depends on S4Vectors.  it may only be tested
>     with the release
>          > version.  You
>          > can see at
>     https://travis-ci.org/github/ropensci/iheatmapr/jobs/698340792
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1toYZijsIXYXOR4zKGyDP7D87ey2EH-2DPxaCkim9T1DT0pvFx6FsE-5FVJB4nz0pjeqALv31old7FYtdr-2DrpkSDgjhNZ-5F-5F-5Fk2qnRRfJIaPq71xuxJBmBMfni8somrI-5FiZqUMK13nOQQmm5bLdh9-2DkDE-2DN5fWr6lHIP-5FzP4OfdkzPJ3XDsGIgFntgmMVGn8Lr7c1jxrbwjjM0jKzq08i2c2bUm1CTyNaEnjIMtHxFK4cMvlPgkcAm44HgS5V9Xxf9xvjTPuyqsYXu9PFIvp03yR44hWquLfDEHemNIOyMHP-2Dv9c2UBGlmBtvKSYYV-5F0Oq6Rrbhudfj-5FtpoQEfp09-5FHbHmoQ_https-253A-252F-252Ftravis-2Dci.org-252Fgithub-252Fropensci-252Fiheatmapr-252Fjobs-252F698340792&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=Ol2RXowKakW3QTRuo1MygsQslBjzJYzEcEkZm-e0P2o&e=>
>     that
>          > iheatmapr
>          > is passing its tests.  i don't know how to determine what
>     packages were
>          > used in the tests.
>          >
>          > you might want to condition out your example for now. 
>     perhaps you can
>          > debug iheatmapr against
>          > current S4Vectors and suggest the solution to iheatmapr authors
>          >
>          >
>          > On Wed, Jun 17, 2020 at 1:26 AM Ahmed Mohamed
>     <mohamed using kuicr.kyoto-u.ac.jp <mailto:mohamed using kuicr.kyoto-u.ac.jp>>
>          > wrote:
>          >
>          >> Hi all,
>          >>
>          >> My package "lipidr" has been failing checks for a while,
>     giving the error
>          >> below:
>          >>
>          >> Error in .wrap_in_length_one_list_like_object(value, name, x) :
>          >>   failed to coerce 'list(value)' to a IheatmapPlots object
>     of length 1
>          >>
>          >> (Full report here:
>          >>
>          >>
>     http://bioconductor.org/checkResults/devel/bioc-LATEST/lipidr/malbec1-checksrc.html
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_1BmOiFuqUzjQClVteG9kNuRUbaCYyUKcVPJCpRdxSZP0gTKw8ameWB9wiERTs4z4PDu0QUk7LJm2OtnUAbfa1I4j5le5O8d07Gbm-5Farj2XtmSi7lZHl75jGmsThiQv-2DFeQUH0gDkZMb1RiNWpPJVd8-5FhN84qX8baWqAWsMFZv17HnyHwYSd9-2DznXCojeUOB7q26Ht-5FB-2D5sVwuAJS3uKTt7NuarJEkEJYKU9iQdGqcyPlKNjZfbJkB-5Fz-5FmLtmcP8IHBQIcFFw5x30MSqPtogb0jSShK0GCo9zcC6Y3EpsqMFfkFiwrti6ne5hwKWY-5FWW6lEAw5zaPZ-5FzADRAqJGOkAhjFLLUHt7nDJlEa59HTg3EM_http-253A-252F-252Fbioconductor.org-252FcheckResults-252Fdevel-252Fbioc-2DLATEST-252Flipidr-252Fmalbec1-2Dchecksrc.html&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=Flv1K5xmBQs4Ul9Q0Kc62ea1zNaZ5fXNiOsiyudoF2Y&e=>
>          >> )
>          >>
>          >> The error seems to originate from S4Vectors package, which
>     lipidr depends
>          >> on (indirectly through SummarizedExperiment). However, I am
>     completely
>          >> unable to reproduce this error. This is what I did:
>          >> - Installed Bioc-devel docker image
>          >> - run the faulty example alone, as well as
>     devtools::check(), both without
>          >> errors.
>          >> - Ran BiocManager::install(update = TRUE) to pick up updates not
>          >> propagated
>          >> to the docker image
>          >> - I even installed S4Vector from GitHub, just in case the
>     git checkout is
>          >> ahead of Bioc.
>          >>
>          >> Faulty example:
>          >>
>     https://github.com/ahmohamed/lipidr/blob/master/R/plot.R#L345
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1OunJfN09-2D2MUlC7zx-2DCAGzhzcy7ZNxORtmk8rEtDuTbXlAvs4PoW4aX4j30HNb9yu3UixDykENvVjaeKhVQ4zultTujUqR9FIbHpE7MyhKt98YBG0tVROeEey6EXpQyiKKn-5FpiPHRd1vk80mfoYM-5FeaK6OCAuNgCEgigOERqksAttGjZmGj0WoWr-5F2PXYjh3mbH8fQaA5ctz19a8hAIEheM3Kib2PqIGxtI3eoEVuUG6qpXG4vsTxzc4o-5F1UQxEfUqP-2DCeAFOiWzilfvghN-5Fv1yDZklXca71b2V6Bec-2D4C06ZSqgQS4Nfm99TkLx0MjQ-5FMVzsmzCAKl9Kfnu9ukuTg_https-253A-252F-252Fgithub.com-252Fahmohamed-252Flipidr-252Fblob-252Fmaster-252FR-252Fplot.R-2523L345&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=7nWznxWtROBskBNWuHV-Y6DOI0p-pOmZMvsdpoHZVrc&e=>
>          >>
>          >> Any suggestions would be appreciated.
>          >> Thanks.
>          >> Ahmed.
>          >>
>          >>         [[alternative HTML version deleted]]
>          >>
>          >> _______________________________________________
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>          >>
>          >
>          > The information in this e-mail is intended only for
>     th...{{dropped:15}}
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