Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the flowPeaks package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowPeaks.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 715/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowPeaks 1.47.0 (landing page) Yongchao Ge
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: flowPeaks |
Version: 1.47.0 |
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings flowPeaks_1.47.0.tar.gz |
StartedAt: 2023-06-05 22:33:14 -0000 (Mon, 05 Jun 2023) |
EndedAt: 2023-06-05 22:33:59 -0000 (Mon, 05 Jun 2023) |
EllapsedTime: 44.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flowPeaks.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings flowPeaks_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowPeaks.Rcheck’ * using R version 4.3.0 (2023-04-21) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘flowPeaks/DESCRIPTION’ ... OK * this is package ‘flowPeaks’ version ‘1.47.0’ * checking package namespace information ... OK * checking package dependencies ... 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 ‘flowPeaks’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 R 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Call with DUP: .C("Rpack_kmeans", as.double(t(data.matrix(x))), as.integer(n), as.integer(p), as.integer(K), cluster = integer(n), m = double(K * p), nc = integer(K), S = double(K * p * p), Nb = integer(K * K), twss = double(1), as.double(stime), DUP = FALSE, PACKAGE = "flowPeaks") DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE getS0K : <anonymous>: no visible global function definition for ‘nclass.FD’ getS0K: no visible global function definition for ‘median’ plot.flowPeaks: no visible global function definition for ‘hist’ plot.flowPeaks: no visible global function definition for ‘points’ plot.flowPeaks: no visible global function definition for ‘text’ plot.flowPeaks: no visible global function definition for ‘par’ plot.flowPeaks: no visible global function definition for ‘segments’ traditional.kmeans: no visible global function definition for ‘kmeans’ traditional.kmeans: no visible global function definition for ‘var’ Undefined global functions or variables: hist kmeans median nclass.FD par points segments text var Consider adding importFrom("grDevices", "nclass.FD") importFrom("graphics", "hist", "par", "points", "segments", "text") importFrom("stats", "kmeans", "median", "var") to your NAMESPACE file. * 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 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * 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/R/R-4.3.0/site-library/flowPeaks/libs/flowPeaks.so’: 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘flowPeaks-guide.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/flowPeaks.Rcheck/00check.log’ for details.
flowPeaks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL flowPeaks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘flowPeaks’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c Rpack.cpp -o Rpack.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c Rregistrate.cpp -o Rregistrate.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c flowPeaks.cpp -o flowPeaks.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c func_collect.cpp -o func_collect.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c func_collect_supp.cpp -o func_collect_supp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c gvector_gmatrix.cpp -o gvector_gmatrix.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c kd_tree.cpp -o kd_tree.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include `gsl-config --cflags` -fPIC -g -O2 -c kmns.cpp -o kmns.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o flowPeaks.so Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o -L/usr/local/lib -lgsl -lgslcblas -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-flowPeaks/00new/flowPeaks/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 (flowPeaks)
flowPeaks.Rcheck/flowPeaks-Ex.timings
name | user | system | elapsed | |
flowPeaks | 2.743 | 0.103 | 2.848 | |