Trouble installing ampvis2

[kasperskytte]

Trouble installing ampvis2

[KasperSkytte]

Hi there Try install.packages(c("curl", "httr")) and try again. If that doesnt fix it, try with devtools instead of remotes with host set: devtools::install_github("madsalbertsen/ampvis2", host = "https://api.github.com") Regards / MVH Kasper Skytte Andersen

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On 9 May 2019, at 18.53, atxange ***@***.***> wrote: I used ampvis2 recently, but got a new computer to needed to re-install all my old R packages. When trying to install ampvis2 by your instructions online, I got this: remotes::install_github("MadsAlbertsen/ampvis2") Error in curl::curl_fetch_memory(url, handle = h) : Timeout was reached: Connection timed out after 10000 milliseconds Tried installing older versions of ampvis2 with ***@***.***") but got the same error. Ideas? R version 3.5.2 Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[atxange]

I tried both, and I'm still getting the same error! :/

[KasperSkytte]

I need more information then. Please provide the output of sessionInfo(). If you run Linux it's probably just a system package that needs to be installed. Have you looked further up in the console output for messages during the installation? Maybe you need to install libcurl4-openssl-dev.

[atxange]

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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] grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] usethis_1.5.0 devtools_2.0.2 caret_6.0-84 ropls_1.14.1 ARTool_0.10.6 emmeans_1.3.4
[7] qvalue_2.14.1 FSA_0.8.23 openxlsx_4.1.0 broom_0.5.2 xlsx_0.6.1 RColorBrewer_1.1-2
[13] data.table_1.12.2 mixOmics_6.6.2 reshape_0.8.8 tibble_2.1.1 microbiome_1.4.2 psych_1.8.12
[19] vegan_2.5-4 lattice_0.20-38 permute_0.9-5 lmerTest_3.1-0 multcomp_1.4-10 TH.data_1.0-10
[25] MASS_7.3-51.4 survival_2.44-1.1 mvtnorm_1.0-10 lme4_1.1-21 Matrix_1.2-17 nlme_3.1-137
[31] dplyr_0.8.0.1 ade4_1.7-13 ggplot2_3.1.1 ape_5.3 scales_1.0.0 phyloseq_1.26.1

loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.1.4 plyr_1.8.4 igraph_1.2.4.1 lazyeval_0.2.2 splines_3.5.2
[7] digest_0.6.18 foreach_1.4.4 magrittr_1.5 memoise_1.1.0 cluster_2.0.9 remotes_2.0.4
[13] recipes_0.1.5 Biostrings_2.50.2 gower_0.2.0 matrixStats_0.54.0 rARPACK_0.11-0 sandwich_2.5-1
[19] prettyunits_1.0.2 colorspace_1.4-1 haven_2.1.0 callr_3.2.0 crayon_1.3.4 jsonlite_1.6
[25] zoo_1.8-5 iterators_1.0.10 glue_1.3.1 gtable_0.3.0 ipred_0.9-9 zlibbioc_1.28.0
[31] XVector_0.22.0 car_3.0-2 pkgbuild_1.0.3 Rhdf5lib_1.4.3 BiocGenerics_0.28.0 abind_1.4-5
[37] Rcpp_1.0.1 xtable_1.8-4 foreign_0.8-71 stats4_3.5.2 lava_1.6.5 prodlim_2018.04.18
[43] pkgconfig_2.0.2 rJava_0.9-11 nnet_7.3-12 tidyselect_0.2.5 labeling_0.3 rlang_0.3.4
[49] reshape2_1.4.3 munsell_0.5.0 cellranger_1.1.0 tools_3.5.2 cli_1.1.0 generics_0.0.2
[55] biomformat_1.10.1 stringr_1.4.0 yaml_2.2.0 fs_1.3.1 ModelMetrics_1.2.2 processx_3.3.1
[61] zip_2.0.1 purrr_0.3.2 compiler_3.5.2 pbkrtest_0.4-7 rstudioapi_0.10 curl_3.3
[67] stringi_1.4.3 ps_1.3.0 desc_1.2.0 RSpectra_0.14-0 forcats_0.4.0 nloptr_1.2.1
[73] multtest_2.38.0 pillar_1.3.1 estimability_1.3 corpcor_1.6.9 R6_2.4.0 gridExtra_2.3
[79] rio_0.5.16 IRanges_2.16.0 sessioninfo_1.1.1 codetools_0.2-16 boot_1.3-22 assertthat_0.2.1
[85] pkgload_1.0.2 rhdf5_2.26.2 xlsxjars_0.6.1 rprojroot_1.3-2 withr_2.1.2 mnormt_1.5-5
[91] S4Vectors_0.20.1 mgcv_1.8-28 parallel_3.5.2 hms_0.4.2 rpart_4.1-15 timeDate_3043.102
[97] tidyr_0.8.3 class_7.3-15 minqa_1.2.4 carData_3.0-2 numDeriv_2016.8-1 Biobase_2.42.0
[103] lubridate_1.7.4 ellipse_0.4.1

[KasperSkytte]

The problem is the curl package which is used by the remotes package to install ampvis2. I don't know the exact cause of the problem since I'm not a developer of that package. But I suspect it has something to do with your network or DNS settings or similar, see jeroen/curl#72.
You can try updating curl to the newest development version using install.packages("https://github.com/jeroen/curl/archive/master.tar.gz", repos = NULL) or update R to the newest version 3.6 and reinstall your packages. If none of that worked, I have no more ideas.