Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD check --install=check:stPipe.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings stPipe_1.0.1.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck’* using R version 4.5.0 (2025-04-11)* using platform: aarch64-unknown-linux-gnu* R was compiled by    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0    GNU Fortran (GCC) 14.2.0* running under: openEuler 24.03 (LTS)* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’* checking installed package size ... INFO  installed size is 27.4Mb  sub-directories of 1Mb or more:    extdata   5.0Mb    libs     22.2Mb* 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 ... 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 ‘/home/biocbuild/R/R-4.5.0/site-library/stPipe/libs/stPipe.so’:  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (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)  Found ‘stderr’, possibly from ‘stderr’ (C)  Found ‘stdout’, possibly from ‘stdout’ (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 214.077 22.578 239.251* 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  ‘/home/biocbuild/bbs-3.22-bioc/meat/stPipe.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL stPipe###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘stPipe’ ...** this is package ‘stPipe’ version ‘1.0.1’** using staged installation** libsusing C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/testthat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/testthat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c st_demul.cpp -o st_demul.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/testthat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c test-example.cpp -o test-example.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/testthat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o stPipe.so RcppExports.o st_demul.o test-example.o test-runner.o /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/R/R-4.5.0/lib -lRinstalling to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-linux-gnuR 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!OpenMP is working. 1 threads.Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000Computing input similarities...Building tree...Done in 0.01 seconds (sparsity = 0.940200)!Learning embedding...Iteration 50: error is 57.387578 (50 iterations in 0.02 seconds)Iteration 100: error is 61.016266 (50 iterations in 0.02 seconds)Iteration 150: error is 60.527993 (50 iterations in 0.02 seconds)Iteration 200: error is 61.386374 (50 iterations in 0.02 seconds)Iteration 250: error is 63.208559 (50 iterations in 0.02 seconds)Iteration 300: error is 1.668661 (50 iterations in 0.01 seconds)Iteration 350: error is 1.395694 (50 iterations in 0.01 seconds)Iteration 400: error is 1.033246 (50 iterations in 0.01 seconds)Iteration 450: error is 0.836994 (50 iterations in 0.01 seconds)Iteration 500: error is 0.834622 (50 iterations in 0.01 seconds)Iteration 550: error is 0.834034 (50 iterations in 0.01 seconds)Iteration 600: error is 0.834608 (50 iterations in 0.01 seconds)Iteration 650: error is 0.834995 (50 iterations in 0.01 seconds)Iteration 700: error is 0.834650 (50 iterations in 0.01 seconds)Iteration 750: error is 0.835225 (50 iterations in 0.01 seconds)Iteration 800: error is 0.835814 (50 iterations in 0.01 seconds)Iteration 850: error is 0.835596 (50 iterations in 0.01 seconds)Iteration 900: error is 0.835646 (50 iterations in 0.01 seconds)Iteration 950: error is 0.835017 (50 iterations in 0.01 seconds)Iteration 1000: error is 0.835651 (50 iterations in 0.01 seconds)Fitting performed in 0.24 seconds.Using the following FASTQ files:/home/biocbuild/tmp/RtmpbjxXJU/data2d70446cd72d9/sample_R1_1.fastq/home/biocbuild/tmp/RtmpbjxXJU/data2d70446cd72d9/sample_R1_2.fastq/home/biocbuild/tmp/RtmpbjxXJU/data2d70446cd72d9/sample_R2.fastqUsing the following FASTQ files:/home/biocbuild/tmp/RtmpbjxXJU/data2d70413c91178/sample_R1.fastq/home/biocbuild/tmp/RtmpbjxXJU/data2d70413c91178/sample_R2.fastqtrimming fastq file...pass QC: 0removed_have_N: 0removed_low_qual: 0time elapsed: 0 milliseconds[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ][ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]> > proc.time()   user  system elapsed  17.934   0.742  18.717