mikessh / homebrew-repseq Goto Github PK

Hi,
I'm getting this error for vdjdb when following the instructions in: https://github.com/mikessh/homebrew-repseq

Error: No available formula with the name "vdjdb"
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
==> Searching taps...
==> Searching taps on GitHub...
Error: No formulae found in taps.

any advice?
thanks
ibseq

to 1.6.1

Hello,

I wanted to install vdjtools on macOS MOjave. Then it showed following error.

==> Installing vdjtools from mikessh/repseq
==> Downloading https://github.com/mikessh/vdjtools/releases/download/1.2.1/vdjtools-1.2.1.zip
Already downloaded: /Users/Sumanta.Barman/Library/Caches/Homebrew/downloads/2bfaacb2fc90ef908cae13fb3c7a646c00da682b21071ca90c11b830c054031e--vdjtools-1.2.1.zip
==> /usr/local/Cellar/vdjtools/1.2.1/bin/vdjtools RInstall
Last 15 lines from /Users/Sumanta.Barman/Library/Logs/Homebrew/vdjtools/01.vdjtools:
2019-06-18 12:56:27 +0200

/usr/local/Cellar/vdjtools/1.2.1/bin/vdjtools
RInstall

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/mikessh/homebrew-repseq/issues

Then I used the direct vdjtools-1.2.1.jar file to run the program and installed R packages (java -jar vdjtools.jar Rinstall). But "ape" and "gplots" packages are failed to install and shows following error.

[RUtil] Executing Rscript test.r reshape2 FField reshape gplots gridExtra circlize ggplot2 grid VennDiagram RColorBrewer plotrix ape MASS scales
[1] "FAILED to install gplots"
[1] "FAILED to install ape"
[RInstall] Finished

So I can't visualize all data. Afterward, I installed that two packages manually by running the command in R. But when I run TrackClonotypes command, then it still cannot find gplots so cannot generate all visualization file and shows following error.

[ERROR] Loading required package: gplots
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘gplots’
Error in heatmap.2(x, labRow = df$cdr3aa, labCol = t, Colv = FALSE, dendrogram = "row", :
could not find function "heatmap.2"
Execution halted

Could be you please help how I can solve this problem?

Hello,

I wanted to install vdjtools on macOS Big Sur, then problem coming when I typed "brew install vdjtools" in terminal (after "brew tap brewsci/science" and "brew tap mikessh/repseq" ):

**Updating Homebrew...
Warning: Calling depends_on :java is deprecated! Use "depends_on "openjdk@11", "depends_on "openjdk@8" or "depends_on "openjdk" instead.
Please report this issue to the mikessh/repseq tap (not Homebrew/brew or Homebrew/core), or even better, submit a PR to fix it:
/usr/local/Homebrew/Library/Taps/mikessh/homebrew-repseq/Formula/vdjtools.rb:8

==> Installing vdjtools from mikessh/repseq
Warning: Calling depends_on :java is deprecated! Use depends_on "openjdk@11", depends_on "openjdk@8" or depends_on "openjdk" instead.
Warning: Calling depends_on :java is deprecated! Use depends_on "openjdk@11", depends_on "openjdk@8" or depends_on "openjdk" instead.
==> Downloading https://github.com/mikessh/vdjtools/releases/download/1.2.1/vdjt
Already downloaded: /Users/wen-qing/Library/Caches/Homebrew/downloads/2bfaacb2fc90ef908cae13fb3c7a646c00da682b21071ca90c11b830c054031e--vdjtools-1.2.1.zip
Warning: Calling depends_on :java is deprecated! Use depends_on "openjdk@11", depends_on "openjdk@8" or depends_on "openjdk" instead.
Warning: Calling depends_on :java is deprecated! Use "depends_on "openjdk@11", "depends_on "openjdk@8" or "depends_on "openjdk" instead.
Please report this issue to the mikessh/repseq tap (not Homebrew/brew or Homebrew/core), or even better, submit a PR to fix it:
/usr/local/Homebrew/Library/Taps/mikessh/homebrew-repseq/Formula/vdjtools.rb:8

Warning: Calling depends_on :java is deprecated! Use depends_on "openjdk@11", depends_on "openjdk@8" or depends_on "openjdk" instead.
==> /usr/local/Cellar/vdjtools/1.2.1/bin/vdjtools RInstall
Last 15 lines from /Users/wen-qing/Library/Logs/Homebrew/vdjtools/01.vdjtools:
2021-01-21 23:00:21 +0800

/usr/local/Cellar/vdjtools/1.2.1/bin/vdjtools
RInstall

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/mikessh/homebrew-repseq/issues

These open issues may also help:
vdjtools installation problem on macOS MOjave #5**

I am attempting to install vdjtools using homebrew, but it keeps failing at the "RInstall" step despite having the most recent version of r downloaded and linked. Could this be related to homebrew/science being deprecated? Is there maybe a dependency missing? Any insight would be greatly appreciated.