Shian Su
| Snapshot Date: 2024-11-20 13:40 -0500 (Wed, 20 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/scPipe |
| git_branch: devel |
| git_last_commit: 19a3041 |
| git_last_commit_date: 2024-10-29 10:23:12 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-21 11:33 -0500 (Thu, 21 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| 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 1878/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scPipe 2.7.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: scPipe |
| Version: 2.7.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scPipe_2.7.0.tar.gz |
| StartedAt: 2024-11-21 05:57:40 -0500 (Thu, 21 Nov 2024) |
| EndedAt: 2024-11-21 06:09:10 -0500 (Thu, 21 Nov 2024) |
| EllapsedTime: 690.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scPipe.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scPipe_2.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scPipe.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘2.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Imports includes 40 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 ‘scPipe’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 25.8Mb
sub-directories of 1Mb or more:
extdata 11.6Mb
libs 12.9Mb
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
QC_metrics.Rd: SingleCellExperiment
UMI_dup_info.Rd: SingleCellExperiment
create_sce_by_dir.Rd: SingleCellExperiment
demultiplex_info.Rd: SingleCellExperiment
feature_info.Rd: SingleCellExperiment
feature_type.Rd: SingleCellExperiment
gene_id_type.Rd: SingleCellExperiment
organism.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 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 ... 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/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 30.758 19.957 50.015
sc_sample_data 6.115 0.170 6.286
plot_QC_pairs 5.757 0.118 5.876
calculate_QC_metrics 1.944 0.142 5.451
convert_geneid 1.087 0.161 5.255
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/scPipe.Rcheck/00check.log’
for details.
scPipe.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scPipe
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c FragmentThread.cpp -o FragmentThread.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c FragmentUtils.cpp -o FragmentUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c ResizeArray.cpp -o ResizeArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c ThreadOutputFile.cpp -o ThreadOutputFile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c bam.c -o bam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cellbarcode.cpp -o cellbarcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c check_barcode_reads.cpp -o check_barcode_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c parsecount.cpp -o parsecount.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-cpp.cpp -o test-cpp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-example.cpp -o test-example.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-fragmentThread.cpp -o test-fragmentThread.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-resizearray.cpp -o test-resizearray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-str_utils.cpp -o test-str_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test-trie_matching.cpp -o test-trie_matching.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c transcriptmapping.cpp -o transcriptmapping.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c tsscreatebins.cpp -o tsscreatebins.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -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/zlibbioc/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)
scPipe.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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.
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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> 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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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-3.21-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
14.581 0.914 15.487
scPipe.Rcheck/scPipe-Ex.timings
| name | user | system | elapsed | |
| QC_metrics | 0.184 | 0.046 | 0.231 | |
| UMI_dup_info | 0.139 | 0.002 | 0.141 | |
| UMI_duplication | 0.090 | 0.005 | 0.095 | |
| anno_import | 2.236 | 0.038 | 2.275 | |
| anno_to_saf | 0 | 0 | 0 | |
| calculate_QC_metrics | 1.944 | 0.142 | 5.451 | |
| cell_barcode_matching | 0.100 | 0.004 | 0.104 | |
| convert_geneid | 1.087 | 0.161 | 5.255 | |
| create_processed_report | 0 | 0 | 0 | |
| create_report | 0 | 0 | 0 | |
| create_sce_by_dir | 0.104 | 0.009 | 0.111 | |
| demultiplex_info | 0.102 | 0.011 | 0.112 | |
| detect_outlier | 0.250 | 0.023 | 0.272 | |
| gene_id_type | 0.11 | 0.01 | 0.12 | |
| get_ercc_anno | 0.258 | 0.011 | 0.269 | |
| get_genes_by_GO | 1.687 | 0.269 | 3.250 | |
| get_read_str | 0.001 | 0.000 | 0.001 | |
| organism | 0.123 | 0.003 | 0.126 | |
| plot_QC_pairs | 5.757 | 0.118 | 5.876 | |
| plot_UMI_dup | 0.401 | 0.041 | 0.442 | |
| plot_demultiplex | 0.271 | 0.012 | 0.283 | |
| plot_mapping | 0.598 | 0.033 | 0.631 | |
| remove_outliers | 0.243 | 0.014 | 0.257 | |
| sc_aligning | 0 | 0 | 0 | |
| sc_atac_bam_tagging | 30.758 | 19.957 | 50.015 | |
| sc_atac_cell_calling | 0.000 | 0.000 | 0.001 | |
| sc_atac_create_sce | 0 | 0 | 0 | |
| sc_atac_feature_counting | 0.000 | 0.001 | 0.000 | |
| sc_atac_peak_calling | 0 | 0 | 0 | |
| sc_atac_pipeline | 0.002 | 0.000 | 0.002 | |
| sc_atac_tfidf | 0 | 0 | 0 | |
| sc_atac_trim_barcode | 0.246 | 0.007 | 0.252 | |
| sc_correct_bam_bc | 0.002 | 0.000 | 0.001 | |
| sc_count_aligned_bam | 0.000 | 0.000 | 0.001 | |
| sc_demultiplex | 0.002 | 0.000 | 0.002 | |
| sc_demultiplex_and_count | 0.001 | 0.000 | 0.001 | |
| sc_detect_bc | 0 | 0 | 0 | |
| sc_exon_mapping | 0.001 | 0.000 | 0.001 | |
| sc_gene_counting | 0.001 | 0.000 | 0.001 | |
| sc_integrate | 0.000 | 0.001 | 0.000 | |
| sc_sample_data | 6.115 | 0.170 | 6.286 | |
| sc_sample_qc | 0.599 | 0.003 | 0.602 | |
| sc_trim_barcode | 0 | 0 | 0 | |