[R-SIG-Mac] odd warning looking up Bioconductor packages

Wed Dec 13 17:56:37 CET 2017

> 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
> 
> 
> 
> 
> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law