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 <hpa...@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.tri...@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 < > lcoll...@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.tri...@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 < > lcoll...@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@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@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel