[Bioc-devel] EXTERNAL: Re: 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
Tue Aug 7 15:57:14 CEST 2018
Sorry about that Martin. Here's my thank you reply to Hervé from August 2nd.
----
Thanks Hervé and no problem about the Windows binary.
Richard did get DelayedArray installed today (I think using biocLite)! ^^
Best,
Leo
On Fri, Aug 3, 2018 at 8:27 AM Martin Morgan
<martin.morgan using roswellpark.org> wrote:
>
>
> The large number of people cc'd on this thread causes the mailman
> software to block posts. I'm removing individuals, please respond to
> this message.
>
> On 08/02/2018 01:57 PM, Hervé Pagès 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=
> >>
> >>
> >
>
>
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