Dear Ecotyper team,
Thank you for providing such a powerful software. I have been tried to run your tutorial 1 on the example data. But I encountered some issues, and I don't know how to solve. I hope you can help me.
The error message as following:
[biostack@localhost ecotyper-master]$ Rscript EcoTyper_recovery_bulk.R -d Carcinoma -m example_data/bulk_lung_data.txt -a example_data/bulk_lung_annotation.txt -c Tissue -o RecoveryOutput
Warning messages:
1: package ‘argparse’ was built under R version 4.4.1
2: package ‘data.table’ was built under R version 4.4.1
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Mast.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: NK.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Dendritic.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: PCs...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: B.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: CD8.T.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: CD4.T.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: PMNs...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Monocytes.and.Macrophages...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Fibroblasts...
E^HError in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Endothelial.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Epithelial.cells...
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in RunJobQueue() :
EcoTyper failed. Please check the error message above!
Execution halted
It seemed that some dependency packages are missing, however, I have installed 'tidyverse' and 'rlang' packages. I don't know the reason of this error.
Thank you again for your attention. I am really appreciated for your help.
This is the session info:
sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: CentOS Linux 8
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[5] purrr_1.1.0 readr_2.1.5 tidyr_1.3.1 tibble_3.3.0
[9] ggplot2_3.5.2 tidyverse_2.0.0 rlang_1.1.6
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.5 stringi_1.8.7 generics_0.1.4
[5] glue_1.8.0 hms_1.1.3 scales_1.4.0 grid_4.4.1
[9] tzdb_0.5.0 lifecycle_1.0.4 compiler_4.4.1 RColorBrewer_1.1-3
[13] timechange_0.3.0 pkgconfig_2.0.3 farver_2.1.2 R6_2.6.1
[17] dichromat_2.0-0.1 tidyselect_1.2.1 pillar_1.11.0 magrittr_2.0.3
[21] tools_4.4.1 withr_3.0.2 gtable_0.3.6
Dear Ecotyper team,
Thank you for providing such a powerful software. I have been tried to run your tutorial 1 on the example data. But I encountered some issues, and I don't know how to solve. I hope you can help me.
The error message as following:
[biostack@localhost ecotyper-master]$ Rscript EcoTyper_recovery_bulk.R -d Carcinoma -m example_data/bulk_lung_data.txt -a example_data/bulk_lung_annotation.txt -c Tissue -o RecoveryOutput
Warning messages:
1: package ‘argparse’ was built under R version 4.4.1
2: package ‘data.table’ was built under R version 4.4.1
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Mast.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: NK.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Dendritic.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: PCs...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: B.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: CD8.T.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: CD4.T.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: PMNs...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Monocytes.and.Macrophages...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Fibroblasts...
E^HError in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Endothelial.cells...
Warning messages:
1: package ‘NMF’ was built under R version 4.4.1
2: package ‘cluster’ was built under R version 4.4.1
3: package ‘ComplexHeatmap’ was built under R version 4.4.1
4: package ‘circlize’ was built under R version 4.4.1
Running cell state recovery on: Epithelial.cells...
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function 'match': could not find function "%||%"
Calls: [ ... match -> rownames -> rownames -> .handleSimpleError -> h
Execution halted
Error in RunJobQueue() :
EcoTyper failed. Please check the error message above!
Execution halted
It seemed that some dependency packages are missing, however, I have installed 'tidyverse' and 'rlang' packages. I don't know the reason of this error.
Thank you again for your attention. I am really appreciated for your help.
This is the session info:
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[5] purrr_1.1.0 readr_2.1.5 tidyr_1.3.1 tibble_3.3.0
[9] ggplot2_3.5.2 tidyverse_2.0.0 rlang_1.1.6
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.5 stringi_1.8.7 generics_0.1.4
[5] glue_1.8.0 hms_1.1.3 scales_1.4.0 grid_4.4.1
[9] tzdb_0.5.0 lifecycle_1.0.4 compiler_4.4.1 RColorBrewer_1.1-3
[13] timechange_0.3.0 pkgconfig_2.0.3 farver_2.1.2 R6_2.6.1
[17] dichromat_2.0-0.1 tidyselect_1.2.1 pillar_1.11.0 magrittr_2.0.3
[21] tools_4.4.1 withr_3.0.2 gtable_0.3.6