* installing *source* package 'HRDscoreAlteraBam' ...
** using staged installation
** libs
using C compiler: 'x86_64-conda-linux-gnu-cc (conda-forge gcc 15.2.0-18) 15.2.0'
using Fortran compiler: 'GNU Fortran (conda-forge gcc 15.2.0-18) 15.2.0'
installing to /tmp/nxf.X6nidOkbVP/R_libs/00LOCK-hrd_score_altera_bam/00new/HRDscoreAlteraBam/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HRDscoreAlteraBam)
Loading required package: pctGCdata
Attaching package: 'HRDscoreAlteraBam'
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Attaching package: 'dplyr'
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Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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Loading required package: IRanges
Attaching package: 'IRanges'
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Loading required package: GenomeInfoDb
Loading required package: NMF
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Attaching package: 'pkgmaker'
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Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 383/384
To enable shared memory capabilities, try: install.extras('
NMF
')
Attaching package: 'NMF'
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Attaching package: 'data.table'
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Loading required package: gridExtra
Attaching package: 'gridExtra'
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Attaching package: 'purrr'
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Taking input= as a system command because it contains a space ('gunzip -c dbsnp_baseline_altera.260120.tsv.gz'). If it's a filename please remove the space, or use file= explicitly. A variable is being passed to input= and when this is taken as a system command there is a security concern if you are creating an app, the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command because it contains a space ('gunzip -c 1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.pileup.csv.gz'). If it's a filename please remove the space, or use file= explicitly. A variable is being passed to input= and when this is taken as a system command there is a security concern if you are creating an app, the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Writing to ./FACETS
Fontconfig warning: using without calling FcInit()
Fontconfig error: No writable cache directories
/opt/conda/envs/env_tih_hrd_running_env/var/cache/fontconfig
/.cache/fontconfig
/.fontconfig
Attaching package: 'XVector'
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Attaching package: 'Biostrings'
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Attaching package: 'rtracklayer'
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Writing ./1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.hrd_score_results.tsv
COMPLETE HRDscore