Error: unused argument (fftempdir = fftempdir)

[brooklynnrm]

Hello, I have been trying to use the ramclustr function for deconvolution of an XCMS feature table. I have tried my own data as well as the example data and everything has thrown the error below:

Error in rc.ramclustr(ramclustObj = ramclustObj, st = st, sr = sr, maxt = maxt, : unused argument (fftempdir = fftempdir)

My input is: ure table gc_feature_table<- read.table("E:/Galaxy/Bacarelli - Additional Samples/Galaxy processing files/XCMS_Test_231017_XCMSv3.22.0_Peak.min_Peak.max.txt", sep="\t", header=TRUE)

create mz_time vector

mz_time<- paste(gc_feature_table$mz, gc_featuretable$rt, sep="") mz_time[1:10]

transcribe intensities

t_gc_int<- data.frame(t(gc_feature_table[,10:ncol(gc_feature_table)]))

add mz_time vector to transcribed matrix

t_gc_int_1<- rbind(mz_time,t_gc_int)

add sample_id vector to transcribed matrix

sample_id<- c("sample",rownames(t_gc_int)) t_gc_int_2<- cbind(sample_id,t_gc_int_1) t_gc_int_23 <- t_gc_int_2[1:10,1:20]

write output

setwd("E:/XCMS Projects/RamClustR/") write.table(t_gc_int_23, "XCMS_Test_231018_RAMClustR.csv", sep=",", row.names=FALSE, col.names=FALSE)

library(RAMClustR)

out_file<- "E:/XCMS Projects/RamClustR/" dir.create(out_file) setwd(out_file)

experiment_GC <- defineExperiment(csv = "E:/XCMS Projects/RamClustR/ExpDes.csv")

GC_Clust <- ramclustR(ms = "E:/XCMS Projects/RamClustR/XCMS_Test_231018RAMClustR.csv", featdelim = "", st = 5, ExpDes=experiment_GC, sampNameCol = 1, minModuleSize=1, mzdec=5, fftempdir = NULL)

[cbroeckl]

@brooklynnrm - what is the error message you receive?

can you also add the output from sessionInfo()?

[brooklynnrm]

R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8 time zone: America/New_York tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] scatterplot3d_0.3-44 corpcor_1.6.10 JADE_2.0-4 waveslim_1.8.4 [5] WaveICA_0.1.0 InterpretMSSpectrum_1.3.8 ggplot2_3.4.4 pcaMethods_1.92.0 [9] gplots_3.1.3 e1071_1.7-13 preprocessCore_1.62.1 fastcluster_1.2.3 [13] RCurl_1.98-1.12 curl_5.1.0 stringi_1.7.12 testthat_3.2.0 [17] BiocManager_1.30.22 xcms_3.22.0 MSnbase_2.26.0 ProtGenerics_1.32.0 [21] S4Vectors_0.38.2 mzR_2.34.1 Rcpp_1.0.11 Biobase_2.60.0 [25] BiocGenerics_0.46.0 BiocParallel_1.34.2 rmarkdown_2.25 knitr_1.44 [29] dynamicTreeCut_1.63-1 RAMClustR_1.3.0 loaded via a namespace (and not attached): [1] bitops_1.0-7 pROC_1.18.4 gridExtra_2.3 fdrtool_1.2.17 [5] rlang_1.1.1 magrittr_2.0.3 clue_0.3-65 snakecase_0.11.1 [9] MassSpecWavelet_1.66.0 matrixStats_1.0.0 compiler_4.3.1 vctrs_0.6.4 [13] stringr_1.5.0 pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1 [17] XVector_0.40.0 caTools_1.18.2 utf8_1.2.3 ggfortify_0.4.16 [21] purrr_1.0.2 xfun_0.40 zlibbioc_1.46.0 GenomeInfoDb_1.36.4 [25] DelayedArray_0.26.7 parallel_4.3.1 cluster_2.1.4 R6_2.5.1 [29] RColorBrewer_1.1-3 limma_3.56.2 brio_1.1.3 GenomicRanges_1.52.1 [33] lubridate_1.9.3 SummarizedExperiment_1.30.2 iterators_1.0.14 IRanges_2.34.1 [37] Matrix_1.6-1.1 splines_4.3.1 timechange_0.2.0 tidyselect_1.2.0 [41] rstudioapi_0.15.0 abind_1.4-5 doParallel_1.0.17 codetools_0.2-19 [45] affy_1.78.2 lattice_0.21-8 tibble_3.2.1 plyr_1.8.9 [49] withr_2.5.1 evaluate_0.22 survival_3.5-5 proxy_0.4-27 [53] pillar_1.9.0 affyio_1.70.0 MatrixGenerics_1.12.3 KernSmooth_2.23-22 [57] foreach_1.5.2 MALDIquant_1.22.1 ncdf4_1.21 generics_0.1.3 [61] munsell_0.5.0 scales_1.2.1 gtools_3.9.4 class_7.3-22 [65] glue_1.6.2 janitor_2.2.0 MsFeatures_1.8.0 tools_4.3.1 [69] plsdepot_0.2.0 mzID_1.38.0 robustbase_0.99-0 enviPat_2.6 [73] vsn_3.68.0 RANN_2.6.1 XML_3.99-0.14 grid_4.3.1 [77] impute_1.74.1 tidyr_1.3.0 MsCoreUtils_1.12.0 colorspace_2.1-0 [81] GenomeInfoDbData_1.2.10 cli_3.6.1 fansi_1.0.5 S4Arrays_1.0.6 [85] dplyr_1.1.3 gtable_0.3.4 DEoptimR_1.1-3 digest_0.6.33 [89] htmltools_0.5.6.1 multtest_2.56.0 lifecycle_1.0.3 MASS_7.3-60 --   > | > >

[brooklynnrm]

@cbroeckl The error is below:

organizing dataset replaced 75 of 171 total feature values ( 44 % ) normalizing dataset Error in rc.ramclustr(ramclustObj = ramclustObj, st = st, sr = sr, maxt = maxt, : unused argument (fftempdir = fftempdir)

[cbroeckl]

I am fairly certain this is an artifact of a reorganization of code we recently performed. i would request that you try to install from github, try again, and let me know how it goes.

detach('package:RAMClustR') devtools::install_github("cbroeckl/RAMClustR", dependencies = FALSE)

[brooklynnrm]

I just re-installed and tried again. Still getting the error:

Error in rc.ramclustr(ramclustObj = ramclustObj, st = st, sr = sr, maxt = maxt, : unused argument (fftempdir = fftempdir)

[cbroeckl]

alright - just pushed an edit. i think i found the reference causing the problem. Please try again. if this doesn't fix the issue i will ask for input files and will try to replicate the error here first.

[cbroeckl]

detach('package:RAMClustR') devtools::install_github("cbroeckl/RAMClustR", dependencies = FALSE)

[brooklynnrm]

Thank you so much for your help! This has fixed the issue!