Multiple platform build/check report for BioC 3.20 - CHECK results for FLAMES on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4451
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4417
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4456
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4489
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4436
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4435
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*

CHECK results for FLAMES on teran2

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.

raw results

Summary

Package: FLAMES

Version: 1.11.2

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FLAMES_1.11.2.tar.gz

StartedAt: 2024-09-27 01:28:43 -0400 (Fri, 27 Sep 2024)

EndedAt: 2024-09-27 01:37:40 -0400 (Fri, 27 Sep 2024)

EllapsedTime: 536.8 seconds

RetCode: 1

Status: ERROR

CheckDir: FLAMES.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FLAMES_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FLAMES.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FLAMES/DESCRIPTION’ ... OK
* this is package ‘FLAMES’ version ‘1.11.2’
* 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 ... 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FLAMES.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  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 ... 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 ... NOTE
Namespace in Imports field not imported from: 'IRanges'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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'
homopolymer_pct : <anonymous>: no visible binding for global variable
  'Freq'
homopolymer_pct : <anonymous>: no visible binding for global variable
  'pct'
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'
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'
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'
transcript_coverage: no visible binding for global variable 'mat'
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 FSM_match FlankEditDist Freq HeatmapAnnotation
  allele_count bam_index barcode cell_id cell_total_reads cnt count
  counts_no_ins everything expr gene_id label length_bin mat
  mutation_index n name nucleotide pct pos ref tr_id transcript value
  which_label x y
* 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
File ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 ... 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 (!any(is.na(find_bin(c("minimap2", "k8"))))) {
+   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)
+   )
+ }
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
Warning in check_forbidden_install("Conda Environments") :
  cannot install Conda Environments during R CMD check
+ /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/0/bin/conda create --yes --prefix /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/FLAMES/1.11.2/flames_env 'python=3.12.3' --quiet -c conda-forge -c bioconda --override-channels
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/FLAMES/1.11.2/flames_env

  added / updated specs:
    - python=3.12.3


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-3.12.3              |hab00c5b_0_cpython        30.5 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        30.5 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1 
  libexpat           conda-forge/linux-64::libexpat-2.6.3-h5888daf_0 
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5 
  libgcc             conda-forge/linux-64::libgcc-14.1.0-h77fa898_1 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.1.0-h69a702a_1 
  libgomp            conda-forge/linux-64::libgomp-14.1.0-h77fa898_1 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 
  ncurses            conda-forge/linux-64::ncurses-6.5-he02047a_1 
  openssl            conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0 
  pip                conda-forge/noarch::pip-24.2-pyh8b19718_1 
  python             conda-forge/linux-64::python-3.12.3-hab00c5b_0_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8228510_1 
  setuptools         conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2024a-h8827d51_1 
  wheel              conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0 
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/0/bin/conda install --yes --prefix /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/FLAMES/1.11.2/flames_env 'python=3.12.3' -c conda-forge -c bioconda --override-channels
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.7.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

+ /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/0/bin/conda install --yes --prefix /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/FLAMES/1.11.2/flames_env -c conda-forge -c bioconda 'python=3.12.3' 'python=3.12.3' 'numpy=2.1.1' 'scipy=1.14.1' 'pysam=0.22.1' 'cutadapt=4.9' 'tqdm=4.66.5' 'pandas=2.2.3' 'oarfish=0.6.2' 'minimap2=2.28' 'samtools=1.21' 'k8=0.2.5' --override-channels
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.7.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



## Package Plan ##

  environment location: /media/volume/teran2_disk/biocbuild/.cache/R/basilisk/1.17.2/FLAMES/1.11.2/flames_env

  added / updated specs:
    - cutadapt=4.9
    - k8=0.2.5
    - minimap2=2.28
    - numpy=2.1.1
    - oarfish=0.6.2
    - pandas=2.2.3
    - pysam=0.22.1
    - python[version='3.12.3.*,3.12.3.*']
    - samtools=1.21
    - scipy=1.14.1
    - tqdm=4.66.5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cffi-1.17.1                |  py312h06ac9bb_0         288 KB  conda-forge
    cutadapt-4.9               |  py312hf67a6ed_1         335 KB  bioconda
    dnaio-1.2.1                |  py312hf67a6ed_2         150 KB  bioconda
    htslib-1.21                |       h5efdd21_0         3.0 MB  bioconda
    numpy-2.1.1                |  py312h58c1407_0         8.1 MB  conda-forge
    oarfish-0.6.2              |       hc9368f3_0         2.5 MB  bioconda
    pandas-2.2.3               |  py312hf9745cd_1        14.7 MB  conda-forge
    pysam-0.22.1               |  py312hcfdcdd7_2         4.4 MB  bioconda
    python-isal-1.7.1          |  py312h66e93f0_0          66 KB  conda-forge
    python-zlib-ng-0.5.1       |  py312h27ca174_0          56 KB  conda-forge
    samtools-1.21              |       h50ea8bc_0         462 KB  bioconda
    scipy-1.14.1               |  py312h7d485d2_0        16.9 MB  conda-forge
    xopen-2.0.2                |     pyh707e725_1          21 KB  conda-forge
    zlib-ng-2.2.2              |       h5888daf_0         103 KB  conda-forge
    zstandard-0.23.0           |  py312hef9b889_1         410 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        51.4 MB

The following NEW packages will be INSTALLED:

  c-ares             conda-forge/linux-64::c-ares-1.33.1-heb4867d_0 
  cffi               conda-forge/linux-64::cffi-1.17.1-py312h06ac9bb_0 
  colorama           conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 
  cutadapt           bioconda/linux-64::cutadapt-4.9-py312hf67a6ed_1 
  dnaio              bioconda/linux-64::dnaio-1.2.1-py312hf67a6ed_2 
  htslib             bioconda/linux-64::htslib-1.21-h5efdd21_0 
  isa-l              conda-forge/linux-64::isa-l-2.31.0-h4bc722e_2 
  k8                 bioconda/linux-64::k8-0.2.5-hdcf5f25_4 
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libblas            conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas 
  libcurl            conda-forge/linux-64::libcurl-8.8.0-hca28451_1 
  libdeflate         conda-forge/linux-64::libdeflate-1.21-h4bc722e_0 
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libgfortran        conda-forge/linux-64::libgfortran-14.1.0-h69a702a_1 
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_1 
  libgfortran5       conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_1 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-14.1.0-hc0a3c3a_1 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-14.1.0-h4852527_1 
  minimap2           bioconda/linux-64::minimap2-2.28-he4a0461_3 
  numpy              conda-forge/linux-64::numpy-2.1.1-py312h58c1407_0 
  oarfish            bioconda/linux-64::oarfish-0.6.2-hc9368f3_0 
  pandas             conda-forge/linux-64::pandas-2.2.3-py312hf9745cd_1 
  pbzip2             conda-forge/linux-64::pbzip2-1.1.13-h1fcc475_2 
  pigz               conda-forge/linux-64::pigz-2.8-h2797004_0 
  pycparser          conda-forge/noarch::pycparser-2.22-pyhd8ed1ab_0 
  pysam              bioconda/linux-64::pysam-0.22.1-py312hcfdcdd7_2 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 
  python-isal        conda-forge/linux-64::python-isal-1.7.1-py312h66e93f0_0 
  python-tzdata      conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0 
  python-zlib-ng     conda-forge/linux-64::python-zlib-ng-0.5.1-py312h27ca174_0 
  python_abi         conda-forge/linux-64::python_abi-3.12-5_cp312 
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 
  samtools           bioconda/linux-64::samtools-1.21-h50ea8bc_0 
  scipy              conda-forge/linux-64::scipy-1.14.1-py312h7d485d2_0 
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 
  tqdm               conda-forge/noarch::tqdm-4.66.5-pyhd8ed1ab_0 
  xopen              conda-forge/noarch::xopen-2.0.2-pyh707e725_1 
  zlib               conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6 
  zlib-ng            conda-forge/linux-64::zlib-ng-2.2.2-h5888daf_0 
  zstandard          conda-forge/linux-64::zstandard-0.23.0-py312hef9b889_1 
  zstd               conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0 

The following packages will be DOWNGRADED:

  libsqlite                               3.46.1-hadc24fc_0 --> 3.46.0-hde9e2c9_0 
  libzlib                                  1.3.1-h4ab18f5_1 --> 1.2.13-h4ab18f5_6 



Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR: Could not find a version that satisfies the requirement fast-edit-distance==1.2.1 (from versions: none)
ERROR: No matching distribution found for fast-edit-distance==1.2.1
Error in setupBasiliskEnv(envpath, packages = .getPackages(env), channels = .getChannels(env),  : 
  failed to install additional packages via pip
Calls: find_bin -> file.path -> <Anonymous> -> setupBasiliskEnv
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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 6 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FLAMES.Rcheck/00check.log’
for details.

Installation output

FLAMES.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FLAMES
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘FLAMES’ ...
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppFunctions.cpp -o RcppFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c classes/BamRecord.cpp -o classes/BamRecord.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c classes/GFFRecord.cpp -o classes/GFFRecord.o
In file included from classes/GFFRecord.cpp:8:
classes/../utility/utility.h: In function ‘std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |         for (int i = 0; i < s.size(); i++) {
      |                         ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c classes/GeneAnnotationParser.cpp -o classes/GeneAnnotationParser.o
In file included from classes/GeneAnnotationParser.cpp:15:
classes/../utility/utility.h: In function ‘std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |         for (int i = 0; i < s.size(); i++) {
      |                         ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c classes/Isoforms.cpp -o classes/Isoforms.o
In file included from classes/Isoforms.cpp:16:
classes/../utility/utility.h: In function ‘std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |         for (int i = 0; i < s.size(); i++) {
      |                         ~~^~~~~~~~~~
classes/Isoforms.cpp: In member function ‘void Isoforms::update_all_splice()’:
classes/Isoforms.cpp:233:35: warning: comparison of integer expressions of different signedness: ‘std::vector<StartEndPair>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  233 |                 if (blocks.size() >= (int)this->Min_sup_cnt) {
      |                     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
classes/Isoforms.cpp: In member function ‘void Isoforms::filter_TSS_TES(std::ofstream&, DoubleJunctions, float)’:
classes/Isoforms.cpp:368:33: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  368 |         if ((left_counts.size() < (int)this->Min_sup_cnt) ||
      |              ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
classes/Isoforms.cpp:369:38: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  369 |                 (right_counts.size() < (int)this->Min_sup_cnt)) {
      |                  ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
classes/Isoforms.cpp: In member function ‘void Isoforms::match_known_annotation(const std::unordered_map<std::__cxx11::basic_string<char>, Junctions>&, const std::unordered_map<std::__cxx11::basic_string<char>, Pos>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<StartEndPair> >&, GeneBlocks, std::unordered_map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >)’:
classes/Isoforms.cpp:662:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare]
  662 |                                 for (int j = 0; j < std::min(raw_iso_key.size() - 1, junction.junctions.size()); j++) {
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
classes/Isoforms.cpp:713:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  713 |                         for (int i = 0; i < new_exons.size(); ++i) {
      |                                         ~~^~~~~~~~~~~~~~~~~~
classes/Isoforms.cpp:725:46: warning: comparisons like ‘X<=Y<=Z’ do not have their mathematical meaning [-Wparentheses]
  725 |                                 } else if (0 < i < raw_iso_key.size() - 1) { // a site from the middle somewhere
      |                                            ~~^~~
classes/Isoforms.cpp: In member function ‘std::string Isoforms::isoform_to_gff3(float)’:
classes/Isoforms.cpp:1140:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1140 |                         for (int i = 0; i < exons.size(); i+=2) {
      |                                         ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c classes/junctions.cpp -o classes/junctions.o
In file included from classes/junctions.cpp:12:
classes/../utility/utility.h: In function ‘std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |         for (int i = 0; i < s.size(); i++) {
      |                         ~~^~~~~~~~~~
classes/junctions.cpp: In function ‘std::unordered_map<std::__cxx11::basic_string<char>, std::vector<StartEndPair> > get_gene_flat(const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<StartEndPair> >&)’:
classes/junctions.cpp:166:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<StartEndPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |         for (int i = 1; i < exons.size(); i++) {
      |                         ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c main-functions/find_isoform.cpp -o main-functions/find_isoform.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c main-functions/flexiplex.cpp -o main-functions/flexiplex.o
main-functions/flexiplex.cpp: In function ‘unsigned int edit_distance(const std::string&, const std::string&, unsigned int&, int)’:
main-functions/flexiplex.cpp:119:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  119 |       if (min_value <= max_editd)
      |           ~~~~~~~~~~^~~~~~~~~~~~
main-functions/flexiplex.cpp: In function ‘Barcode get_barcode(const std::string&, const std::unordered_set<std::__cxx11::basic_string<char> >&, int, int, const std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&)’:
main-functions/flexiplex.cpp:225:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  225 |     if (i_pattern >= subpattern_ends[i_subpattern]) {
main-functions/flexiplex.cpp:286:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  286 |     if (editDistance == barcode.editd) {
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:288:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  288 |     } else if (editDistance < barcode.editd &&
      |                ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:289:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  289 |                editDistance <= barcode_max_editd) { // if best so far, update
      |                ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp: In function ‘std::vector<Barcode> big_barcode_search(const std::string&, const std::unordered_set<std::__cxx11::basic_string<char> >&, int, int, const std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&)’:
main-functions/flexiplex.cpp:351:29: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  351 |       if (barcode.flank_end == std::string::npos) {
      |           ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp: In function ‘void print_stats(const std::string&, const std::vector<Barcode>&, std::ostream&)’:
main-functions/flexiplex.cpp:376:38: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  376 |                << (barcode.flank_end == std::string::npos ? "True" : "False")
      |                    ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp: In function ‘void print_read(const std::string&, const std::string&, const std::string&, const std::vector<Barcode>&, std::ofstream&, std::unordered_set<std::__cxx11::basic_string<char> >&, bool)’:
main-functions/flexiplex.cpp:401:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Barcode>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  401 |   for (int b = 0; b < vec_bc.size(); b++) {
      |                   ~~^~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:412:32: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  412 |     if (vec_bc.at(b).flank_end == std::string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:417:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Barcode>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  417 |     for (int f = 0; f < vec_bc.size(); f++) {
      |                     ~~^~~~~~~~~~~~~~~
main-functions/flexiplex.cpp: In function ‘int flexiplex_cpp(Rcpp::String, Rcpp::String, bool, int, int, Rcpp::StringVector, Rcpp::String, Rcpp::String, Rcpp::String, int)’:
main-functions/flexiplex.cpp:636:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<SearchResult> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  636 |     for (int t = 0; t < sr_v.size();
      |                     ~~^~~~~~~~~~~~~
main-functions/flexiplex.cpp:641:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SearchResult>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  641 |       for (int r = 0; r < sr_v[t].size(); r++) { // loop over the reads
      |                       ~~^~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:643:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Barcode>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  643 |         for (int b = 0; b < sr_v[t][r].vec_bc_for.size(); b++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:645:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Barcode>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  645 |         for (int b = 0; b < sr_v[t][r].vec_bc_rev.size(); b++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c main-functions/get_transcript_seq.cpp -o main-functions/get_transcript_seq.o
main-functions/get_transcript_seq.cpp: In function ‘void write_fa(const std::string&, const std::string&, const std::string&, int)’:
main-functions/get_transcript_seq.cpp:87:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   87 |     while (i < seq.size()) {
      |            ~~^~~~~~~~~~~~
main-functions/get_transcript_seq.cpp:88:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   88 |         if (i + wrap_len > seq.size()) {
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c main-functions/group_bam2isoform.cpp -o main-functions/group_bam2isoform.o
In file included from main-functions/group_bam2isoform.cpp:18:
main-functions/../utility/utility.h: In function ‘std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
main-functions/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |         for (int i = 0; i < s.size(); i++) {
      |                         ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c main-functions/pileup_readid.cpp -o main-functions/pileup_readid.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c tests/test-junctions.cpp -o tests/test-junctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c tests/test-parsing.cpp -o tests/test-parsing.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c utility/cigars.cpp -o utility/cigars.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c utility/bam.c -o utility/bam.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-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 /media/volume/teran2_disk/biocbuild/bbs-3.20-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)

Tests output

FLAMES.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
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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/RtmpQigSs7/file61cbe69e3ea9d/config_file_400574.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/RtmpQigSs7/bc_allow.tsv
Number of known barcodes: 143
Searching for barcodes...
Number of reads processed: 10
Number of reads where a barcode was found: 0
Number of reads where more than one barcode was found: 0
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/RtmpQigSs7/bc_allow.tsv
Number of known barcodes: 143
Searching for barcodes...
Number of reads processed: 393
Number of reads where a barcode was found: 368
Number of reads where more than one barcode was found: 4
All done!
Skipping TSO trimming...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 17.987   0.998  19.009

Example timings

FLAMES.Rcheck/FLAMES-Ex.timings

name	user	system	elapsed
annotation_to_fasta	1.289	0.120	1.556
blaze	0.243	0.054	1.717