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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FLAMES_2.1.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FLAMES.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FLAMES/DESCRIPTION’ ... OK
* this is package ‘FLAMES’ version ‘2.1.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 43 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FLAMES’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
Found the following additional notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.21-bioc/meat/FLAMES.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
* 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 code 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
create_spe: no visible binding for global variable 'barcode'
filter_coverage: no visible global function definition for
  'starts_with'
filter_coverage: no visible binding for global variable 'filter_res'
find_barcode: no visible binding for global variable 'Sample'
find_barcode: no visible binding for global variable 'Outfile'
find_variants_grange: no visible binding for global variable
  'which_label'
find_variants_grange: no visible binding for global variable
  'nucleotide'
find_variants_grange: no visible binding for global variable 'pos'
find_variants_grange: no visible binding for global variable 'count'
find_variants_grange: no visible binding for global variable
  'counts_no_ins'
find_variants_grange: no visible binding for global variable 'ref'
generate_sc_sce: no visible binding for global variable 'FSM_match'
get_coverage: no visible binding for global variable 'Freq'
homopolymer_pct : <anonymous>: no visible binding for global variable
  'Freq'
homopolymer_pct : <anonymous>: no visible binding for global variable
  'pct'
parse_oarfish_sc_output: no visible binding for global variable '.'
plot_coverage: no visible binding for global variable 'tr_length'
plot_coverage: no visible binding for global variable 'read_counts'
plot_coverage: no visible binding for global variable 'total_counts'
plot_coverage: no visible binding for global variable 'cumpct'
plot_coverage: no visible binding for global variable 'length_bin'
plot_coverage: no visible binding for global variable 'min_length'
plot_coverage: no visible binding for global variable 'max_length'
plot_coverage: no visible global function definition for 'head'
plot_coverage: no visible binding for global variable 'transcript'
plot_demultiplex: no visible binding for global variable 'CellBarcode'
plot_demultiplex: no visible binding for global variable 'Sample'
plot_demultiplex: no visible binding for global variable 'UMI'
plot_demultiplex: no visible binding for global variable 'UMI_count'
plot_demultiplex: no visible binding for global variable 'barcode_rank'
plot_demultiplex: no visible binding for global variable
  'FlankEditDist'
plot_demultiplex: no visible binding for global variable 'n_reads'
plot_demultiplex: no visible binding for global variable
  'BarcodeEditDist'
plot_demultiplex: no visible binding for global variable 'total reads'
plot_demultiplex: no visible binding for global variable 'demultiplexed
  reads'
plot_demultiplex: no visible binding for global variable 'single match
  reads'
plot_demultiplex: no visible binding for global variable
  'undemultiplexted reads'
plot_demultiplex: no visible binding for global variable
  'multi-matching reads'
plot_demultiplex: no visible binding for global variable 'Type'
plot_demultiplex: no visible binding for global variable 'Reads'
plot_demultiplex: no visible binding for global variable 'input'
plot_demultiplex: no visible binding for global variable 'output'
plot_demultiplex: no visible binding for global variable
  'read1_with_adapter'
plot_demultiplex: no visible binding for global variable 'Count'
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'
plot_isoform_heatmap : group_annotation: no visible global function
  definition for 'HeatmapAnnotation'
plot_isoform_reduced_dim: no visible binding for global variable 'x'
plot_isoform_reduced_dim: no visible binding for global variable 'y'
plot_isoform_reduced_dim: no visible binding for global variable 'expr'
plot_spatial_isoform: no visible global function definition for 'head'
plot_spatial_pie: no visible global function definition for 'head'
plot_spatial_pie: no visible binding for global variable 'imageY'
plot_spatial_pie: no visible binding for global variable 'imageX'
relative_mutation_positions: no visible binding for global variable
  'region'
relative_mutation_positions_single: no visible binding for global
  variable 'type'
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 binding for global variable '.'
sc_mutations: no visible binding for global variable 'mutation_index'
sc_mutations: no visible binding for global variable 'bam_index'
variant_count_tb: no visible binding for global variable 'barcode'
variant_count_tb: no visible binding for global variable 'allele_count'
variant_count_tb: no visible binding for global variable
  'cell_total_reads'
Undefined global functions or variables:
  . BarcodeEditDist CellBarcode Count FSM_match FlankEditDist Freq
  HeatmapAnnotation Outfile Reads Sample Type UMI UMI_count
  allele_count bam_index barcode barcode_rank cell_id cell_total_reads
  cnt count counts_no_ins cumpct demultiplexed reads everything expr
  filter_res gene_id head imageX imageY input label length_bin
  max_length min_length multi-matching reads mutation_index n_reads
  name nucleotide output pct pos read1_with_adapter read_counts ref
  region single match reads starts_with total reads total_counts tr_id
  tr_length transcript type undemultiplexted reads value which_label x
  y
Consider adding
  importFrom("base", "match", "single")
  importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bulk_long_pipeline.Rd: SummarizedExperiment
  sc_long_multisample_pipeline.Rd: SingleCellExperiment
  sc_long_pipeline.Rd: SingleCellExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... INFO
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
File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/FLAMES/libs/FLAMES.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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)
> se <- bulk_long_pipeline(
+   annotation = annotation, fastq = fastq_dir, outdir = outdir, genome_fa = genome_fa,
+   config_file = create_config(outdir, type = "sc_3end", threads = 1, no_flank = TRUE)
+ )
Writing configuration parameters to:  /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/config_file_2774863.json 
#### Input parameters:
{
  "pipeline_parameters": {
    "seed": [2022],
    "threads": [1],
    "do_barcode_demultiplex": [true],
    "do_gene_quantification": [true],
    "do_genome_alignment": [true],
    "do_isoform_identification": [true],
    "bambu_isoform_identification": [false],
    "multithread_isoform_identification": [false],
    "do_read_realignment": [true],
    "do_transcript_quantification": [true],
    "oarfish_quantification": [true]
  },
  "barcode_parameters": {
    "max_bc_editdistance": [2],
    "max_flank_editdistance": [8],
    "pattern": {
      "primer": ["CTACACGACGCTCTTCCGATCT"],
      "BC": ["NNNNNNNNNNNNNNNN"],
      "UMI": ["NNNNNNNNNNNN"],
      "polyT": ["TTTTTTTTT"]
    },
    "strand": ["-"],
    "TSO_seq": ["AAGCAGTGGTATCAACGCAGAGTACATGGG"],
    "TSO_prime": [5],
    "cutadapt_minimum_length": [10],
    "full_length_only": [false]
  },
  "isoform_parameters": {
    "generate_raw_isoform": [false],
    "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": [5],
    "min_cnt_pct": [0.001],
    "min_sup_pct": [0.2],
    "bambu_trust_reference": [true],
    "strand_specific": [0],
    "remove_incomp_reads": [4],
    "downsample_ratio": [1]
  },
  "alignment_parameters": {
    "use_junctions": [true],
    "no_flank": [true]
  },
  "realign_parameters": {
    "use_annotation": [true]
  },
  "transcript_counting": {
    "min_tr_coverage": [0.4],
    "min_read_coverage": [0.4]
  }
} 
gene annotation: /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/2a574f5d55c3ec_SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf 
genome fasta: /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/2a574f651911f8_SIRV_isoforms_multi-fasta_170612a.fasta 
input fastq files: /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/fastq_dir/2a574f59ce604f_sample1.fastq.gz
 /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/fastq_dir/2a574f673df12a_sample2.fastq.gz
output directory: /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177 
minimap2 path: 
k8 path: 
#### Aligning reads to genome using minimap2
	Aligning sample  2a574f59ce604f_sample1 ...
10:47:05 Tue Jan 28 2025 minimap2_align
[M::mm_idx_gen::0.016*0.88] collected minimizers
[M::mm_idx_gen::0.027*0.93] sorted minimizers
[M::main::0.027*0.93] loaded/built the index for 7 target sequence(s)
[M::mm_mapopt_update::0.029*0.93] mid_occ = 14
[M::mm_idx_stat] kmer size: 14; skip: 5; is_hpc: 0; #seq: 7
[M::mm_idx_stat::0.031*0.94] distinct minimizers: 39103 (61.08% are singletons); average occurrences: 1.935; average spacing: 2.947; total length: 223019
[M::worker_pipeline::8.403*0.99] mapped 2500 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: /usr/bin/minimap2 -ax splice -t 1 -k14 --secondary=no --seed 2022 --splice-flank=no --junc-bed /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/tmp_splice_anno.bed12 --junc-bonus 1 /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/2a574f651911f8_SIRV_isoforms_multi-fasta_170612a.fasta /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/fastq_dir/2a574f59ce604f_sample1.fastq.gz
[M::main] Real time: 8.409 sec; CPU: 8.286 sec; Peak RSS: 0.079 GB
	Aligning sample  2a574f673df12a_sample2 ...
10:47:14 Tue Jan 28 2025 minimap2_align
[M::mm_idx_gen::0.015*0.83] collected minimizers
[M::mm_idx_gen::0.025*0.90] sorted minimizers
[M::main::0.025*0.90] loaded/built the index for 7 target sequence(s)
[M::mm_mapopt_update::0.028*0.91] mid_occ = 14
[M::mm_idx_stat] kmer size: 14; skip: 5; is_hpc: 0; #seq: 7
[M::mm_idx_stat::0.029*0.91] distinct minimizers: 39103 (61.08% are singletons); average occurrences: 1.935; average spacing: 2.947; total length: 223019
[M::worker_pipeline::8.507*0.99] mapped 2500 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: /usr/bin/minimap2 -ax splice -t 1 -k14 --secondary=no --seed 2022 --splice-flank=no --junc-bed /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/tmp_splice_anno.bed12 --junc-bonus 1 /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/2a574f651911f8_SIRV_isoforms_multi-fasta_170612a.fasta /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/fastq_dir/2a574f673df12a_sample2.fastq.gz
[M::main] Real time: 8.513 sec; CPU: 8.417 sec; Peak RSS: 0.112 GB
10:47:22 Tue Jan 28 2025 find_isoform
#### Read gene annotations
	Removed similar transcripts in gene annotation: Counter({'duplicated_transcripts': 2})
#### find isoforms
SIRV1
SIRV2
SIRV3
SIRV4
SIRV5
SIRV6
SIRV7
#### Realign to transcript using minimap2
	Realigning sample  2a574f59ce604f_sample1 ...
10:47:25 Tue Jan 28 2025 minimap2_realign
[M::mm_idx_gen::0.004*1.03] collected minimizers
[M::mm_idx_gen::0.007*1.60] sorted minimizers
[M::main::0.007*1.60] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.008*1.56] mid_occ = 20
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.008*1.53] distinct minimizers: 4801 (32.41% are singletons); average occurrences: 3.318; average spacing: 5.400; total length: 86023
[M::worker_pipeline::1.244*2.52] mapped 2500 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: /usr/bin/minimap2 --eqx -N 100 -ax map-ont /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/transcript_assembly.fa /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/fastq_dir/2a574f59ce604f_sample1.fastq.gz
[M::main] Real time: 1.247 sec; CPU: 3.138 sec; Peak RSS: 0.032 GB
file renamed to  2a574f59ce604f_sample1_realign2transcript.bam 
Warning in file.remove(file.path(outdir, paste0(prefix, "tmp_align.bam"))) :
  cannot remove file '/home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/2a574f59ce604f_sample1_tmp_align.bam', reason 'No such file or directory'
	Realigning sample  2a574f673df12a_sample2 ...
10:47:27 Tue Jan 28 2025 minimap2_realign
[M::mm_idx_gen::0.005*0.64] collected minimizers
[M::mm_idx_gen::0.008*1.43] sorted minimizers
[M::main::0.008*1.42] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.008*1.39] mid_occ = 20
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.009*1.37] distinct minimizers: 4801 (32.41% are singletons); average occurrences: 3.318; average spacing: 5.400; total length: 86023
[M::worker_pipeline::0.906*2.48] mapped 2500 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: /usr/bin/minimap2 --eqx -N 100 -ax map-ont /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/transcript_assembly.fa /home/biocbuild/tmp/RtmpcVfmTN/file2a574f1d8a34f7/fastq_dir/2a574f673df12a_sample2.fastq.gz
[M::main] Real time: 0.908 sec; CPU: 2.250 sec; Peak RSS: 0.028 GB
file renamed to  2a574f673df12a_sample2_realign2transcript.bam 
Warning in file.remove(file.path(outdir, paste0(prefix, "tmp_align.bam"))) :
  cannot remove file '/home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/2a574f673df12a_sample2_tmp_align.bam', reason 'No such file or directory'
#### Generating transcript count matrix
2025-01-28T10:47:28.083090Z  INFO oarfish: setting user-provided filter parameters.
2025-01-28T10:47:28.084848Z  INFO oarfish::alignment_parser: read header from BAM file /home/biocbuild/tmp/RtmpcVfmTN/file2a574f771b4177/2a574f59ce604f_sample1_realign2transcript.bam, contains 86 reference sequences.
thread 'main' panicked at src/alignment_parser.rs:29:10:
has inner header
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Error in run_oarfish(realign_bam, outdir, threads = config$pipeline_parameters$threads,  : 
  error running oarfish:
134
Calls: bulk_long_pipeline ... quantify_transcript -> quantify_transcript_oarfish -> run_oarfish
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
blaze 0.423  0.066   6.472
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/FLAMES.Rcheck/00check.log’
for details.