Closed feefee20 closed 1 year ago
Hello, what version of mgcv is available for R3.5.1 ? The current mgcv seems to work in >= R3.6.0 (https://cran.r-project.org/web/packages/mgcv/index.html).
[solved] installed mgcv_1.8-33 (https://cran.r-project.org/src/contrib/Archive/mgcv/mgcv_1.8-33.tar.gz) that works in R3.5.1
I am trying to learn the tool by following your tutorial with the following commands and .hic file downloaded from your server: '4DNFI1UEG1HD.hic'.
Would you please help me out to fix the issue? Thanks again.
cat Flamingo.R library(FLAMINGOr) library(GenomicFeatures) library(Matrix) setwd("/home/usr/test/") all_size <- getChromInfoFromUCSC("hg38") chr_name='1' chr_name = as.numeric(chr_name) chr_size = all_size[chr_name,2] chr_name <- paste0('chr',chr_name) res = flamingo.main_func_large(hic_data_low='4DNFI1UEG1HD.hic', file_format='hic', domain_res=1e6,frag_res=5e3, chr_size=chr_size, chr_name=chr_name, normalization='KR', downsampling_rates=0.75, lambda=10,max_dist=0.01,nThread=10,n_row=30000)
cat R-Rout
Loading required package: BiocGenerics Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Download and preprocess the 'chrominfo' data frame ... OK [1] "Contact map is too large, large matrix mod is on" [1] "Dividing domains..." [1] "Processing Fragments..." [1] "caching datasets..." x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table x being coerced from class: matrix to data.table [1] "Reconstructing backbones..." Loading required package: nlme
Attaching package: ‘nlme’
The following object is masked from ‘package:IRanges’:
collapse
Our system is under:
PRETTY_NAME="Debian GNU/Linux bookworm/sid" NAME="Debian GNU/Linux" VERSION_CODENAME=bookworm
Thanks for using our software!
I guess there might be version conflicts with the imported packages. Below are the specific versions we used. Let us know if it works or not. Thanks!
strawr_0.0.9 mgcv_1.8-24 data.table_1.14.2 Matrix_1.2-14
Hello, thanks for leaving your comments.
I tried to run with same input file using the specific versions you used. It was stopped in the same step: Would be there any other possibilities?
Hi, thanks for reaching out. Based on the output file, I think your code has been run successfully. Only thing is that you need to save the res
data.
Thanks for checking. All set! Thanks again!
Hello,
Thanks for the useful tool! I am trying to add your tool in conda. Would you please provide all dependencies/environments to stabilize your tool in conda? Thanks for your help.
Here's my environment in conda:
Python 3.7.0 | packaged by conda-forge | (default, Nov 12 2018, 20:15:55) [GCC 7.3.0] :: Anaconda, Inc. on linux
R version 3.5.1 (2018-07-02)