Here is the detailed version of the installation tutorial, the installation process encountered errors, you can find detailed solutions in this article.
If the following solutions do not help you, please leave a comment on the website. We will solve the problem as soon as possible and add the solution to this document for more users to read.
In the Ubuntu system, when installing the ape dependency
package, there may be the following problems:
# error "/usr/bin/ld: cannot find -llapack"
# error "/usr/bin/ld: cannot find -lgfortran"This is due to a lack of basic tools from the system. Install these tools using shell commands:
sudo apt install liblapack-dev libopenblas-dev gfortranThe development environment of itol.toolkit package is
R4.2.0. Since R version 4.0.0, some important language habit updates
have been released, among which the updates of Rcpp, rlang
and other underlying packages have a great impact on users below R
version 4.0.0. itol.toolkit running in versions earlier
than R4.0.0 may cause some errors caused by underlying dependency
packages. Run itol.toolkit at R 4.0.0 or later
possibly.
The following error occurs when running the quickstart tutorial:
unit <- create_unit(data = df_group,
key = "Quickstart",
type = "DATASET_COLORSTRIP",
tree = tree)
# Error in char (data[[potential_color]]) :
# 'nchar()' requires a character vectorThe best way is to install itol.toolkit v1.1.2 and
later, where we removed the nchar dependency in favor of
stringr::str_length, which is more stable across R
versions.
The temporary solution is to explicitly define the color parameter in
the create_unit
function.
unit <- create_unit(data = df_group,
key = "Quickstart",
type = "DATASET_COLORSTRIP",
color = "Set1",
tree = tree)R packages from the Bioconductor platform cannot be
automatically installed by install.packages or
devtools::install_github. This will result in an error
similar to the following:
# error "package ‘Biostrings’ is not available (for R version 3.6.3)"The best way is to use pak package to
install itol.toolkit package. See the main
document for the method.
Another way is to install dependency packages using
BiocManager:
# install.packages("BiocManager")
BiocManager::install("Biostrings")This is a typical indirectly dependcy package.
# Error: package or namespace load failed for 'itol.toolkit' in library.dynam(lib, package, package.lib):
# DLL ‘fansi’ not found: maybe not installed for this architecture?
# Error: loading failed
# Stop
# *** arch - x64
# ERROR: loading failed for 'i386'
# * removing 'C:/Users/86139/Documents/R/win-library/4.1/itol.toolkit'
# Warning message:
# In i.p(...) :
# installation of package ‘C:/Users/86139/AppData/Local/Temp/Rtmpycftoi/file45b02cc43b42/itol.toolkit_1.1.2.tar.gz’ had non-zero exit statusThe best solution is using pak to install:
install.packages("pak")
# from CRAN
pak::pak('itol.toolkit')
# from GitHub
# not work for this status https://github.com/r-lib/pak/issues/473
pak::pak('TongZhou2017/itol.toolkit') The complete dependency package information is as follows. If you have network problems, download the dependency package manually and install it locally. See the next section for details.
| package | platform | function in itol.toolkit |
|---|---|---|
| dplyr | CRAN | Data processing |
| stringr | CRAN | String processing; nchar repalce |
| data.table | CRAN | Data processing |
| methods | CRAN | Object base function |
| stats | CRAN | Data processing |
| tidyr | CRAN | Data frame processing |
| purrr | CRAN | Data screening |
| seqinr | CRAN | Tree file processing |
| ape | CRAN | Tree file processing |
| Biostrings | Bioconductor | fasta format sequence read |
| wesanderson | CRAN | Color scheme |
| ggsci | CRAN | Color scheme |
| RColorBrewer | CRAN | Color scheme |
| rstudioapi | CRAN | RStudio Plug-in base |
| shiny | CRAN | RStudio Plug-in base |
| miniUI | CRAN | RStudio Plug-in base |
| colourpicker | CRAN | RStudio Plug-in base |
If you encounter similar errors caused by network problems:
# Warning in install.packages :
# unable to access index for repository https://cran.rstudio.com/src/contrib:
# cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
# Installing package into ‘C:/Users/25757/Documents/R/win-library/4.0’
# (as ‘lib’ is unspecified)
#
# Warning in install.packages :
# unable to access index for repository https://cran.rstudio.com/src/contrib:
# cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
#
# Warning in install.packages :
# package ‘ape’ is not available (for R version 4.0.0)
#
# Warning in install.packages :
# unable to access index for repository https://cran.rstudio.com/bin/windows/contrib/4.0:
# cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/PACKAGES'Please download the R packages manually from the package homepages in the previous section, and then install them locally using the following command:
install.packages(PathToPkgFile,repos=NULL,type="source")IOCAS, 2575760336@qq.com↩︎
IOCAS, tongzhou2017@gmail.com↩︎