[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
Wed Mar 31 11:55:51 CEST 2021
Thank you very much, Hervé!
On Wed, Mar 31, 2021 at 8:25 AM Hervé Pagès <hpages.on.github using gmail.com>
wrote:
> Hi Stian,
>
> I know I know, this thread is almost 1 year old. I had s sticker hanging
> around to remind me about this, and, today, I spent the entire afternoon
> looking into this, found the problem, and implemented a fix.
>
> Long story short: On our Mac builders, the png() device was using the
> "Xlib" type by default. Problem is that png(type="Xlib") does not
> support semi-transparency (and this seems to be the case on all Mac and
> Linux systems). I changed this to use the "cairo" type by default (this
> is the default on Linux). With this change, I was finally able to run 'R
> CMD build chimeraviz' successfully on the machine.
>
> I also found out that this problem was also breaking the srnadiff package.
>
> We won't see the effect of that change on today's build report, but
> hopefully we will on tomorrow's report.
>
> Cheers,
> H.
>
>
> On 4/23/20 11:33 PM, Stian Lågstad wrote:
> > Thank you very much for the help so far!
> >
> > On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès <hpages using fredhutch.org
> > <mailto: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>
> > >> <mailto: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=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=Ctw0qHipP04y4qx-EQjnkqzp78H_pYbqbG_EiKD10Ck&e=
> >
> >
> > >>
> > <
> 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=
> > <
> 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
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fgit.bioconductor.org-252Fpackages-252Fchimeraviz-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132939427-26amp-3Bsdata-3DcTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=AXA8I4gFAwdgs59Y6c4xB0rKpoJxZBRSmj7CF6rk8oY&e=
> >
> > >>
> > >> 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>
> > >>>> <mailto: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://urldefense.proofpoint.com/v2/url?u=http-3A__kuwisdelu.github.io&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=aHFesaMDD1xg6qfVuQHWI8uVD0SjqQYShilwF3LXitI&e=
> >
> >
> > >>>>>
> > <
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fkuwisdelu.github.io-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DCO4n-5F-5FSJ6oQxnPyEFpNoDuHw2Pa0aC-5FCznlpINGGORQ-2526s-253DNl-2DSFGWHUlZqtDsccYwD2EHptbV-5F1lbboQkoGIwfeKI-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132939427-26amp-3Bsdata-3DwWHZczFLad0imdTwrpSBsiqqdYyTX09n0MNXkpdpFVo-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=UX2KssuP147meAevPkdWXdnsU2FL7Eb7AwzQjVu647I&e=
> >>
> >
> > >>>>>
> > <
> 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://urldefense.proofpoint.com/v2/url?u=https-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-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132939427-26amp-3Bsdata-3DzcOG-252BEG-252Bk16OXD2SN6pCGrZrQX8Rpwpx07gqYuBGPBE-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=pBQU-kt89IsXMVmzhkQKstOEQnAdLuyYSqJDympr0Qg&e=
> >
> >
> > >>>>>
> > <
> 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
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-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-2D253Dhttps-2D2D3A-2D5F-2D5Fkuwisdelu.github.io-2D2526d-2D253DDwMGaQ-2D2526c-2D253DeRAMFD45gAfqt84VtBcfhQ-2D2526r-2D253DBK7q3XeAvimeWdGbWY-2D5FwJYbW0WYiZvSXAJJKaaPhzWA-2D2526m-2D253DiIfSQOsSomvKm-2D5F1GHwSPKYxnfvicYz3rNyk04PTXhxU-2D2526s-2D253DitZMZz7G1z4hEn-2D5Fh6m-2D2DWLnSXgIbD-2D2D41KOovzdseVHT4-2D2526e-2D253D-2D26amp-2D3Bdata-2D3D02-2D257C01-2D257Ck.bemis-2D2540northeastern.edu-2D257C557e92d7107a41f63ec208d7e8098af2-2D257Ca8eec281aaa34daeac9b9a398b9215e7-2D257C0-2D257C0-2D257C637233000008658074-2D26amp-2D3Bsdata-2D3D9TmRy1lpNBJjGLZcqPqJY-2D252BMP32z2kgbsmTdvSn4RUk8-2D253D-2D26amp-2D3Breserved-2D3D0-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DCO4n-5F-5FSJ6oQxnPyEFpNoDuHw2Pa0aC-5FCznlpINGGORQ-2526s-253DhNiYK5Qxom3Q8JMAgB15vH-5FK86oAT1s-2DZFy1NFMtBcw-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132949421-26amp-3Bsdata-3DF9edg0Pf5jT9RZGC8B-252FIxJvV4DpW8Ztv3ZUDkw06tcs-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=2IO475KGvDe0YZL08WIHwh6hWOihqMx7vuTj-8l7Nks&e=
> >>>
> > >>>>>> On Apr 23, 2020, at 11:28 PM, Hervé Pagès
> > <hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> > >>>>>> <mailto:hpages using fredhutch.org <mailto: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 <mailto: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://urldefense.proofpoint.com/v2/url?u=https-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-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132949421-26amp-3Bsdata-3D-252BST-252B9JRGaOFHqb2h49INMs6j-252FmHm0PRG9q7OF5uQoa4-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=DPPCsOoDgnxzMGQHzcgNILTAy4LkBlQQnn1sHeAWMaE&e=
> >
> >
> > >>>>>>>>>
> > <
> 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://urldefense.proofpoint.com/v2/url?u=https-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-2D257C557e92d7107a41f63ec208d7e8098af2-2D257Ca8eec281aaa34daeac9b9a398b9215e7-2D257C0-2D257C0-2D257C637233000008658074-2D26amp-2D3Bsdata-2D3D8wwh50TVSe-2D252Fg8Sc5v4byXWZkGcPD8yFlOZ-2D252BXokB06Ek-2D253D-2D26amp-2D3Breserved-2D3D0-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DCO4n-5F-5FSJ6oQxnPyEFpNoDuHw2Pa0aC-5FCznlpINGGORQ-2526s-253DViG1kLLmQ4IsrAfoOC2NlhmKzDfQMaiTazXwnIYAfuQ-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132949421-26amp-3Bsdata-3DO1L2hRELSaa12YA27PJTTGV2xYSXNrJjPEVUugiHIvk-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=PZzU2vbTUDgTCF2ZjzMX6oxRmZZhR0K5ZASxcgeCNwU&e=
> >>
> >
> > >>>>>>>>>
> > <
> 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://urldefense.proofpoint.com/v2/url?u=https-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-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132949421-26amp-3Bsdata-3DrQh-252FUV6sIvnCnD48zlsTyRsX7fASsifp-252FJWyKKMaHOI-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=nJ9jG6zUxUi6FzHLsanvcCG78aeVBaCo3Fiv2trGHzU&e=
> >
> >
> > >>>>>>>>>
> > <
> 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
> > <
> 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:E-mail%3Ahpages using fredhutch.org> <mailto:hpages using fredhutch.org
> > <mailto: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 <mailto: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://urldefense.proofpoint.com/v2/url?u=https-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-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132949421-26amp-3Bsdata-3DBdf8dvgaOBLd7EvbwojiUrB1cuLxzLq4FoIqWHj6aKA-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=sf_oqqXGOjYWrVP2lvkzrXwYssGSxkNujZo9hMlHL3A&e=
> >
> >
> > >>>>>>
> > <
> 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://urldefense.proofpoint.com/v2/url?u=https-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-2D257C557e92d7107a41f63ec208d7e8098af2-2D257Ca8eec281aaa34daeac9b9a398b9215e7-2D257C0-2D257C0-2D257C637233000008658074-2D26amp-2D3Bsdata-2D3DcvG4Wy-2D252Fl-2D252BP5pSYfwgdDJiHwZwvlTGBbKmFFSJoruaMg-2D253D-2D26amp-2D3Breserved-2D3D0-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DCO4n-5F-5FSJ6oQxnPyEFpNoDuHw2Pa0aC-5FCznlpINGGORQ-2526s-253D4og1ORz-2D6-5FeQYm-2DM4A52k-5Fq-2DzwqtsZzzQd1ZKgDmQ9o-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132959412-26amp-3Bsdata-3DOtPn85TZoVi80MjQRWODH4-252FHvfMS53mg9byP0DMg8W0-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=7oAkWLXDKn_jTWvmd9hBbQvbCInz8emWYaXlmzQRqSY&e=
> >>
> >
> > >>>>>>
> > <
> 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://urldefense.proofpoint.com/v2/url?u=https-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-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132959412-26amp-3Bsdata-3DF5tQarKC-252B3TgOvA2eHlKKycL5pb5a4X879efzDBm7R4-253D-26amp-3Breserved-3D0&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=spDwGebzwvYFmsfil8jbkf1ixWYz45Vu5uuTNE1srvo&s=BEfagcSzqnbDfv-Zp0aC_xxqAoVPWio7bpDlRDOuRXM&e=
> >
> >
> > >>>>>>
> > <
> 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
> > <
> 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>
> > <mailto: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 <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 <mailto:hpages using fredhutch.org>
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> >
> >
> >
> > --
> > Stian Lågstad
> > +47 41 80 80 25
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
--
Stian Lågstad
+47 41 80 80 25
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