[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
|co||@dotor @end|ng |rom gm@||@com
Wed Sep 18 06:26:51 CEST 2019
Hi,
I'm happy to report that this was never a connection issue. I was just
mislead by https://stackoverflow.com/questions/25487593/r-what-does-incomplete-block-on-file-mean
which suggested that the download was incomplete as well as the timing
of the connection issue with the non-bioc website. It turns out that
the installation of clusterProfiler's dependencies DO.db, GO.db and
other packages that have no Windows binary can be resolved by editing
the TMP and TEMP environment variables to a path with no spaces for a
Windows user whose username includes a space. Doing so leads to a
utils::tempdir() with no spaces, which is used to form the destination
directory with default arguments when using utils::install.packages().
I wrote more about this at
http://lcolladotor.github.io/2019/09/18/windows-user-space-issues-with-installing-r-packages/#.XYGsZJNKg0o
Thank you again for your help on this a year ago! If any of you have
other solutions, we'd love to learn about them.
Best,
Leo
On Thu, Aug 2, 2018 at 2:22 PM Leonardo Collado Torres <lcollado using jhu.edu> wrote:
>
> 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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