Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1896/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPipe 2.6.0  (landing page)
Shian Su
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/scPipe
git_branch: RELEASE_3_20
git_last_commit: a29d66c
git_last_commit_date: 2024-10-29 10:23:12 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for scPipe on nebbiolo2

To the developers/maintainers of the scPipe package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scPipe.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: scPipe
Version: 2.6.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scPipe_2.6.0.tar.gz
StartedAt: 2024-12-20 05:16:37 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:24:33 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 476.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scPipe.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scPipe_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scPipe.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘scPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scPipe’ version ‘2.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scPipe’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 37.2Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
    libs     23.8Mb
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘flexmix’ ‘vctrs’
  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
sc_atac_feature_counting: warning in sc_atac_create_sce(input_folder =
  output_folder, organism = organism, sample = sample_name,
  feature_type = feature_type, pheno_data = pheno_data, report =
  create_report): partial argument match of 'sample' to 'sample_name'
sc_aligning: no visible binding for global variable ‘Var1’
sc_aligning: no visible binding for global variable ‘Freq’
sc_atac_bam_tagging: no visible binding for global variable ‘.N’
sc_atac_bam_tagging: no visible binding for global variable ‘count’
sc_atac_bam_tagging: no visible binding for global variable ‘.SD’
sc_atac_create_cell_qc_metrics: no visible binding for global variable
  ‘seqnames’
sc_atac_create_cell_qc_metrics: no visible binding for global variable
  ‘start’
sc_atac_create_cell_qc_metrics: no visible binding for global variable
  ‘end’
sc_atac_create_cell_qc_metrics: no visible binding for global variable
  ‘barcode’
sc_atac_create_cell_qc_metrics: no visible binding for global variable
  ‘count’
sc_atac_feature_counting: no visible binding for global variable
  ‘start’
sc_atac_feature_counting: no visible binding for global variable ‘end’
sc_atac_feature_counting: no visible global function definition for
  ‘write.csv’
sc_atac_plot_cells_per_feature: no visible binding for global variable
  ‘log_cells_per_feature’
sc_atac_plot_cells_per_feature: no visible binding for global variable
  ‘..count..’
sc_atac_plot_features_per_cell: no visible binding for global variable
  ‘log_features_per_cell’
sc_atac_plot_features_per_cell: no visible binding for global variable
  ‘..count..’
sc_atac_plot_fragments_cells_per_feature: no visible binding for global
  variable ‘log_counts_per_feature’
sc_atac_plot_fragments_cells_per_feature: no visible binding for global
  variable ‘log_cells_per_feature’
sc_atac_plot_fragments_features_per_cell: no visible binding for global
  variable ‘log_counts_per_cell’
sc_atac_plot_fragments_features_per_cell: no visible binding for global
  variable ‘log_features_per_cell’
sc_atac_plot_fragments_per_cell: no visible binding for global variable
  ‘log_counts_per_cell’
sc_atac_plot_fragments_per_cell: no visible binding for global variable
  ‘..count..’
sc_atac_plot_fragments_per_feature: no visible binding for global
  variable ‘log_counts_per_feature’
sc_atac_plot_fragments_per_feature: no visible binding for global
  variable ‘..count..’
sc_get_umap_data: no visible global function definition for ‘irlba’
sc_get_umap_data: no visible binding for global variable ‘value’
sc_get_umap_data: no visible binding for global variable ‘cluster’
sc_interactive_umap_plot : server: no visible binding for global
  variable ‘UMAP1’
sc_interactive_umap_plot : server: no visible binding for global
  variable ‘UMAP2’
sc_interactive_umap_plot : server: no visible binding for global
  variable ‘barcode’
sc_mae_plot_umap : <anonymous>: no visible global function definition
  for ‘irlba’
sc_mae_plot_umap : <anonymous>: no visible binding for global variable
  ‘value’
sc_mae_plot_umap : <anonymous>: no visible binding for global variable
  ‘cluster’
sc_mae_plot_umap : <anonymous>: no visible global function definition
  for ‘experiments’
sc_mae_plot_umap: no visible binding for global variable ‘UMAP1’
sc_mae_plot_umap: no visible binding for global variable ‘UMAP2’
Undefined global functions or variables:
  ..count.. .N .SD Freq UMAP1 UMAP2 Var1 barcode cluster count end
  experiments irlba log_cells_per_feature log_counts_per_cell
  log_counts_per_feature log_features_per_cell seqnames start value
  write.csv
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/scPipe/libs/scPipe.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
sc_atac_bam_tagging  32.299 19.775  51.320
plot_QC_pairs         6.112  0.054   6.167
sc_sample_data        5.213  0.124   5.338
calculate_QC_metrics  3.172  0.171   7.499
* 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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scPipe.Rcheck/00check.log’
for details.


Installation output

scPipe.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c FragmentThread.cpp -o FragmentThread.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c FragmentUtils.cpp -o FragmentUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c ResizeArray.cpp -o ResizeArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c ThreadOutputFile.cpp -o ThreadOutputFile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c Trie.cpp -o Trie.o
Trie.cpp: In member function ‘void Trie::SeqMismatchAux(std::vector<MismatchResult>&, const std::string&, trie_node*, int, int, int) const’:
Trie.cpp:265:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<trie_node*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  265 |                 for (int i = 0; i < valid_nodes.size(); i++) {
      |                                 ~~^~~~~~~~~~~~~~~~~~~~
Trie.cpp:274:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<trie_node*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  274 |                         for (int i = 0; i < valid_nodes.size(); i++) {
      |                                         ~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bam.c -o bam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c cellbarcode.cpp -o cellbarcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c check_barcode_reads.cpp -o check_barcode_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c parsecount.cpp -o parsecount.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-cpp.cpp -o test-cpp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-example.cpp -o test-example.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-fragmentThread.cpp -o test-fragmentThread.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-resizearray.cpp -o test-resizearray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-str_utils.cpp -o test-str_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-trie_matching.cpp -o test-trie_matching.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c transcriptmapping.cpp -o transcriptmapping.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function ‘std::vector<int> sc_atac_paired_fastq_to_fastq(const char*, std::vector<std::__cxx11::basic_string<char> >, const char*, const char*, const char*, bool, bool, bool, int, int, bool)’:
trimbarcode.cpp:981:16: warning: ‘fq3’ may be used uninitialized [-Wmaybe-uninitialized]
  981 |         gzclose(fq3);
      |         ~~~~~~~^~~~~
trimbarcode.cpp:720:16: note: ‘fq3’ was declared here
  720 |         gzFile fq3;
      |                ^~~
trimbarcode.cpp:812:31: warning: ‘seq3’ may be used uninitialized [-Wmaybe-uninitialized]
  812 |             if((l3 = kseq_read(seq3)) < 0){
      |                      ~~~~~~~~~^~~~~~
trimbarcode.cpp:749:13: note: ‘seq3’ was declared here
  749 |     kseq_t *seq3;
      |             ^~~~
trimbarcode.cpp: In function ‘std::vector<int> sc_atac_paired_fastq_to_csv(char*, char*, char*, char*, char*, int, int, char*, bool, bool, bool, int, int, int, int, int, int)’:
trimbarcode.cpp:1498:16: warning: ‘fq3’ may be used uninitialized [-Wmaybe-uninitialized]
 1498 |         gzclose(fq3);
      |         ~~~~~~~^~~~~
trimbarcode.cpp:1108:12: note: ‘fq3’ was declared here
 1108 |     gzFile fq3;
      |            ^~~
trimbarcode.cpp:1116:13: warning: ‘seq3’ may be used uninitialized [-Wmaybe-uninitialized]
 1116 |     kseq_t *seq3;
      |             ^~~~
trimbarcode.cpp:1203:9: warning: ‘bc1_end’ may be used uninitialized [-Wmaybe-uninitialized]
 1203 |         if (bc1_end > (int)seq1->seq.l) {
      |         ^~
trimbarcode.cpp:1162:9: note: ‘bc1_end’ was declared here
 1162 |     int bc1_end, bc2_end; // get end position in the read of barcode and umi
      |         ^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c tsscreatebins.cpp -o tsscreatebins.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o scPipe.so FragmentThread.o FragmentUtils.o Gene.o Interval.o RcppExports.o ResizeArray.o ThreadOutputFile.o Trie.o bam.o cellbarcode.o check_barcode_reads.o detect_barcode.o parsebam.o parsecount.o qc_per_bc_file_helper.o rcpp_scPipe_func.o sc_atac_create_fragments.o test-cpp.o test-example.o test-fragmentThread.o test-resizearray.o test-runner.o test-str_utils.o test-trie_matching.o transcriptmapping.o trimbarcode.o tsscreatebins.o utils.o /home/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
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-scPipe/00new/scPipe/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scPipe)

Tests output

scPipe.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scPipe)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians



Linux/MacOS detected! 

Checking if samtools is installed ... 

samtools was not located. Please specify the path of it when running sc_atac_remove_duplicates()
> 
> test_check("scPipe")
Successful; continuing with program.
Invalid barcode start index given, with only 0 percent of reads containing a barcode match. However, a better barcode start location is 0 , where 55 percent of barcodes were found.
Unsuccessful. No location was found with a high number of barcode matches. Did both smallbarcode1col.csv and /home/biocbuild/bbs-3.20-bioc/R/site-library/scPipe/extdata/simu_R1.fastq.gz come from the same provider?
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 121 ]
> 
> proc.time()
   user  system elapsed 
 14.709   0.912  15.611 

Example timings

scPipe.Rcheck/scPipe-Ex.timings

nameusersystemelapsed
QC_metrics0.2340.0020.236
UMI_dup_info0.1260.0020.129
UMI_duplication0.1250.0030.128
anno_import2.6000.0512.651
anno_to_saf000
calculate_QC_metrics3.1720.1717.499
cell_barcode_matching0.1040.0010.105
convert_geneid1.0250.0472.229
create_processed_report000
create_report000
create_sce_by_dir0.0960.0000.097
demultiplex_info0.0930.0060.100
detect_outlier0.240.000.24
gene_id_type0.1000.0020.102
get_ercc_anno0.2430.0030.247
get_genes_by_GO0.8150.0221.881
get_read_str0.0010.0000.000
organism0.1390.0020.141
plot_QC_pairs6.1120.0546.167
plot_UMI_dup0.3850.0030.388
plot_demultiplex0.2460.0030.249
plot_mapping0.6430.0110.654
remove_outliers0.2890.0020.291
sc_aligning000
sc_atac_bam_tagging32.29919.77551.320
sc_atac_cell_calling000
sc_atac_create_sce000
sc_atac_feature_counting000
sc_atac_peak_calling0.0000.0000.001
sc_atac_pipeline0.0010.0000.001
sc_atac_tfidf000
sc_atac_trim_barcode0.2310.0060.237
sc_correct_bam_bc0.0010.0000.001
sc_count_aligned_bam000
sc_demultiplex0.0010.0000.001
sc_demultiplex_and_count0.0010.0000.000
sc_detect_bc000
sc_exon_mapping0.0010.0000.001
sc_gene_counting0.0010.0000.001
sc_integrate000
sc_sample_data5.2130.1245.338
sc_sample_qc0.6840.0090.692
sc_trim_barcode000