"no package" Problem

[sean-bigsheng]

`Sat May 28 22:32:30 GMT+08:00 2022 SegmentUsage] Processing sample ERR3445170.clonotypes.TRB
[RUtil] Executing Rscript vexpr_plot.r ./results/desease_state.segments.wt.V.txt 57 0 1 FALSE ./results/desease_state.segments.wt.V.pdf
[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'
Loading required package: RColorBrewer
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'RColorBrewer'
Loading required package: ggplot2
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ggplot2'
Loading required package: plotrix
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'plotrix'
Error in brewer.pal(nlevels, "Set2") :
could not find function "brewer.pal"
Calls: colorRampPalette -> colorRamp -> t -> col2rgb -> %in%
Execution halted

[RUtil] Executing Rscript vexpr_plot.r ./results/desease_state.segments.wt.J.txt 13 0 1 FALSE ./results/desease_state.segments.wt.J.pdf
[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'
Loading required package: RColorBrewer
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'RColorBrewer'
Loading required package: ggplot2
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ggplot2'
Loading required package: plotrix
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'plotrix'
Error in brewer.pal(nlevels, "Set2") :
could not find function "brewer.pal"
Calls: colorRampPalette -> colorRamp -> t -> col2rgb -> %in%
Execution halted`

So I turn to the RStudio, and found this:
attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] RColorBrewer_1.1-3 ggplot2_3.3.6 plotrix_3.8-2
[4] gplots_3.1.3

loaded via a namespace (and not attached):
[1] fansi_1.0.3 gtools_3.9.2.1 withr_2.5.0
[4] utf8_1.2.2 crayon_1.5.1 bitops_1.0-7
[7] grid_4.2.0 R6_2.5.1 lifecycle_1.0.1
[10] gtable_0.3.0 magrittr_2.0.3 scales_1.2.0
[13] pillar_1.7.0 KernSmooth_2.23-20 rlang_1.0.2
[16] cli_3.3.0 vctrs_0.4.1 ellipsis_0.3.2
[19] tools_4.2.0 glue_1.6.2 munsell_0.5.0
[22] compiler_4.2.0 pkgconfig_2.0.3 colorspace_2.0-3
[25] caTools_1.18.2 tibble_3.1.7

I saw the same issue in Error on R step #54, and I still have idea to deal with it.
Could somebody can help? Thanks!

[sean-bigsheng]

[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 795694 0.08793043221498285 TGCGCCAGCAGCCTAGGACAGAGCACAGATACGCAGTATTTT CASSLGQSTDTQYF TRBV5-1 TRBD1 TRBJ2-3 11 15 20 21 for MiXcr input type: Some mandatory columns are absent in the input file., see _vdjtools_error.log for details
I also have this issue. The version of mixCR is mixcr-3.0.13. I ignored it because I think the result can be used by VDJtools directly. Did this cause the issue above?