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.mor...@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.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= > >> > >> > > > > > This email message may contain legally privileged and/or... > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ 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