Installing "immunedeconv" package

[wangxlab]

Hi,

I tried to install "immunedeconv" package to a supercomputer that my university uses. It is Centos ver7. According to the instruction, I installed it through Bioconda but it doesn't work. I pasted the command line that I typed to install below. Could you tell me what I did wrong?

Install immunedeconv package

$ interact --egress $ module load anaconda5/5.0.0-3.6
$ conda create --prefix /pylon5/mc5fppp/biotech/.conda/envs/deconvolution
$ source activate deconvolution $ conda install -c bioconda -c conda-forge r-immunedeconv

When I load the reticulate library

$ interact --egress $ module load anaconda5/5.0.0-3.6 $ module load R/3.6.0-mkl $ source activate deconvolution
$ R

library(inmunedeconve) Error in library(inmunedeconve) : there is no package called ‘inmunedeconve’

[grst]

You seem to have a typo: It's library(immunedeconv).

On Mon, Oct 28, 2019, 14:31 Xiaosong Wang Lab notifications@github.com wrote:

Hi,

I tried to install "immunedeconv" package to a supercomputer that my university uses. It is Centos ver7. According to the instruction, I installed it through Bioconda but it doesn't work. I pasted the command line that I typed to install below. Could you tell me what I did wrong? Install immunedeconv package

$ interact --egress $ module load anaconda5/5.0.0-3.6 $ conda create --prefix /pylon5/mc5fppp/biotech/.conda/envs/deconvolution $ source activate deconvolution $ conda install -c bioconda -c conda-forge r-immunedeconv When I load the reticulate library

$ interact --egress $ module load anaconda5/5.0.0-3.6 $ module load R/3.6.0-mkl $ source activate deconvolution $ R

library(inmunedeconve) Error in library(inmunedeconve) : there is no package called ‘inmunedeconve’

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[wangxlab]

Sorry that is typo. I typed a correct spelling, but still it doesn't work and it says there is no package.

It sounds like my installing command line is correct. But, I don't know why library calling doesn't work. Maybe the supercomputer system problem..? Do you have any adivce?

[grst]

You could try not to load the R module. R should have been installed within the conda env.

You can use which R to check if you are using the right one.

On Mon, Oct 28, 2019, 15:26 Xiaosong Wang Lab notifications@github.com wrote:

Sorry that is type. I typed a correct spelling, but still it doesn't work and it says there is no package.

It sounds like my installing command line is correct. But, I don't know why library calling doesn't work. Maybe the supercomputer system problem..? Do you have any adivce?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/icbi-lab/immunedeconv/issues/24?email_source=notifications&email_token=ABVZRV6ILIOQGXY4AM4I4Q3QQ3ZCHA5CNFSM4JF2FONKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECNB2AI#issuecomment-546970881, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABVZRVYHHQKRIJSPHSTVHCLQQ3ZCHANCNFSM4JF2FONA .

[JianGuoZhou3]

sclc_quantiseq=immunedeconv::deconvolute(tibble.sclc1, "quantiseq")

Running quantiseq

Running quanTIseq deconvolution module

Gene expression normalization and re-annotation (arrays: FALSE)

Removing 17 noisy genes

Removing 15 genes with high expression in tumors

Signature genes found in data set: 111/138 (80.43%)

Mixture deconvolution (method: lsei)

Deconvolution sucessful!

sclc_timer=immunedeconv::deconvolute(tibble.sclc1, "timer")

Running timer assertion failed: indications fit to mixture matrix Error: length(indications) == ncol(gene_expression_matrix) is not TRUE sclc_timer=immunedeconv::deconvolute(tibble.sclc1, "timer")

Running timer assertion failed: indications fit to mixture matrix Error: length(indications) == ncol(gene_expression_matrix) is not TRUE sclc_epic=immunedeconv::deconvolute(tibble.sclc1, "epic")

Running epic Warning messages: 1: In (function (bulk, reference = NULL, mRNA_cell = NULL, mRNA_cell_sub = NULL, : The optimization didn't fully converge for some samples: GSM1219462; GSM1219466

• check fit.gof for the convergeCode and convergeMessage 2: In (function (bulk, reference = NULL, mRNA_cell = NULL, mRNA_cell_sub = NULL, : mRNA_cell value unknown for some cell types: CAFs, Endothelial - using the default value of 0.4 for these but this might bias the true cell proportions from all cell types. sclc_mcp_counter=immunedeconv::deconvolute(tibble.sclc1, "mcp_counter")

Running mcp_counter Warning message: In (function (expression, featuresType = c("affy133P2_probesets", : Found no markers for population(s): CD8 T cells sclc_cibersort_abs=immunedeconv::deconvolute(tibble.sclc1, "cibersort_abs")

Running cibersort_abs Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) :

Error in file(filename, "r", encoding = encoding) : cannot open the connection @grst

[JianGuoZhou3]

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] preprocessCore_1.44.0 e1071_1.7-2 tibble_2.1.3 immunedeconv_2.0.0
[5] EPIC_1.1.5 tidyr_0.8.3 ggplot2_3.2.1 dplyr_0.8.3

loaded via a namespace (and not attached): [1] Biobase_2.42.0 bit64_0.9-7 splines_3.5.2 assertthat_0.2.1
[5] stats4_3.5.2 blob_1.2.0 cellranger_1.1.0 yaml_2.2.0
[9] remotes_2.1.0 pillar_1.4.2 RSQLite_2.1.2 backports_1.1.5
[13] lattice_0.20-38 glue_1.3.1 limma_3.38.3 quadprog_1.5-7
[17] digest_0.6.22 testit_0.10 colorspace_1.4-1 Matrix_1.2-15
[21] XML_3.98-1.20 lpSolve_5.6.13.3 pkgconfig_2.0.3 genefilter_1.64.0
[25] purrr_0.3.3 xtable_1.8-4 scales_1.0.0 MCPcounter_1.1.0
[29] BiocParallel_1.16.6 annotate_1.60.1 mgcv_1.8-27 IRanges_2.16.0
[33] withr_2.1.2 BiocGenerics_0.28.0 lazyeval_0.2.2 survival_2.43-3
[37] magrittr_1.5 crayon_1.3.4 readxl_1.3.1 memoise_1.1.0
[41] data.tree_0.7.11 nlme_3.1-137 MASS_7.3-51.1 class_7.3-15
[45] tools_3.5.2 hms_0.5.2 matrixStats_0.55.0 stringr_1.4.0
[49] S4Vectors_0.20.1 munsell_0.5.0 limSolve_1.5.5.3 AnnotationDbi_1.44.0 [53] compiler_3.5.2 rlang_0.4.1 grid_3.5.2 RCurl_1.95-4.12
[57] rstudioapi_0.10 bitops_1.0-6 gtable_0.3.0 DBI_1.0.0
[61] curl_4.2 R6_2.4.0 bit_1.1-14 zeallot_0.1.0
[65] readr_1.3.1 stringi_1.4.3 sva_3.30.1 Rcpp_1.0.3
[69] vctrs_0.2.0 tidyselect_0.2.5

[grst]

Did you specify the path to the CIBERSORT binary? https://icbi-lab.github.io/immunedeconv/articles/immunedeconv.html#special-case-cibersort

Also, in the future, please use backticks to format your code/console outputs.

code

https://guides.github.com/features/mastering-markdown/

[JianGuoZhou3]

cibersort_binary = "/vip/jgzhou/jianguo.zhou/CIBERSORT.R"
cibersort_mat = "/vip/jgzhou/jianguo.zhou/CIBERSORT/LM22.txt"
res_cibersort = deconvolute(tibble.sclc1, "cibersort")

Running cibersort Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) :

Error in file(filename, "r", encoding = encoding) : cannot open the connection

sclc_timer=immunedeconv::deconvolute(tibble.sclc1, "timer")

Running timer assertion failed: indications fit to mixture matrix Error: length(indications) == ncol(gene_expression_matrix) is not TRUE

sclc_cibersort=immunedeconv::deconvolute(tibble.sclc1, "cibersort")

Running cibersort Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) :

Error in file(filename, "r", encoding = encoding) : cannot open the connection

[grst]

you need to use the set_xxx functions. It's all in the documentation.