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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:retrofit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings retrofit_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/retrofit.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘retrofit/DESCRIPTION’ ... OK
* this is package ‘retrofit’ version ‘1.6.0’
* 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'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘retrofit’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) decompose.Rd:44: Lost braces; missing escapes or markup?
    44 | the function returns factorized {W, H, Theta}.
       |                                 ^
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/retrofit.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL retrofit
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘retrofit’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decompose_measure_error.cpp -o decompose_measure_error.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decompose_step2.cpp -o decompose_step2.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decompose_step3.cpp -o decompose_step3.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decompose_step4.cpp -o decompose_step4.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decompose_step5.cpp -o decompose_step5.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o retrofit.so RcppExports.o decompose_measure_error.o decompose_step2.o decompose_step3.o decompose_step4.o decompose_step5.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-retrofit/00new/retrofit/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 (retrofit)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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(retrofit)
Loading required package: Rcpp

Attaching package: 'retrofit'

The following object is masked from 'package:stats':

    decompose

> 
> test_check("retrofit")
[1] "!is.null(rownames(sc_ref)) is not TRUE"
[1] "dim(decomp_w)[1] == dim(sc_ref)[1] is not TRUE"
[1] "dim(decomp_w)[2] == dim(decomp_h)[1] is not TRUE"
[1] "cell_types( 2 ) are fewer than the mapping target K( 5 )."
[1] "dim(decomp_w)[2] == dim(decomp_h)[1] is not TRUE"
[Rcpp] first original: 1
[Rcpp] first original: 0.356564
[Rcpp] first original: 0.381625
[1] "iteration: 1 0.055 Seconds"
[1] "iteration: 2 0.055 Seconds"
[1] "iteration: 3 0.055 Seconds"
[1] "iteration: 4 0.056 Seconds"
[1] "iteration: 5 0.055 Seconds"
[1] "iteration: 6 0.056 Seconds"
[1] "iteration: 7 0.055 Seconds"
[1] "iteration: 8 0.055 Seconds"
[1] "iteration: 9 0.055 Seconds"
[1] "iteration: 10 0.059 Seconds"
[1] "Iteration mean:  0.056  seconds  total:  0.557  seconds"
[1] "iteration: 1 0 Seconds"
[1] "iteration: 2 0 Seconds"
[1] "iteration: 3 0 Seconds"
[1] "iteration: 4 0 Seconds"
[1] "iteration: 5 0 Seconds"
[1] "iteration: 6 0 Seconds"
[1] "iteration: 7 0 Seconds"
[1] "iteration: 8 0 Seconds"
[1] "iteration: 9 0 Seconds"
[1] "iteration: 10 0 Seconds"
[1] "Iteration mean:  0  seconds  total:  0.001  seconds"
[1] "!is.null(x) is not TRUE"
[1] "!is.null(L) is not TRUE"
[1] "!is.null(iterations) is not TRUE"
[1] "!is.null(lambda) is not TRUE"
[1] "!is.null(kappa) is not TRUE"
[1] "is.numeric(L) && as.integer(L) > 0 is not TRUE"
[1] "is.numeric(iterations) && as.integer(iterations) > 0 is not TRUE"
[1] "is.numeric(kappa) && kappa > 0 is not TRUE"
[1] "is.list(init_param) is not TRUE"
[1] "\"alpha_w_0\" %in% names(init_param) && is.numeric(init_param$alpha_w_0) is not TRUE"
[1] "\"alpha_w_0\" %in% names(init_param) && is.numeric(init_param$alpha_w_0) is not TRUE"
[1] "\"alpha_th_k\" %in% names(init_param) is not TRUE"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 61 ]
> 
> proc.time()
   user  system elapsed 
  2.939   0.086   3.023