Movatterモバイル変換

################################################################################################################################################################## 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_1.0.1.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘stPipe/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘stPipe’ version ‘1.0.1’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 21 non-default packages.Importing from so many packages makes the package vulnerable to any ofthem becoming unavailable.  Move as many as possible to Suggests anduse 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 15.0.0 (clang-1500.0.40.1)’* used SDK: ‘MacOSX11.3.1.sdk’* checking installed package size ... INFO  installed size is  9.7Mb  sub-directories of 1Mb or more:    extdata   5.0Mb    libs      4.6Mb* 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 ... NOTENamespace 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 ... NOTERun_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 fieldcontains '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 ... INFOGNU 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 ... WARNINGNote: information on .o files is not availableFile ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/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 norwrite to stdout/stderr instead of to the console, nor use Fortran I/Onor system RNGs nor [v]sprintf. The detected symbols are linked intothe 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 ... OKExamples with CPU (user + system) or elapsed time > 5s          user  system elapsedRun_ST 409.186 258.691 951.149* 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* DONEStatus: 1 WARNING, 2 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL stPipe###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘stPipe’ ...** this is package ‘stPipe’ version ‘1.0.1’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c st_demul.cpp -o st_demul.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-example.cpp -o test-example.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.oclang++ -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 stPipe.so RcppExports.o st_demul.o test-example.o test-runner.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -F/Library/Frameworks/R.framework/.. -framework Rld: warning: ignoring duplicate libraries: '-lz'installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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 PCARead the 100 x 50 data matrix successfully!Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000Computing input similarities...Building tree...Done in 0.01 seconds (sparsity = 0.941600)!Learning embedding...Iteration 50: error is 59.003610 (50 iterations in 0.02 seconds)Iteration 100: error is 62.212000 (50 iterations in 0.02 seconds)Iteration 150: error is 58.652265 (50 iterations in 0.02 seconds)Iteration 200: error is 58.324788 (50 iterations in 0.02 seconds)Iteration 250: error is 58.346545 (50 iterations in 0.02 seconds)Iteration 300: error is 1.643468 (50 iterations in 0.02 seconds)Iteration 350: error is 1.292064 (50 iterations in 0.01 seconds)Iteration 400: error is 0.930466 (50 iterations in 0.01 seconds)Iteration 450: error is 0.860881 (50 iterations in 0.01 seconds)Iteration 500: error is 0.853097 (50 iterations in 0.01 seconds)Iteration 550: error is 0.849987 (50 iterations in 0.01 seconds)Iteration 600: error is 0.850607 (50 iterations in 0.01 seconds)Iteration 650: error is 0.851342 (50 iterations in 0.01 seconds)Iteration 700: error is 0.850595 (50 iterations in 0.01 seconds)Iteration 750: error is 0.850188 (50 iterations in 0.01 seconds)Iteration 800: error is 0.850555 (50 iterations in 0.01 seconds)Iteration 850: error is 0.851515 (50 iterations in 0.01 seconds)Iteration 900: error is 0.851178 (50 iterations in 0.01 seconds)Iteration 950: error is 0.850978 (50 iterations in 0.01 seconds)Iteration 1000: error is 0.850126 (50 iterations in 0.01 seconds)Fitting performed in 0.26 seconds.Using the following FASTQ files:/tmp/RtmpQz1DNl/data36b145d5a0c5/sample_R1_1.fastq/tmp/RtmpQz1DNl/data36b145d5a0c5/sample_R1_2.fastq/tmp/RtmpQz1DNl/data36b145d5a0c5/sample_R2.fastqUsing the following FASTQ files:/tmp/RtmpQz1DNl/data36b1308ef808/sample_R1.fastq/tmp/RtmpQz1DNl/data36b1308ef808/sample_R2.fastqtrimming fastq file...pass QC: 0removed_have_N: 0removed_low_qual: 0time 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  17.995   0.944  26.246