[Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0
Leonardo Collado Torres
lcoll@do @ending from jhu@edu
Thu Aug 2 20:22:38 CEST 2018
Thanks Hervé and no problem about the Windows binary.
Richard did get DelayedArray installed today (I think using biocLite)! ^^
Best,
Leo
On Thu, Aug 2, 2018 at 1:59 PM Hervé Pagès <hpages using fredhutch.org> wrote:
>
> Hi Leonardo,
>
> Hope you were able to solve your connection problems.
> Just to let you that I fixed the DelayedArray timeout on
> Windows and the zip files are now available for this
> platform:
>
> https://bioconductor.org/packages/DelayedArray
>
> Sorry for the inconvenience.
>
> Cheers,
> H.
>
>
> On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
> > Hi,
> >
> > Just as a quick update. Everything worked yesterday when Richard used
> > another PC computer from his home (another network). So it's
> > definitely not a Bioc problem.
> >
> > Yet I have no idea how to troubleshoot it beyond burning it all and
> > starting from scratch: re-installing R and everything and checking if
> > that works. Well, or testing using a hotspot wifi connection with one
> > of our phones and seeing if that works to bypass the wifi network from
> > work.
> >
> > Best,
> > Leo
> >
> > On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr. <tim.triche using gmail.com>
> wrote:
> >>
> >> are you sure his tmp directory isn't full
> >>
> >> --t
> >>
> >>
> >> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres <
> lcollado using jhu.edu> wrote:
> >>>
> >>> From Richard:
> >>>
> >>>> BiocManager::install("DelayedArray")
> >>>
> >>> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
> >>>
> >>> Installing package(s) 'BiocVersion', 'DelayedArray'
> >>>
> >>> trying URL '
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ&e=
> '
> >>>
> >>> Content type 'application/zip' length 8649 bytes
> >>>
> >>> downloaded 8649 bytes
> >>>
> >>>
> >>>
> >>> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
> >>>
> >>>
> >>>
> >>> The downloaded binary packages are in
> >>>
> >>> C:\Users\Richard
> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
> >>>
> >>> installing the source package ‘DelayedArray’
> >>>
> >>>
> >>>
> >>> trying URL '
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY&e=
> '
> >>>
> >>> Content type 'application/x-gzip' length 486139 bytes (474 KB)
> >>>
> >>> downloaded 474 KB
> >>>
> >>>
> >>>
> >>> Error in untar2(tarfile, files, list, exdir, restore_times) :
> >>>
> >>> incomplete block on file
> >>>
> >>> In R CMD INSTALL
> >>>
> >>>
> >>>
> >>> The downloaded source packages are in
> >>>
> >>> ‘C:\Users\Richard
> >>> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
> >>>
> >>> installation path not writeable, unable to update packages: foreign,
> >>> MASS, mgcv, survival
> >>>
> >>> Update old packages: 'openssl', 'stringi'
> >>>
> >>> Update all/some/none? [a/s/n]:
> >>>
> >>> n
> >>>
> >>> Warning message:
> >>>
> >>> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
> >>>
> >>> installation of package ‘DelayedArray’ had non-zero exit status
> >>>
> >>>>
> >>>
> >>>
> >>>
> >>> Also, at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_bioc_html_DelayedArray.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=sIiQvz3aJN2aHqxD1FLQLygGYRequcJnj2ywQlGrkds&e=
> >>> I don't see the tar for the Windows binary.
> >>>
> >>>
> >>>
> >>>
> >>> On Mon, Jul 30, 2018 at 2:57 PM Tim Triche, Jr. <tim.triche using gmail.com>
> wrote:
> >>>>
> >>>> BiocManager::install(whatever) doesn't work?
> >>>>
> >>>> biocLite is supposed to die, you see...
> >>>>
> >>>>
> >>>> --t
> >>>>
> >>>>
> >>>> On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres <
> lcollado using jhu.edu> wrote:
> >>>>>
> >>>>> Hi bioc-devel,
> >>>>>
> >>>>> A co-worker of mine (Richard) tried several times to install the
> >>>>> DelayedArray package. We got a couple of errors but it ultimately
> >>>>> looks like it's an internet connection problem. The truth is that
> >>>>> might be something affecting us on our side since I can't access
> >>>>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.comunidadbioinfo.org_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=mqn4K670CsFEqikTzeMFSYQasmpt-lJcGZNmmpMUFFA&e=
> either but collaborators in Mexico
> >>>>> (cc'ed) can right now. Me (on a Mac) and Emily (on a PC) on the same
> >>>>> network can't access that website.
> >>>>>
> >>>>> One of the errors we saw with Richard (on a PC) was about a missing
> >>>>> tar block. We failed to save that error message (for what's it's
> >>>>> worth, that was using RStudio). We then tried again and ran into this
> >>>>> error:
> >>>>>
> >>>>>> ## try http:// if https:// URLs are not supported
> >>>>>
> >>>>>> source("
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_biocLite.R&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=iQdulMCYkOcfK1OVbMaabLmodIoXbm_0o-E_wljDJq8&e=
> ")
> >>>>>
> >>>>> Error in file(filename, "r", encoding = encoding) :
> >>>>>
> >>>>> cannot open the connection
> >>>>>
> >>>>> In addition: Warning message:
> >>>>>
> >>>>> In file(filename, "r", encoding = encoding) :
> >>>>>
> >>>>> InternetOpenUrl failed: 'A connection with the server could not be
> >>>>> established'
> >>>>>
> >>>>>> source("
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_biocLite.R&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=E_aXM9k6x5bj6QJvBcCq62cBqo8bRrI8t2yBsLDIip0&e=
> ")
> >>>>>
> >>>>> Error in file(filename, "r", encoding = encoding) :
> >>>>>
> >>>>> cannot open the connection
> >>>>>
> >>>>> In addition: Warning message:
> >>>>>
> >>>>> In file(filename, "r", encoding = encoding) :
> >>>>>
> >>>>> InternetOpenUrl failed: 'A connection with the server could not be
> >>>>> established'
> >>>>>
> >>>>>> sessionInfo()
> >>>>>
> >>>>> R version 3.5.0 (2018-04-23)
> >>>>>
> >>>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
> >>>>>
> >>>>> Running under: Windows 10 x64 (build 17134)
> >>>>>
> >>>>>
> >>>>>
> >>>>> Matrix products: default
> >>>>>
> >>>>>
> >>>>>
> >>>>> locale:
> >>>>>
> >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> >>>>> States.1252 LC_MONETARY=English_United States.1252
> >>>>>
> >>>>> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
> >>>>>
> >>>>>
> >>>>>
> >>>>> attached base packages:
> >>>>>
> >>>>> [1] stats graphics grDevices utils datasets methods base
> >>>>>
> >>>>>
> >>>>>
> >>>>> loaded via a namespace (and not attached):
> >>>>>
> >>>>> [1] compiler_3.5.0
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On my Mac however, I can install DelayedArray.
> >>>>>
> >>>>>> source('
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_biocLite.R&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=E_aXM9k6x5bj6QJvBcCq62cBqo8bRrI8t2yBsLDIip0&e=
> ')
> >>>>> Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> >>>>>> biocLite('DelayedArray')
> >>>>> BioC_mirror:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=ONhQc9D8pZG8vfLdgX0Q1AWOwuPxDBzEW2Ifp06nmsQ&e=
> >>>>> Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
> >>>>> Installing package(s) ‘DelayedArray’
> >>>>> trying URL '
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_macosx_el-2Dcapitan_contrib_3.5_DelayedArray-5F0.6.2.tgz&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=Kpu3S3I2bAtZswJFljWMnqN-QA1hE9ZDjSWJ0J-kBm0&e=
> '
> >>>>> Content type 'application/x-gzip' length 1308365 bytes (1.2 MB)
> >>>>> ==================================================
> >>>>> downloaded 1.2 MB
> >>>>>> sessionInfo()
> >>>>> R version 3.5.1 (2018-07-02)
> >>>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> >>>>> Running under: macOS High Sierra 10.13.6
> >>>>>
> >>>>> Matrix products: default
> >>>>> BLAS:
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> >>>>> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.5/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
> >>>>>
> >>>>> other attached packages:
> >>>>> [1] BiocInstaller_1.30.0
> >>>>>
> >>>>> loaded via a namespace (and not attached):
> >>>>> [1] compiler_3.5.1 tools_3.5.1
> >>>>>
> >>>>>
> >>>>> So, I have no idea how to approach this and just wanted to double
> >>>>> check that things are ok from your side.
> >>>>>
> >>>>>
> >>>>> Thanks,
> >>>>> Leo
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioc-devel using r-project.org mailing list
> >>>>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=YRPQuTB5uy8tiE-k-5akRFXnJhoNwjhnS3ooygAEUQU&e=
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos&s=YRPQuTB5uy8tiE-k-5akRFXnJhoNwjhnS3ooygAEUQU&e=
> >
>
> --
> 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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