Shian Su
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/scPipe |
| git_branch: RELEASE_3_17 |
| git_last_commit: 2d9cb4c |
| git_last_commit_date: 2023-04-25 10:57:21 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:37 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1854/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scPipe 2.0.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 2.0.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scPipe.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scPipe_2.0.0.tar.gz |
| StartedAt: 2023-10-16 06:35:04 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 06:43:40 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 515.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scPipe.Rcheck |
| Warnings: 1 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scPipe.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scPipe_2.0.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/scPipe.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scPipe' version '2.0.0'
* 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 whether package 'scPipe' can be installed ... WARNING
Found the following significant warnings:
trimbarcode.cpp:354:15: warning: pointer 'old_name_adr' used after 'void* realloc(void*, size_t)' [-Wuse-after-free]
See 'F:/biocbuild/bbs-3.17-bioc/meat/scPipe.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 23.7Mb
sub-directories of 1Mb or more:
extdata 12.0Mb
libs 10.3Mb
* 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 R 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'flexmix'
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_create_sce: no visible binding for global variable
'output_folder'
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
'makeGRangesFromDataFrame'
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 makeGRangesFromDataFrame
output_folder 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/scPipe/libs/x64/scPipe.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 34.71 4.69 40.19
plot_QC_pairs 6.33 0.14 6.51
sc_sample_data 5.57 0.16 5.73
calculate_QC_metrics 1.73 0.22 84.22
convert_geneid 0.79 0.10 13.20
get_genes_by_GO 0.56 0.07 10.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/scPipe.Rcheck/00check.log'
for details.
scPipe.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL scPipe
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'scPipe' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentThread.cpp -o FragmentThread.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentUtils.cpp -o FragmentUtils.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ResizeArray.cpp -o ResizeArray.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadOutputFile.cpp -o ThreadOutputFile.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 long unsigned int'} [-Wsign-compare]
274 | for (int i = 0; i < valid_nodes.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cellbarcode.cpp -o cellbarcode.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_barcode_reads.cpp -o check_barcode_reads.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parsecount.cpp -o parsecount.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-cpp.cpp -o test-cpp.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-example.cpp -o test-example.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-fragmentThread.cpp -o test-fragmentThread.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-resizearray.cpp -o test-resizearray.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-trie_matching.cpp -o test-trie_matching.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transcriptmapping.cpp -o transcriptmapping.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function 'void paired_fastq_to_bam(char*, char*, char*, read_s, filter_s)':
trimbarcode.cpp:354:15: warning: pointer 'old_name_adr' used after 'void* realloc(void*, size_t)' [-Wuse-after-free]
354 | memcpy(new_name_adr, old_name_adr, n_char_copied);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trimbarcode.cpp:353:38: note: call to 'void* realloc(void*, size_t)' here
353 | seq1->name.s = (char*)realloc(old_name_adr, new_name_length);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trimbarcode.cpp: In function 'void paired_fastq_to_fastq(char*, char*, char*, read_s, filter_s, bool)':
trimbarcode.cpp:613:24: warning: 'o_stream_gz' may be used uninitialized [-Wmaybe-uninitialized]
613 | fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
trimbarcode.cpp:458:12: note: 'o_stream_gz' was declared here
458 | gzFile o_stream_gz;
| ^~~~~~~~~~~
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:814:31: warning: 'seq3' may be used uninitialized [-Wmaybe-uninitialized]
814 | if((l3 = kseq_read(seq3)) < 0){
| ~~~~~~~~~^~~~~~
trimbarcode.cpp:751:13: note: 'seq3' was declared here
751 | kseq_t *seq3;
| ^~~~
trimbarcode.cpp:983:16: warning: 'fq3' may be used uninitialized [-Wmaybe-uninitialized]
983 | gzclose(fq3);
trimbarcode.cpp:722:16: note: 'fq3' was declared here
722 | gzFile fq3;
| ^~~
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:1164:9: warning: 'bc1_end' may be used uninitialized [-Wmaybe-uninitialized]
1164 | int bc1_end, bc2_end; // get end position in the read of barcode and umi
| ^~~~~~~
trimbarcode.cpp:1420:54: warning: 'seq3' may be used uninitialized [-Wmaybe-uninitialized]
1420 | seq3->name.s = (char*)realloc(seq3->name.s, new_name_length1 + 1); // allocate additional memory
| ~~~~~~~~~~~^
trimbarcode.cpp:1118:13: note: 'seq3' was declared here
1118 | kseq_t *seq3;
| ^~~~
trimbarcode.cpp:1500:16: warning: 'fq3' may be used uninitialized [-Wmaybe-uninitialized]
1500 | gzclose(fq3);
trimbarcode.cpp:1110:12: note: 'fq3' was declared here
1110 | gzFile fq3;
| ^~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsscreatebins.cpp -o tsscreatebins.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
g++ -shared -s -static-libgcc -o scPipe.dll tmp.def 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-trie_matching.o transcriptmapping.o trimbarcode.o tsscreatebins.o utils.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-scPipe/00new/scPipe/libs/x64
** 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
** 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 version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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, setdiff, sort, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
Windows platform detected, sc_atac_peak_calling() and sc_atac_remove_duplicates() function may not operate. Please call peaks and remove duplicate reads outside the package.
>
> 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 F:/biocbuild/bbs-3.17-bioc/R/library/scPipe/extdata/simu_R1.fastq.gz come from the same provider?
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 110 ]
>
> proc.time()
user system elapsed
14.17 1.18 16.28
scPipe.Rcheck/scPipe-Ex.timings
| name | user | system | elapsed | |
| QC_metrics | 0.33 | 0.00 | 0.32 | |
| UMI_dup_info | 0.21 | 0.04 | 0.25 | |
| UMI_duplication | 0.22 | 0.04 | 0.27 | |
| anno_import | 2.10 | 0.05 | 2.23 | |
| anno_to_saf | 0 | 0 | 0 | |
| calculate_QC_metrics | 1.73 | 0.22 | 84.22 | |
| cell_barcode_matching | 0.20 | 0.01 | 0.24 | |
| convert_geneid | 0.79 | 0.10 | 13.20 | |
| create_processed_report | 0 | 0 | 0 | |
| create_report | 0 | 0 | 0 | |
| create_sce_by_dir | 0.23 | 0.03 | 0.27 | |
| demultiplex_info | 0.2 | 0.0 | 0.2 | |
| detect_outlier | 0.44 | 0.01 | 0.45 | |
| gene_id_type | 0.19 | 0.02 | 0.21 | |
| get_ercc_anno | 0.22 | 0.02 | 0.29 | |
| get_genes_by_GO | 0.56 | 0.07 | 10.14 | |
| get_read_str | 0 | 0 | 0 | |
| organism | 0.36 | 0.02 | 0.38 | |
| plot_QC_pairs | 6.33 | 0.14 | 6.51 | |
| plot_UMI_dup | 0.48 | 0.06 | 0.63 | |
| plot_demultiplex | 0.33 | 0.00 | 0.33 | |
| plot_mapping | 0.72 | 0.00 | 0.72 | |
| remove_outliers | 0.33 | 0.00 | 0.32 | |
| sc_aligning | 0 | 0 | 0 | |
| sc_atac_bam_tagging | 34.71 | 4.69 | 40.19 | |
| sc_atac_cell_calling | 0 | 0 | 0 | |
| sc_atac_create_sce | 0 | 0 | 0 | |
| sc_atac_feature_counting | 0 | 0 | 0 | |
| sc_atac_peak_calling | 0 | 0 | 0 | |
| sc_atac_pipeline | 0 | 0 | 0 | |
| sc_atac_tfidf | 0 | 0 | 0 | |
| sc_atac_trim_barcode | 0.36 | 0.03 | 0.39 | |
| sc_correct_bam_bc | 0 | 0 | 0 | |
| sc_count_aligned_bam | 0 | 0 | 0 | |
| sc_demultiplex | 0 | 0 | 0 | |
| sc_demultiplex_and_count | 0 | 0 | 0 | |
| sc_detect_bc | 0 | 0 | 0 | |
| sc_exon_mapping | 0 | 0 | 0 | |
| sc_gene_counting | 0.02 | 0.00 | 0.02 | |
| sc_integrate | 0 | 0 | 0 | |
| sc_sample_data | 5.57 | 0.16 | 5.73 | |
| sc_sample_qc | 0.83 | 0.00 | 0.83 | |
| sc_trim_barcode | 0 | 0 | 0 | |