[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
Hervé Pagès
hp@ge@ @ending from fredhutch@org
Thu Aug 2 19:57:57 CEST 2018
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=
>
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>
--
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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