fix(vignette): fix incorrect CRAN links in the Introduction vignette

Author: Vadim Nazarov

vignettes/v1_introduction.Rmd

@@ -104,7 +104,7 @@ If you can not install `devtools`, check sections 1 and 2 below.
 
 If you run in any other trouble, try the following steps:
 
-1. Check your R version. Run `version` command in the console to get your R versions. If the R version is below 3.5.0 (for example, `R version 3.1.0`), try updating your R version to the latest one. Check this [this link](http://cran.r-project.org/bin/linux/ubuntu/README.html) if you are on Ubuntu. Note: if you try to install a package after the update and it still fails with the following message:
+1. Check your R version. Run `version` command in the console to get your R versions. If the R version is below 3.5.0 (for example, `R version 3.1.0`), try updating your R version to the latest one. Check this [this link](https://cran.r-project.org/bin/linux/ubuntu/README.html) if you are on Ubuntu. Note: if you try to install a package after the update and it still fails with the following message:
 
    ```
    ERROR: dependencies ‘httr’, ‘usethis’ are not available for package ‘devtools’
@@ -208,23 +208,13 @@ Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
 
 9. For Windows users. If you have issues with the package installation, or if you want to change the folder for R packages, feel free to check [this forum post](http://community.rstudio.com/t/help-regarding-package-installation-renviron-rprofile-r-libs-r-libs-site-and-r-libs-user-oh-my/13888/8).
 
-9. For Windows users. Make sure to install [Rtools](http://cran.r-project.org/bin/windows/Rtools/). Before installation close RStudio, install Rtools and re-open it afterwards. To check if Rtools installed correctly, run the `devtools::find_rtools()` command (after installing the devtools package). If you have an error, check [this link](http://github.com/r-lib/devtools/issues/1941) for help.
+9. For Windows users. Make sure to install [Rtools](https://cran.r-project.org/bin/windows/Rtools/). Before installation close RStudio, install Rtools and re-open it afterwards. To check if Rtools installed correctly, run the `devtools::find_rtools()` command (after installing the devtools package). If you have an error, check [this link](http://github.com/r-lib/devtools/issues/1941) for help.
 
 9. If you can not install dependencies for `immunarch`, please try manual installation of all dependencies by executing the following command in R console:
 
    ```
 install.packages(c("rematch", "prettyunits", "forcats", "cellranger", "progress", "zip", "backports", "ellipsis", "zeallot", "SparseM", "MatrixModels", "sp", "haven", "curl", "readxl", "openxlsx", "minqa", "nloptr", "RcppEigen", "utf8", "vctrs", "carData", "pbkrtest", "quantreg", "maptools", "rio", "lme4", "labeling", "munsell", "cli", "fansi", "pillar", "viridis", "car", "ellipse", "flashClust", "leaps", "scatterplot3d", "modeltools", "DEoptimR", "digest", "gtable", "lazyeval", "rlang", "scales", "tibble", "viridisLite", "withr", "assertthat", "glue", "magrittr", "pkgconfig", "R6", "tidyselect", "BH", "plogr", "purrr", "ggsci", "cowplot", "ggsignif", "polynom", "fastcluster", "plyr", "abind", "dendextend", "FactoMineR", "mclust", "flexmix", "prabclus", "diptest", "robustbase", "kernlab", "GlobalOptions", "shape", "colorspace", "stringi", "hms", "clipr", "crayon", "httpuv", "mime", "jsonlite", "xtable", "htmltools", "sourcetools", "later", "promises", "gridBase", "RColorBrewer", "yaml", "ggplot2", "dplyr", "dtplyr", "dbplyr", "data.table", "gridExtra", "ggpubr", "pheatma3", "ggrepel", "reshape2", "DBI", "factoextra", "fpc", "circlize", "tidyr", "Rtsne", "readr", "readxl", "shiny", "shinythemes", "treemap", "igraph", "airr", "ggseqlogo", "UpSetR", "stringr", "ggalluvial", "Rcpp"))
    ```
-
-9. If you can not install `immunarch` using `install_url()`, try the manual installation. First, you need to download the package file from [our GitHub](http://github.com/immunomind/immunarch/raw/master/immunarch.tar.gz).
-
-   Note that you **should not un-archive it**!
-   
-   After downloading the file, you need to run R command from the `devtools` package to install `immunarch`. Upon completion the dependencies will have been already downloaded and installed. Run the following command:
-   
-   ```
-devtools::install_local("path/to/your/folder/with/immunarch.tar.gz", dependencies=T)
-   ```
 
 9. If you encounter the following error while running the `devtools::install_local` function: