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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:stPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings stPipe_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
    libs      4.9Mb
* 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 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 ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/stPipe/libs/stPipe.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (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 339.841 285.142  694.58
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL stPipe
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘stPipe’ ...
** this is package ‘stPipe’ version ‘1.0.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c st_demul.cpp -o st_demul.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-example.cpp -o test-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o stPipe.so RcppExports.o st_demul.o test-example.o test-runner.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.940000)!
Learning embedding...
Iteration 50: error is 52.384913 (50 iterations in 0.01 seconds)
Iteration 100: error is 50.363508 (50 iterations in 0.01 seconds)
Iteration 150: error is 54.555519 (50 iterations in 0.01 seconds)
Iteration 200: error is 53.266526 (50 iterations in 0.01 seconds)
Iteration 250: error is 53.555184 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.726431 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.453328 (50 iterations in 0.01 seconds)
Iteration 400: error is 1.222957 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.911922 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.866924 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.852586 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.854163 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.839032 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.836025 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.836425 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.835677 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.836199 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.834424 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.833508 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.833761 (50 iterations in 0.01 seconds)
Fitting performed in 0.15 seconds.
Using the following FASTQ files:
/var/folders/db/4tvgx8jx4z3fm1gzlnlzw9rc0000gq/T//Rtmp0YtxQu/data3efe384e703c/sample_R1_1.fastq/var/folders/db/4tvgx8jx4z3fm1gzlnlzw9rc0000gq/T//Rtmp0YtxQu/data3efe384e703c/sample_R1_2.fastq
/var/folders/db/4tvgx8jx4z3fm1gzlnlzw9rc0000gq/T//Rtmp0YtxQu/data3efe384e703c/sample_R2.fastq
Using the following FASTQ files:
/var/folders/db/4tvgx8jx4z3fm1gzlnlzw9rc0000gq/T//Rtmp0YtxQu/data3efe204219c9/sample_R1.fastq
/var/folders/db/4tvgx8jx4z3fm1gzlnlzw9rc0000gq/T//Rtmp0YtxQu/data3efe204219c9/sample_R2.fastq


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

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 18.115   2.532  22.344