[Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

Stian Lågstad @t|@n|@g@t@d @end|ng |rom gm@||@com
Fri Apr 24 08:33:05 CEST 2020 

Thank you very much for the help so far!

On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès <hpages using fredhutch.org> wrote:

> OK, thanks testing that. This suggests that the problem is on our
> side... sigh! I will need to dig deeper into this.
>
> Best,
> H.
>
>
> On 4/23/20 22:57, Bemis, Kylie wrote:
> > Worked for me without errors or warnings:
> >
> > kuwisdelu using Eva-02-Dash Projects % R CMD build chimeraviz
> > * checking for file ‘chimeraviz/DESCRIPTION’ ... OK
> > * preparing ‘chimeraviz’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... OK
> > * checking for LF line-endings in source and make files and shell scripts
> > * checking for empty or unneeded directories
> > Removed empty directory ‘chimeraviz/docker’
> > * building ‘chimeraviz_1.13.8.tar.gz’
> >
> > kuwisdelu using Eva-02-Dash Projects % R CMD INSTALL chimeraviz_1.13.8.tar.gz
> > * installing to library ‘/Users/kuwisdelu/Library/R/4.0/library’
> > * installing *source* package ‘chimeraviz’ ...
> > ** using staged installation
> > ** 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 from temporary location
> > ** testing if installed package can be loaded from final location
> > ** testing if installed package keeps a record of temporary installation
> > path
> > * DONE (chimeraviz)
> >
> > Under:
> >
> >> sessionInfo()
> > R version 4.0.0 RC (2020-04-18 r78249)
> > Platform: x86_64-apple-darwin17.0 (64-bit)
> > Running under: macOS Catalina 10.15.3
> >
> > Matrix products: default
> > BLAS:
> > /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.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] stats     graphics  grDevices utils     datasets  methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_4.0.0 tools_4.0.0
> >
> > The vignette looks okay as far as I can tell.
> >
> > -Kylie
> >
> >
> >
> >
> >
> >
> >> On Apr 24, 2020, at 1:40 AM, Hervé Pagès <hpages using fredhutch.org
> >> <mailto:hpages using fredhutch.org>> wrote:
> >>
> >> Interesting indeed. Thanks for checking this.
> >>
> >> Even though I'm not sure what conclusion to draw from all this.
> >>
> >> Since you are on a Mac, can I ask you another big favor? Do you think
> >> you could run 'R CMD build' on chimeraviz and see if you can reproduce
> >> the error we see on the build report here:
> >>
> >>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2Fchimeraviz%2Fmachv2-buildsrc.html&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3D&reserved=0
> >> <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fbioconductor.org-252FcheckResults-252F3.11-252Fbioc-2DLATEST-252Fchimeraviz-252Fmachv2-2Dbuildsrc.html-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132939427-26amp-3Bsdata-3Ds9fJRfwSMO0UkPEwdmrW7mZhEM-252FgCOYtQm3HO12DknA-253D-26amp-3Breserved-3D0&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ChvNTQebsUvVKYAGSEtFgFNOcwgSzxXYjQ69oO9oBM0&s=Rkoe-LwrUsVZyqv9zyv00KH__7fWXhf-n8-ZTmYFdP4&e=
> >
> >>
> >> Get the source with
> >>
> >>  git clone
> >>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeraviz&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3D&reserved=0
> >>
> >> Thanks,
> >> H.
> >>
> >>
> >> On 4/23/20 21:55, Bemis, Kylie wrote:
> >>> That’s interesting. I did:
> >>>> BiocManager::install("Cardinal", type="mac.binary.el-capitan”)
> >>>> browseVignettes("Cardinal")
> >>> from R 3.6.3, and the figures using transparency in the vignettes
> >>> look fine to me.
> >>> When I use X11() to reproduce the warning locally, the transparent
> >>> colors get truncated, so that the higher-alpha colors appear opaque
> >>> and the lower-alpha colors don’t appear at all.
> >>> However, in the merida1 vignette, the figures appear as I’d normally
> >>> get form quartz() or pdf() locally, which don’t produce warnings for
> >>> me on macOS 10.15.3.
> >>> -Kylie
> >>>> On Apr 24, 2020, at 12:39 AM, Hervé Pagès <hpages using fredhutch.org
> >>>> <mailto:hpages using fredhutch.org>> wrote:
> >>>>
> >>>> Hi Kylie,
> >>>>
> >>>> I get the warnings on merida1 for Cardinal too e.g. when I run the
> >>>> code in the Cardinal-2-stats vignette:
> >>>>
> >>>>    merida1:vignettes biocbuild$ pwd
> >>>>    /Users/biocbuild/bbs-3.10-bioc/meat/Cardinal/vignettes
> >>>>
> >>>>    merida1:vignettes biocbuild$ R CMD Stangle Cardinal-2-stats.Rmd
> >>>>    Output file:  Cardinal-2-stats.R
> >>>>
> >>>>    merida1:vignettes biocbuild$ R
> >>>>    ...
> >>>>    > source("Cardinal-2-stats.R", echo=TRUE)
> >>>>    ...
> >>>>    There were 14 warnings (use warnings() to see them)
> >>>>    > warnings()
> >>>>    Warning messages:
> >>>>    1: In rect(left, top, r, b, angle = angle, density = density,  ...
> :
> >>>>      semi-transparency is not supported on this device: reported
> >>>> only once per page
> >>>>    2: In rect(left, top, r, b, angle = angle, density = density,  ...
> :
> >>>>      semi-transparency is not supported on this device: reported
> >>>> only once per page
> >>>>    ...
> >>>>
> >>>> The thing is that 'R CMD build' does not display warnings, unless
> >>>> there is an error. Maybe that's why you've never seen them until now
> >>>> because of the error you have on machv2 (and other platforms).
> >>>>
> >>>> It's be interesting to know if the plots included in the vignette
> >>>> are actually OK. Have you checked them? You can do this by
> >>>> installing the Mac binary for Cardinal in BioC 3.10 with:
> >>>>
> >>>>    BiocManager::install("Cardinal", type="mac.el-capitan.binary")
> >>>>
> >>>> (make sure you do this in R 3.6). This will install the vignette
> >>>> generated on merida1. Then open the vignette via
> >>>> browseVignettes("Cardinal") and check the plots. Do they look ok
> >>>> despite the "semi-transparency" problem?
> >>>>
> >>>> Thanks,
> >>>> H.
> >>>>
> >>>>
> >>>>
> >>>> On 4/23/20 20:39, Bemis, Kylie wrote:
> >>>>> I’m now seeing the same "semi-transparency" error on my Mac builds
> >>>>> for Cardinal. My vignettes have used transparency for years now and
> >>>>> this has never been an issue before (on merida1 or otherwise).
> >>>>> I can reproduce the error locally with an X11() device, but not
> >>>>> with quartz(), png(), png(), etc.
> >>>>> (Note that my Cardinal 2.5.9 builds are currently failing due to an
> >>>>> unrelated issue that I’ve since fixed, but the build system hasn’t
> >>>>> gotten to 2.5.11 yet.)
> >>>>> ~~~
> >>>>> Kylie Ariel Bemis (she/her)
> >>>>> Khoury College of Computer Sciences
> >>>>> Northeastern University
> >>>>> kuwisdelu.github.io
> >>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__kuwisdelu.github.io%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DNl-SFGWHUlZqtDsccYwD2EHptbV_1lbboQkoGIwfeKI%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=wWHZczFLad0imdTwrpSBsiqqdYyTX09n0MNXkpdpFVo%3D&reserved=0>
>
> >>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__kuwisdelu.github.io%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DiIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU%26s%3DitZMZz7G1z4hEn_h6m-WLnSXgIbD-41KOovzdseVHT4%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=zcOG%2BEG%2Bk16OXD2SN6pCGrZrQX8Rpwpx07gqYuBGPBE%3D&reserved=0
> >>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fkuwisdelu.github.io-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DiIfSQOsSomvKm-5F1GHwSPKYxnfvicYz3rNyk04PTXhxU-2526s-253DitZMZz7G1z4hEn-5Fh6m-2DWLnSXgIbD-2D41KOovzdseVHT4-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233000008658074-26amp-3Bsdata-3D9TmRy1lpNBJjGLZcqPqJY-252BMP32z2kgbsmTdvSn4RUk8-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DhNiYK5Qxom3Q8JMAgB15vH_K86oAT1s-ZFy1NFMtBcw%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=F9edg0Pf5jT9RZGC8B%2FIxJvV4DpW8Ztv3ZUDkw06tcs%3D&reserved=0
> >>
> >>>>>> On Apr 23, 2020, at 11:28 PM, Hervé Pagès <hpages using fredhutch.org
> >>>>>> <mailto:hpages using fredhutch.org> <mailto:hpages using fredhutch.org>> wrote:
> >>>>>>
> >>>>>> Ok so I'm changing my mind about this. I suspect that the error is
> >>>>>> actually related to the warning. The error comes from the magick
> >>>>>> package (a wrapper around the ImageMagick software) and it
> >>>>>> indicates a failure to crop an empty image. It can easily be
> >>>>>> reproduced with:
> >>>>>>
> >>>>>>  ## Generate an empty image.
> >>>>>>  png("myplot.png", bg="transparent")
> >>>>>>  plot.new()
> >>>>>>  dev.off()
> >>>>>>
> >>>>>>  ## Try to crop it.
> >>>>>>  magick::image_trim(magick::image_read("myplot.png"))
> >>>>>>  # Error in magick_image_trim(image, fuzz) :
> >>>>>>  #   R: GeometryDoesNotContainImage `/Users/biocbuild/myplot.png'
> >>>>>> @ # warning/attribute.c/GetImageBoundingBox/247
> >>>>>>
> >>>>>> So I suspect that what happens is that the images generated on Mac
> >>>>>> by the code in the vignette are empty (because of the
> >>>>>> semi-transparency problem on Mac) which would explain why later
> >>>>>> knitr fails to crop them (it uses magick::image_trim() for that).
> >>>>>>
> >>>>>> I don't exactly understand why we wouldn't have seen the problem
> >>>>>> on merida1 though (same version of knitr (1.28) and magick (2.3)
> >>>>>> on both machines) but it seems that chimeraviz has changed
> >>>>>> significantly between BioC 3.10 and 3.11. Did you start using
> >>>>>> semi-transparency recently in your plots?
> >>>>>>
> >>>>>> Best,
> >>>>>> H.
> >>>>>>
> >>>>>>
> >>>>>> On 4/23/20 19:42, Hervé Pagès wrote:
> >>>>>>> Hi Stian,
> >>>>>>> I went on machv2 and gave this a shot. I can reproduce the
> >>>>>>> GeometryDoesNotContainImage error in an interactive session. I
> >>>>>>> don't have an answer yet but I was curious about the
> >>>>>>> "semi-transparency is not supported on this device" warning and
> >>>>>>> was wondering if it could somehow be related with the error.
> >>>>>>> It turns out that the warning is actually easy to reproduce on a
> >>>>>>> Mac with something like this:
> >>>>>>> plot.new()
> >>>>>>> lines(c(0.1, 0.22), c(0.5, 0.44), type = "l", lwd = 1, col =
> >>>>>>> "#FF000080")
> >>>>>>> I think that the 4th byte (80) in the color specification
> >>>>>>> ("#FF000080") is the level of transparency.
> >>>>>>> I can get this warning on machv2 **and** merida1. Some googling
> >>>>>>> indicates that this is a pretty common warning on Mac. Since we
> >>>>>>> don't get the vignette error on merida1 I think it's unlikely
> >>>>>>> that the warning is related to the error.
> >>>>>>> I'll keep investigating the GeometryDoesNotContainImage error...
> >>>>>>> H.
> >>>>>>> On 4/22/20 01:59, Stian Lågstad wrote:
> >>>>>>>> I'm still unable to reproduce this error on my end. If anyone
> >>>>>>>> with a mac
> >>>>>>>> could try building locally I would be very grateful. Thanks.
> >>>>>>>>
> >>>>>>>> On Sat, Apr 18, 2020 at 4:06 PM Stian Lågstad
> >>>>>>>> <stianlagstad using gmail.com <mailto:stianlagstad using gmail.com>
> >>>>>>>> <mailto:stianlagstad using gmail.com>>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> Hi,
> >>>>>>>>>
> >>>>>>>>> I'm haven't been able to figure out this error for the latest
> >>>>>>>>> machv2 build
> >>>>>>>>> for chimeraviz:
> >>>>>>>>>
> >>>>>>>>> ```
> >>>>>>>>> Warning in doTryCatch(return(expr), name, parentenv, handler) :
> >>>>>>>>> semi-transparency is not supported on this device: reported
> >>>>>>>>> only once
> >>>>>>>>> per page
> >>>>>>>>> Quitting from lines 108-126 (chimeraviz-vignette.Rmd)
> >>>>>>>>> Error: processing vignette 'chimeraviz-vignette.Rmd' failed with
> >>>>>>>>> diagnostics:
> >>>>>>>>> R: GeometryDoesNotContainImage
> >>>>>>>>>
> `/private/tmp/RtmpdBrrvk/Rbuild9ed5154894cc/chimeraviz/vignettes/chimeraviz-vignette_files/figure-html/unnamed-chunk-7-1.png'
> >>>>>>>>> @ warning/attribute.c/GetImageBoundingBox/247
> >>>>>>>>> --- failed re-building ‘chimeraviz-vignette.Rmd’
> >>>>>>>>> ```
> >>>>>>>>>
> >>>>>>>>> The build in question:
> >>>>>>>>>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_chimeraviz_machv2-2Dbuildsrc.html%26d%3DDwIFaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DQ1W5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM%26s%3DA7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=%2BST%2B9JRGaOFHqb2h49INMs6j%2FmHm0PRG9q7OF5uQoa4%3D&reserved=0
> >>>>>>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fbioconductor.org-5FcheckResults-5F3.11-5Fbioc-2D2DLATEST-5Fchimeraviz-5Fmachv2-2D2Dbuildsrc.html-2526d-253DDwIFaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DQ1W5ctHOQ2Hjw49pX7VAGBn7-2Du5l3mAqH1rt9tFNnZM-2526s-253DA7jGEFF5ehz2Hsxmlr-5FvGmPSX3Xy2SwZErgyi1mPIuw-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233000008658074-26amp-3Bsdata-3D8wwh50TVSe-252Fg8Sc5v4byXWZkGcPD8yFlOZ-252BXokB06Ek-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DViG1kLLmQ4IsrAfoOC2NlhmKzDfQMaiTazXwnIYAfuQ%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=O1L2hRELSaa12YA27PJTTGV2xYSXNrJjPEVUugiHIvk%3D&reserved=0>
>
> >>>>>>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fbioconductor.org-5FcheckResults-5F3.11-5Fbioc-2D2DLATEST-5Fchimeraviz-5Fmachv2-2D2Dbuildsrc.html-2526d-253DDwIFaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DQ1W5ctHOQ2Hjw49pX7VAGBn7-2Du5l3mAqH1rt9tFNnZM-2526s-253DA7jGEFF5ehz2Hsxmlr-5FvGmPSX3Xy2SwZErgyi1mPIuw-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C0fefe5ade3994ca1943e08d7e7ff9084-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637232957151727562-26amp-3Bsdata-3Djz-252FO8NrKC2VZTuK4Z-252F7Fo19ExLg9d1C4LpzbZddhcQ8-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DiIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU%26s%3DP62BYr_gq2eIDAUWhWL4PX7IoRmhTn06cUUU4o6QdPE%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=rQh%2FUV6sIvnCnD48zlsTyRsX7fASsifp%2FJWyKKMaHOI%3D&reserved=0
> >>>>>>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fnam05.safelinks.protection.outlook.com-5F-2D3Furl-2D3Dhttps-2D253A-2D252F-2D252Furldefense.proofpoint.com-2D252Fv2-2D252Furl-2D253Fu-2D253Dhttp-2D2D3A-2D5F-2D5Fbioconductor.org-2D5FcheckResults-2D5F3.11-2D5Fbioc-2D2D2DLATEST-2D5Fchimeraviz-2D5Fmachv2-2D2D2Dbuildsrc.html-2D2526d-2D253DDwIFaQ-2D2526c-2D253DeRAMFD45gAfqt84VtBcfhQ-2D2526r-2D253DBK7q3XeAvimeWdGbWY-2D5FwJYbW0WYiZvSXAJJKaaPhzWA-2D2526m-2D253DQ1W5ctHOQ2Hjw49pX7VAGBn7-2D2Du5l3mAqH1rt9tFNnZM-2D2526s-2D253DA7jGEFF5ehz2Hsxmlr-2D5FvGmPSX3Xy2SwZErgyi1mPIuw-2D2526e-2D253D-2D26amp-2D3Bdata-2D3D02-2D257C01-2D257Ck.bemis-2D2540northeastern.edu-2D257C0fefe5ade3994ca1943e08d7e7ff9084-2D257Ca8eec281aaa34daeac9b9a398b9215e7-2D257C0-2D257C0-2D257C637232957151727562-2D26amp-2D3Bsdata-2D3Djz-2D252FO8NrKC2VZTuK4Z-2D252F7Fo19ExLg9d1C4LpzbZddhcQ8-2D253D-2D26amp-2D3Breserved-2D3D0-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DiIfSQOsSomvKm-5F1GHwSPKYxnfvicYz3rNyk04PTXhxU-2526s-253DP62BYr-5Fgq2eIDAUWhWL4PX7IoRmhTn06cUUU4o6QdPE-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233000008658074-26amp-3Bsdata-3DFDVD5ELC9sRWdB3VwJv3Fk9sZI9Zlm6sTh-252B1wYcPC1M-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DEwfAyleMRqJuyYNqmAeQs8dfpFeb8JeajCsvtlSfoOI%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=vxu8Yw6yBfPk0ryXJCqQ%2B5F6xQ7fYOCo4ZxUZPLn1qo%3D&reserved=0
> >>
> >>>>>>>>>
> >>>>>>>>> If anyone has seen something like this before then I'd
> >>>>>>>>> appreciate some
> >>>>>>>>> help. Thank you!
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> Stian Lågstad
> >>>>>>>>> +47 41 80 80 25
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> 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:hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> >>>>>> <mailto:hpages using fredhutch.org>
> >>>>>> Phone:  (206) 667-5791
> >>>>>> Fax:    (206) 667-1319
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
> >>>>>> <mailto:Bioc-devel using r-project.org>mailing list
> >>>>>>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=Bdf8dvgaOBLd7EvbwojiUrB1cuLxzLq4FoIqWHj6aKA%3D&reserved=0
> >>>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fstat.ethz.ch-252Fmailman-252Flistinfo-252Fbioc-2Ddevel-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233000008658074-26amp-3Bsdata-3DcvG4Wy-252Fl-252BP5pSYfwgdDJiHwZwvlTGBbKmFFSJoruaMg-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3D4og1ORz-6_eQYm-M4A52k_q-zwqtsZzzQd1ZKgDmQ9o%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132959412&sdata=OtPn85TZoVi80MjQRWODH4%2FHvfMS53mg9byP0DMg8W0%3D&reserved=0>
>
> >>>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fstat.ethz.ch-252Fmailman-252Flistinfo-252Fbioc-2Ddevel-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C0fefe5ade3994ca1943e08d7e7ff9084-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637232957151727562-26amp-3Bsdata-3D-252BSIWViTvvcbrxJdXzw0IobmTldrBgK4DNLz-252F-252B2QJb-252FI-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DiIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU%26s%3DC9R31cXoa76n1W0GH-SVyVxgikFTCUbcJ9kdZqLu1-g%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132959412&sdata=F5tQarKC%2B3TgOvA2eHlKKycL5pb5a4X879efzDBm7R4%3D&reserved=0
> >>>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fnam05.safelinks.protection.outlook.com-5F-2D3Furl-2D3Dhttps-2D253A-2D252F-2D252Fstat.ethz.ch-2D252Fmailman-2D252Flistinfo-2D252Fbioc-2D2Ddevel-2D26amp-2D3Bdata-2D3D02-2D257C01-2D257Ck.bemis-2D2540northeastern.edu-2D257C0fefe5ade3994ca1943e08d7e7ff9084-2D257Ca8eec281aaa34daeac9b9a398b9215e7-2D257C0-2D257C0-2D257C637232957151727562-2D26amp-2D3Bsdata-2D3D-2D252BSIWViTvvcbrxJdXzw0IobmTldrBgK4DNLz-2D252F-2D252B2QJb-2D252FI-2D253D-2D26amp-2D3Breserved-2D3D0-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DiIfSQOsSomvKm-5F1GHwSPKYxnfvicYz3rNyk04PTXhxU-2526s-253DC9R31cXoa76n1W0GH-2DSVyVxgikFTCUbcJ9kdZqLu1-2Dg-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233000008658074-26amp-3Bsdata-3DL9rgvm-252BjOc-252BBTKrFY5zIclFbhscIsxz7qg67vuboNTU-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DPxStlSRhyaALfrbWZTFzMEQK_jGGExRUIY_1b6fahV8%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132959412&sdata=8OchQZ6XXi4D%2BVW17BTOPlqSJGNnnSGRWQZ%2BX3U4%2Fws%3D&reserved=0
> >>
> >>>>
> >>>> --
> >>>> 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: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> >>>> Phone:  (206) 667-5791
> >>>> Fax:    (206) 667-1319
> >>
> >> --
> >> 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: hpages using fredhutch.org
> >> Phone:  (206) 667-5791
> >> Fax:    (206) 667-1319
> >
>
> --
> 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: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>


-- 
Stian Lågstad
+47 41 80 80 25

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