Changqing Wang
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/FLAMES |
| git_branch: devel |
| git_last_commit: 534d30d |
| git_last_commit_date: 2025-01-05 23:25:58 -0500 (Sun, 05 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 716/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FLAMES 2.1.4 (landing page) Changqing Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the FLAMES package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FLAMES.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: FLAMES |
| Version: 2.1.4 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FLAMES_2.1.4.tar.gz |
| StartedAt: 2025-01-24 22:18:24 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 22:29:59 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 695.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FLAMES.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FLAMES_2.1.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FLAMES.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.21-bioc/meat/FLAMES.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* 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 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 ... 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
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 ... 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 ... 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/bbs-3.21-bioc/R/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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_isoform_reduced_dim 20.007 0.813 20.816
bulk_long_pipeline 19.207 0.987 19.138
sc_long_multisample_pipeline 12.652 5.947 12.690
create_se_from_dir 17.613 0.495 15.686
create_sce_from_dir 6.288 3.203 7.999
find_isoform 6.868 0.199 7.114
get_GRangesList 6.767 0.162 6.994
minimap2_align 6.473 0.134 6.657
relative_mutation_positions 6.230 0.259 6.490
plot_coverage 6.080 0.180 6.295
sc_long_pipeline 3.787 1.755 3.534
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/FLAMES.Rcheck/00check.log’
for details.
FLAMES.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL FLAMES ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘FLAMES’ ... ** this is package ‘FLAMES’ version ‘2.1.4’ ** using non-staged installation via StagedInstall field ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppFunctions.cpp -o RcppFunctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c classes/BamRecord.cpp -o classes/BamRecord.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c classes/GFFRecord.cpp -o classes/GFFRecord.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c classes/GeneAnnotationParser.cpp -o classes/GeneAnnotationParser.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c classes/Isoforms.cpp -o classes/Isoforms.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c classes/junctions.cpp -o classes/junctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c main-functions/find_isoform.cpp -o main-functions/find_isoform.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c main-functions/flexiplex.cpp -o main-functions/flexiplex.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c main-functions/get_transcript_seq.cpp -o main-functions/get_transcript_seq.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c main-functions/group_bam2isoform.cpp -o main-functions/group_bam2isoform.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c main-functions/pileup_readid.cpp -o main-functions/pileup_readid.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c tests/test-junctions.cpp -o tests/test-junctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c tests/test-parsing.cpp -o tests/test-parsing.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c utility/cigars.cpp -o utility/cigars.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -c utility/bam.c -o utility/bam.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppExports.o RcppFunctions.o classes/BamRecord.o classes/GFFRecord.o classes/GeneAnnotationParser.o classes/Isoforms.o classes/junctions.o main-functions/find_isoform.o main-functions/flexiplex.o main-functions/get_transcript_seq.o main-functions/group_bam2isoform.o main-functions/pileup_readid.o tests/test-junctions.o tests/test-parsing.o utility/cigars.o utility/edlib-1.2.7/edlib.o utility/bam.o -pthread -lz /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug FLAMES.so; fi installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (FLAMES)
FLAMES.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(FLAMES)
>
> test_check("FLAMES")
Writing configuration parameters to: /tmp/RtmprCzFKI/file2d6665525a42c0/config_file_2975333.json
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d66653f11797d/bc_allow.tsv
Number of known barcodes: 143
Processing file: /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/extdata/fastq/musc_rps24.fastq.gz
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
Skipping TSO trimming...
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d66653f03526e/bc_allow.tsv
Number of known barcodes: 143
Processing file: /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/extdata/fastq/musc_rps24.fastq.gz
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
Skipping TSO trimming...
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d66653f03526e/bc_allow.tsv
Number of known barcodes: 143
Processing file: /tmp/RtmprCzFKI/file2d66653c7399f0/musc_rps24_1.fastq
Searching for barcodes...
Processing file: /tmp/RtmprCzFKI/file2d66653c7399f0/musc_rps24_2.fastq
Searching for barcodes...
Processing file: /tmp/RtmprCzFKI/file2d66653c7399f0/musc_rps24_3.fastq
Searching for barcodes...
Processing file: /tmp/RtmprCzFKI/file2d66653c7399f0/musc_rps24_4.fastq
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
Skipping TSO trimming...
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d66657eb5b30f/bc_allow.tsv
Number of known barcodes: 143
Processing file: /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/extdata/fastq/musc_rps24.fastq.gz
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
Skipping TSO trimming...
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d66657eb5b30f/bc_allow.tsv
Number of known barcodes: 143
Processing file: /tmp/RtmprCzFKI/file2d66655409b2c5/musc_rps24_1.fastq
Searching for barcodes...
Processing file: /tmp/RtmprCzFKI/file2d66655409b2c5/musc_rps24_2.fastq
Searching for barcodes...
Processing file: /tmp/RtmprCzFKI/file2d66655409b2c5/musc_rps24_3.fastq
Searching for barcodes...
Processing file: /tmp/RtmprCzFKI/file2d66655409b2c5/musc_rps24_4.fastq
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d66657eb5b30f/bc_allow.tsv
Number of known barcodes: 143
Processing file: /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/extdata/fastq/musc_rps24.fastq.gz
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
Skipping TSO trimming...
FLEXIPLEX 0.96.2
Setting max barcode edit distance to 2
Setting max flanking sequence edit distance to 8
Setting read IDs to be replaced
Setting number of threads to 1
Search pattern:
primer: CTACACGACGCTCTTCCGATCT
BC: NNNNNNNNNNNNNNNN
UMI: NNNNNNNNNNNN
polyT: TTTTTTTTT
Setting known barcodes from /tmp/RtmprCzFKI/file2d666573c7bafb/bc_allow.tsv
Number of known barcodes: 143
Processing file: /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/extdata/fastq/musc_rps24.fastq.gz
Searching for barcodes...
Number of reads processed: 393
Number of reads where at least one barcode was found: 368
Number of reads with exactly one barcode match: 364
Number of chimera reads: 1
All done!
Skipping TSO trimming...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
23.586 1.200 24.779
FLAMES.Rcheck/FLAMES-Ex.timings
| name | user | system | elapsed | |
| annotation_to_fasta | 1.306 | 0.086 | 1.394 | |
| blaze | 0.409 | 0.051 | 2.409 | |
| bulk_long_pipeline | 19.207 | 0.987 | 19.138 | |
| combine_sce | 0.881 | 0.078 | 0.959 | |
| convolution_filter | 0.000 | 0.001 | 0.001 | |
| create_config | 0.005 | 0.001 | 0.005 | |
| create_sce_from_dir | 6.288 | 3.203 | 7.999 | |
| create_se_from_dir | 17.613 | 0.495 | 15.686 | |
| cutadapt | 0.000 | 0.000 | 0.001 | |
| filter_annotation | 0.669 | 0.078 | 0.746 | |
| filter_coverage | 4.267 | 0.386 | 4.693 | |
| find_barcode | 0.796 | 0.144 | 0.943 | |
| find_bin | 0.007 | 0.001 | 0.008 | |
| find_isoform | 6.868 | 0.199 | 7.114 | |
| find_variants | 4.033 | 0.519 | 4.551 | |
| get_GRangesList | 6.767 | 0.162 | 6.994 | |
| get_coverage | 3.896 | 0.202 | 4.129 | |
| minimap2_align | 6.473 | 0.134 | 6.657 | |
| minimap2_realign | 0.638 | 0.049 | 0.686 | |
| parse_gff_tree | 0.216 | 0.009 | 0.240 | |
| plot_coverage | 6.080 | 0.180 | 6.295 | |
| plot_demultiplex | 1.151 | 0.050 | 1.201 | |
| plot_isoform_heatmap | 3.452 | 0.080 | 3.534 | |
| plot_isoform_reduced_dim | 20.007 | 0.813 | 20.816 | |
| plot_isoforms | 2.662 | 0.024 | 2.688 | |
| quantify_transcript | 1.885 | 0.045 | 1.983 | |
| quantify_transcript_flames | 1.906 | 0.038 | 1.996 | |
| relative_mutation_positions | 6.230 | 0.259 | 6.490 | |
| sc_DTU_analysis | 2.771 | 2.092 | 2.895 | |
| sc_impute_transcript | 0.649 | 0.056 | 0.705 | |
| sc_long_multisample_pipeline | 12.652 | 5.947 | 12.690 | |
| sc_long_pipeline | 3.787 | 1.755 | 3.534 | |
| sc_mutations | 2.241 | 0.347 | 2.587 | |
| weight_transcripts | 0.038 | 0.023 | 0.061 | |