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

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Fri Apr 24 08:08:18 CEST 2020 

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

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