[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

Martin Morgan m@rtin@morg@n @ending from ro@wellp@rk@org
Fri Aug 3 14:09:24 CEST 2018 

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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= 
>>>>>>
>>
>> _______________________________________________
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>>
>>
> 


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