Cogent NGS Discovery Software notices
The issues described below for the Cogent NGS Discovery Software are ones that have been seen or reported. If you encounter other errors using CogentDS or are unable to resolve the problem using the suggestions below, please:
- Capture a screenshot of the error you see on the screen.
- Send the screenshot to Technical Support, along with a brief description of the issue.
Software issues FAQs
Error pop-up: Choose R installation when running RStudio
Problem description
A pop-up error screen is displaying the title "Choose R installation" with the message "RStudio requires an existing installation of R in order to work. Please select the version of R to use."
Figure 1. Error pop-up seen when RStudio is unable to find the R installation in Windows.
Cause
Either RStudio can't find the installation of R or R is not installed on the computer.
Fix
Please contact your IT specialist for additional assistance.
Error: (converted from warning) cannot remove prior installation of package
Problem description
An error like the following is seen either during installation or an upgrade of Cogent NGS Discovery Software (package name 'glue' is provided as an example only):
Figure 2. Example of an R-dependency package upgrade error message.
Cause
This is an issue within R.
Fix
The workaround is to manually install the package(s) throwing the error(s).
install.packages("<PACKAGENAME>")
where <PACKAGENAME> is replaced with the name of the package to be re-installed.
Example:
install.packages("glue")
Figure 3. Example of a manual installation of the problem R package as depicted in Figure 2. Note the package was successfully unpacked and no error message occurred after the manual install.
Re-run the install/upgrade and repeat as necessary until no additional error messages are seen.
Error in loadNamespace, namespace '<PACKAGENAME>' #.#.# is being loaded, but >= #.#.# is required
Problem description
An error like the following is seen either during installation or an upgrade of Cogent NGS Discovery Software (package name 'processx' is provided as an example only):
Figure 4. Example of an R-dependency package error during installation.
Cause
This is an issue within R.
Fix
The workaround is to manually install the package(s) throwing the error(s).
install.packages("<PACKAGENAME>")
where <PACKAGENAME> is replaced with the name of the package to be re-installed.
Example:
install.packages("processx")
Figure 5. Example of a manual installation of the problem R package as depicted in Figure 4. Note the package was successfully unpacked and no error message occurred after the manual install.
Re-run the install/upgrade and repeat as necessary until no additional error messages are seen.
Error: .onLoad failed in loadNamespace() for '<PACKAGENAME>'
Problem description
In some cases when upgrading an R package using the install.packages() command, it may encounter an error and display a message like the one below (package name 'backports' is provided as an example only):
Figure 6. Example of an R-dependency package error during installation.
Cause
This is an issue within R.
Fix
Uninstall the package using the following command:
remove.packages("<PACKAGENAME>")
where <PACKAGENAME> is replaced with the name of the package to be uninstalled.
Example:
remove.packages("backports")
Re-run the package install (install.packages("<PACKAGENAME>")) and repeat as necessary until no additional error messages are seen.
RNA-seq
Cogent NGS Analysis Pipeline
Analyze RNA-seq data generated by select Takara Bio applications.
Cogent NGS Discovery Software
Visualize RNA-seq data in UMAP or t-SNE charts from the output of the Cogent NGS Analysis Pipeline.
SMART-Seq DE3 Demultiplexer
Demultiplex sequencing data from the SMART-Seq v4 3′ DE Kit into sorted read data files.
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