Hi All, I am using R version 3.4.3 Patched (2017-12-05 r73849) R.app GUI 1.70 (7463) x86_64-apple-darwin15.6.0 on MacOS 10.13.2. Using R.app I am looking for Bioconductor packages, and using the package installer I get the following warning: Warning: unable to access index for repository http://www.bioconductor.org/packages/3.6/extra/bin/macosx/el-capitan/contrib/3.4: cannot open URL 'http://www.bioconductor.org/packages/3.6/extra/bin/macosx/el-capitan/contrib/3.4/PACKAGES? despite the fact I do get a list of available packages (screenshot attached). I emailed the bioconductor devs but it is not clear what is going on, aside than my R is looking for a webpage that is a 404. I was wondering whether this is a peculiarity of my own machine or whether it has been encountered elsewhere. Assuming it is my machine, is there a way of making said warning go away? Cheers F [cid:EC3117B7-6BBF-430A-989C-541AE9067A1E] -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20171211/cb5d9efd/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2017-12-11 at 15.08.15.png Type: image/png Size: 602874 bytes Desc: Screen Shot 2017-12-11 at 15.08.15.png URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20171211/cb5d9efd/attachment-0001.png>
odd warning looking up Bioconductor packages
2 messages · Federico Calboli, David Winsemius
2 days later
On Dec 11, 2017, at 6:11 AM, Federico Calboli <federico.calboli at kuleuven.be> wrote: Hi All, I am using R version 3.4.3 Patched (2017-12-05 r73849) R.app GUI 1.70 (7463) x86_64-apple-darwin15.6.0 on MacOS 10.13.2. Using R.app I am looking for Bioconductor packages, and using the package installer I get the following warning: Warning: unable to access index for repository http://www.bioconductor.org/packages/3.6/extra/bin/macosx/el-capitan/contrib/3.4: cannot open URL 'http://www.bioconductor.org/packages/3.6/extra/bin/macosx/el-capitan/contrib/3.4/PACKAGES? despite the fact I do get a list of available packages (screenshot attached). I emailed the bioconductor devs but it is not clear what is going on, aside than my R is looking for a webpage that is a 404. I was wondering whether this is a peculiarity of my own machine or whether it has been encountered elsewhere. Assuming it is my machine, is there a way of making said warning go away?
I've been getting the same warning for a while. The BioConductor approved way is to use `source("https://bioconductor.org/biocLite.R"); biocLite(c("pkg_name")). It has not affected my ability to install BioC packages, so I've been ignoring it. The other reason I've been ignoring it is that I'm not using the approved method. I thought it is from R.app using an old address with the "http" not being "https" some place in the Package Installer script.
I can get it just by clicking on the "Get List" button of the GUI Package Installer panel with Bioconductor (binaries) selected. If I choose to reinstall pkg:"a4" is get the warning again then
trying URL 'http://www.bioconductor.org/packages/3.6/bioc/bin/macosx/el-capitan/contrib/3.4/a4_1.26.0.tgz'
Content type 'application/x-gzip' length 966139 bytes (943 KB)
.... followed by the reports of success and then another warning. So maybe it's not the "http" but rather the target website.
David. > sessionInfo() R version 3.4.2 Patched (2017-10-04 r73465) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] grDevices utils datasets graphics stats methods base other attached packages: [1] rms_5.1-1 SparseM_1.77 Hmisc_4.0-3 ggplot2_2.2.1 Formula_1.2-2 survival_2.41-3 [7] sos_2.0-0 brew_1.0-6 lattice_0.20-35 loaded via a namespace (and not attached): [1] viridis_0.4.0 tidyr_0.7.2 jsonlite_1.5 viridisLite_0.2.0 splines_3.4.2 [6] assertthat_0.2.0 latticeExtra_0.6-28 gamlss_5.0-5 backports_1.1.1 quantreg_5.34 [11] glue_1.2.0 downloader_0.4 digest_0.6.12 RColorBrewer_1.1-2 checkmate_1.8.5 [16] minqa_1.2.4 colorspace_1.3-2 sandwich_2.4-0 htmltools_0.3.6 Matrix_1.2-12 [21] plyr_1.8.4 XML_3.98-1.9 pkgconfig_2.0.1 DiagrammeR_0.9.2 purrr_0.2.4 [26] mvtnorm_1.0-6 scales_0.5.0 gamlss.data_5.0-0 lme4_1.1-14 MatrixModels_0.4-1 [31] htmlTable_1.11.0 tibble_1.3.4 influenceR_0.1.0 TH.data_1.0-8 nnet_7.3-12 [36] lazyeval_0.2.1 rgexf_0.15.3 magrittr_1.5 polspline_1.1.12 nlme_3.1-131 [41] MASS_7.3-47 foreign_0.8-69 mxnet_0.10.1 Rook_1.1-1 tools_3.4.2 [46] data.table_1.10.4-3 hms_0.4.0 multcomp_1.4-8 stringr_1.2.0 munsell_0.4.3 [51] cluster_2.0.6 bindrcpp_0.2 gamlss.dist_5.0-3 compiler_3.4.2 rlang_0.1.4 [56] nloptr_1.0.4 grid_3.4.2 rstudioapi_0.7 htmlwidgets_0.9 visNetwork_2.0.1 [61] igraph_1.1.2 base64enc_0.1-3 gtable_0.2.0 codetools_0.2-15 R6_2.2.2 [66] gridExtra_2.3 zoo_1.8-0 knitr_1.17 dplyr_0.7.4 bindr_0.1 [71] readr_1.1.1 stringi_1.1.6 parallel_3.4.2 Rcpp_0.12.14 rpart_4.1-11 [76] acepack_1.4.1 > > Cheers > > F > > <Screen Shot 2017-12-11 at 15.08.15.png> > > -- > Federico Calboli > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > Charles Deberiotstraat 32 box 2439 > 3000 Leuven > +32 16 32 87 67 > > > > > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law