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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:stPipe.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings stPipe_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘stPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stPipe’ version ‘1.0.0’
* 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) 13.3.0’
* checking installed package size ... INFO
  installed size is 26.1Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
    libs     20.9Mb
* 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 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.22-bioc/R/site-library/stPipe/libs/stPipe.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (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 206.904 21.337 230.281
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_Run_QC.R:76:3'): EmptyDropletUtils mode applies emptyDrops filter correctly ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  i Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test_Run_QC.R:76:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 38 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘stPipe-vignette.Rmd’ using rmarkdown
trying URL 'https://zenodo.org/records/14920583/files/stPipe_demo_R1.fq.gz?download=1'
Content type 'application/octet-stream' length 74003930 bytes (70.6 MB)
==================================================
downloaded 70.6 MB

trying URL 'https://zenodo.org/records/14920583/files/stPipe_demo_R2.fq.gz?download=1'

Quitting from stPipe-vignette.Rmd:69-85 [input]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://zenodo.org/records/14920583/files/stPipe_demo_R2.fq.gz?download=1'
---
Backtrace:
    ▆
 1. └─utils::download.file(R2_url, R2_path)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'stPipe-vignette.Rmd' failed with diagnostics:
cannot open URL 'https://zenodo.org/records/14920583/files/stPipe_demo_R2.fq.gz?download=1'
--- failed re-building ‘stPipe-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stPipe-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL stPipe
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘stPipe’ ...
** this is package ‘stPipe’ version ‘1.0.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.22-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++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.22-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++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.22-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++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.22-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++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o stPipe.so RcppExports.o st_demul.o test-example.o test-runner.o /home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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 = 0.939600)!
Learning embedding...
Iteration 50: error is 59.609202 (50 iterations in 0.01 seconds)
Iteration 100: error is 55.885076 (50 iterations in 0.01 seconds)
Iteration 150: error is 53.409056 (50 iterations in 0.01 seconds)
Iteration 200: error is 57.893119 (50 iterations in 0.01 seconds)
Iteration 250: error is 56.646372 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.830126 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.542572 (50 iterations in 0.01 seconds)
Iteration 400: error is 1.391124 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.886656 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.847267 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.847750 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.842572 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.839648 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.837402 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.839423 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.837348 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.838645 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.839068 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.838594 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.838267 (50 iterations in 0.01 seconds)
Fitting performed in 0.17 seconds.
Saving _problems/test_Run_QC-100.R
Using the following FASTQ files:
/tmp/RtmpNY1Uyo/data3acc0a565b2071/sample_R1_1.fastq/tmp/RtmpNY1Uyo/data3acc0a565b2071/sample_R1_2.fastq
/tmp/RtmpNY1Uyo/data3acc0a565b2071/sample_R2.fastq
Using the following FASTQ files:
/tmp/RtmpNY1Uyo/data3acc0a5ebbdb08/sample_R1.fastq
/tmp/RtmpNY1Uyo/data3acc0a5ebbdb08/sample_R2.fastq


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

[ FAIL 1 | WARN 1 | SKIP 1 | PASS 38 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Run_QC.R:76:3'): EmptyDropletUtils mode applies emptyDrops filter correctly ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
i Please use `with_mocked_bindings()` instead.
Backtrace:
    ▆
 1. └─testthat::with_mock(...) at test_Run_QC.R:76:3
 2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
 3.     └─lifecycle:::deprecate_stop0(msg)
 4.       └─rlang::cnd_signal(...)

[ FAIL 1 | WARN 1 | SKIP 1 | PASS 38 ]
Error:
! Test failures.
Execution halted