############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings FLAMES_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FLAMES.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FLAMES/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FLAMES’ version ‘1.8.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FLAMES’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/home/biocbuild/bbs-3.18-bioc/meat/FLAMES.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE annotation_to_fasta: no visible global function definition for 'write.table' generate_sc_sce: no visible binding for global variable 'FSM_match' plot_coverage: no visible binding for global variable 'x' plot_coverage: no visible binding for global variable 'transcript' plot_coverage: no visible binding for global variable 'length_bin' plot_demultiplex: no visible binding for global variable 'Freq' plot_demultiplex: no visible binding for global variable '.' plot_demultiplex: no visible binding for global variable 'x' plot_demultiplex: no visible binding for global variable 'FlankEditDist' plot_demultiplex: no visible binding for global variable 'n' plot_demultiplex: no visible binding for global variable 'BarcodeEditDist' plot_flagstat: no visible global function definition for 'everything' plot_flagstat: no visible binding for global variable 'name' plot_flagstat: no visible binding for global variable 'value' sc_DTU_analysis: no visible binding for global variable 'FSM_match' sc_DTU_analysis: no visible binding for global variable 'gene_id' sc_DTU_analysis: no visible binding for global variable '.' sc_DTU_analysis: no visible binding for global variable 'cell_id' sc_DTU_analysis: no visible binding for global variable 'cnt' sc_DTU_analysis: no visible binding for global variable 'tr_id' sc_DTU_analysis: no visible binding for global variable 'label' sc_DTU_analysis : filter_tr: no visible binding for global variable 'gene_id' sc_DTU_analysis : filter_tr: no visible global function definition for 'all_vars' sc_DTU_analysis : filter_tr: no visible binding for global variable '.' sc_DTU_analysis: no visible global function definition for 'all_vars' sc_heatmap_expression: no visible binding for global variable 'transcript_id' sc_heatmap_expression: no visible binding for global variable 'gene_id' sc_heatmap_expression : group_annotation: no visible binding for global variable 'heatmap_annotation_colors' sc_umap_expression: no visible binding for global variable 'transcript_id' sc_umap_expression: no visible binding for global variable 'gene_id' sc_umap_expression: no visible binding for global variable 'x' sc_umap_expression: no visible binding for global variable 'y' sc_umap_expression : plot_idx: no visible binding for global variable 'x' sc_umap_expression : plot_idx: no visible binding for global variable 'y' transcript_coverage: no visible binding for global variable 'mat' Undefined global functions or variables: . BarcodeEditDist FSM_match FlankEditDist Freq all_vars cell_id cnt everything gene_id heatmap_annotation_colors label length_bin mat n name tr_id transcript transcript_id value write.table x y Consider adding importFrom("utils", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘FLAMES-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: bulk_long_pipeline > ### Title: Pipeline for Bulk Data > ### Aliases: bulk_long_pipeline > > ### ** Examples > > # download the two fastq files, move them to a folder to be merged together > temp_path <- tempfile() > bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE) > file_url <- + "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data" > # download the required fastq files, and move them to new folder > fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq1", paste(file_url, "fastq/sample1.fastq.gz", sep = "/")))]] > fastq2 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq2", paste(file_url, "fastq/sample2.fastq.gz", sep = "/")))]] > annotation <- bfc[[names(BiocFileCache::bfcadd(bfc, "annot.gtf", paste(file_url, "SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf", sep = "/")))]] > genome_fa <- bfc[[names(BiocFileCache::bfcadd(bfc, "genome.fa", paste(file_url, "SIRV_isoforms_multi-fasta_170612a.fasta", sep = "/")))]] > fastq_dir <- paste(temp_path, "fastq_dir", sep = "/") # the downloaded fastq files need to be in a directory to be merged together > dir.create(fastq_dir) > file.copy(c(fastq1, fastq2), fastq_dir) [1] TRUE TRUE > unlink(c(fastq1, fastq2)) # the original files can be deleted > > outdir <- tempfile() > dir.create(outdir) > if (is.character(locate_minimap2_dir())) { + se <- bulk_long_pipeline( + annotation = annotation, fastq = fastq_dir, outdir = outdir, genome_fa = genome_fa, + config_file = system.file("extdata/SIRV_config_default.json", package = "FLAMES") + ) + + se_2 <- create_se_from_dir(outdir = outdir, annotation = annotation) + } /usr/bin/minimap2 /usr/bin/minimap2 #### Input parameters: { "comment": ["this is the default config for SIRV spike-in data. use splice annotation on alignment."], "pipeline_parameters": { "seed": [2022], "threads": [1], "do_barcode_demultiplex": [false], "do_gene_quantification": [true], "do_genome_alignment": [true], "do_isoform_identification": [true], "bambu_isoform_identification": [false], "do_read_realignment": [true], "do_transcript_quantification": [true] }, "barcode_parameters": { "max_bc_editdistance": [2], "max_flank_editdistance": [8], "pattern": { "primer": ["CTACACGACGCTCTTCCGATCT"], "BC": ["NNNNNNNNNNNNNNNN"], "UMI": ["NNNNNNNNNNNN"], "polyT": ["TTTTTTTTT"] }, "TSO_seq": ["CCCATGTACTCTGCGTTGATACCACTGCTT"], "TSO_prime": [3], "full_length_only": [false] }, "isoform_parameters": { "generate_raw_isoform": [true], "max_dist": [10], "max_ts_dist": [100], "max_splice_match_dist": [10], "min_fl_exon_len": [40], "max_site_per_splice": [3], "min_sup_cnt": [10], "min_cnt_pct": [0.01], "min_sup_pct": [0.2], "bambu_trust_reference": [true], "strand_specific": [1], "remove_incomp_reads": [5], "downsample_ratio": [1] }, "alignment_parameters": { "use_junctions": [true], "no_flank": [true] }, "realign_parameters": { "use_annotation": [true] }, "transcript_counting": { "min_tr_coverage": [0.75], "min_read_coverage": [0.75] } } gene annotation: /home/biocbuild/tmp/Rtmpg21oWa/file1091117ce668f/10911159b0ded8_SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf genome fasta: /home/biocbuild/tmp/Rtmpg21oWa/file1091117ce668f/109111417158e6_SIRV_isoforms_multi-fasta_170612a.fasta input fastq files: /home/biocbuild/tmp/Rtmpg21oWa/file1091117ce668f/fastq_dir/10911159b92958_sample2.fastq.gz /home/biocbuild/tmp/Rtmpg21oWa/file1091117ce668f/fastq_dir/10911174a45032_sample1.fastq.gz output directory: /home/biocbuild/tmp/Rtmpg21oWa/file10911117252276 directory containing minimap2: /usr/bin #### Aligning reads to genome using minimap2 Aligning sample 10911159b92958_sample2 ... 10:46:17 Thu Nov 02 2023 minimap2_align Error in minimap2_align(config, genome_fa, fastq_files[i], annotation, : Could not locate k8 and/or paftools.js in the minimap2 folder, they are required for converting annotation to bed12 files Calls: bulk_long_pipeline -> minimap2_align Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/FLAMES.Rcheck/00check.log’ for details.