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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:stPipe.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings stPipe_1.1.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/stPipe.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-14 08:33:45 UTC
* checking for file ‘stPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stPipe’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘stPipe’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is 22.2Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
    libs     17.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SummarizedExperiment’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘stPipe_env’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Run_Create_Obj: no visible global function definition for ‘new’
Run_Create_Obj: no visible global function definition for ‘rowData<-’
Run_Visualization: no visible global function definition for ‘reorder’
ref_pos: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  new read.csv reorder rowData<-
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reorder")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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-3.23-bioc/R/site-library/stPipe/libs/stPipe.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (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
Run_ST 215.135   21.1 238.302
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/stPipe.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL stPipe
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘stPipe’ ...
** this is package ‘stPipe’ version ‘1.1.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c st_demul.cpp -o st_demul.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-example.cpp -o test-example.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o stPipe.so RcppExports.o st_demul.o test-example.o test-runner.o /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto -lz -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-stPipe/00new/stPipe/libs
** R
** 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 (stPipe)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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(stPipe)
> 
> test_check("stPipe")
Performing PCA
Read the 100 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.938200)!
Learning embedding...
Iteration 50: error is 55.861810 (50 iterations in 0.01 seconds)
Iteration 100: error is 61.830127 (50 iterations in 0.01 seconds)
Iteration 150: error is 56.400559 (50 iterations in 0.01 seconds)
Iteration 200: error is 53.060081 (50 iterations in 0.01 seconds)
Iteration 250: error is 57.145330 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.656790 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.367857 (50 iterations in 0.01 seconds)
Iteration 400: error is 1.047411 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.871956 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.872082 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.869237 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.868043 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.867031 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.867349 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.867005 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.867192 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.866250 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.866662 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.867509 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.867556 (50 iterations in 0.01 seconds)
Fitting performed in 0.17 seconds.
Using the following FASTQ files:
/tmp/RtmpKGnDVT/data37c9c842edc522/sample_R1_1.fastq/tmp/RtmpKGnDVT/data37c9c842edc522/sample_R1_2.fastq
/tmp/RtmpKGnDVT/data37c9c842edc522/sample_R2.fastq
Using the following FASTQ files:
/tmp/RtmpKGnDVT/data37c9c87de559ae/sample_R1.fastq
/tmp/RtmpKGnDVT/data37c9c87de559ae/sample_R2.fastq


trimming fastq file...
pass QC: 0
removed_have_N: 0
removed_low_qual: 0
time elapsed: 0 milliseconds

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 34 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 13.623   0.696  14.310