> On Dec 11, 2017, at 6:11 AM, Federico Calboli <federico.calb...@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@r-project.org
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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
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