############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:miloR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings miloR_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘miloR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miloR’ version ‘2.2.0’ * package encoding: UTF-8 * 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 ‘miloR’ can be installed ... WARNING Found the following significant warnings: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] See ‘/home/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... NOTE installed size is 23.9Mb sub-directories of 1Mb or more: data 1.8Mb libs 21.4Mb * 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 ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’ plotDAbeeswarm: no visible binding for global variable ‘logFC’ plotDAbeeswarm: no visible binding for global variable ‘is_signif’ plotDAbeeswarm: no visible binding for global variable ‘Nhood’ plotDAbeeswarm: no visible binding for global variable ‘logFC_color’ plotNhoodCounts: no visible binding for global variable ‘cond’ plotNhoodCounts: no visible binding for global variable ‘values’ plotNhoodCounts: no visible binding for global variable ‘y’ plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’ plotNhoodExpressionDA: no visible binding for global variable ‘logFC’ plotNhoodExpressionDA: no visible binding for global variable ‘SpatialFDR’ plotNhoodExpressionDA: no visible binding for global variable ‘logFC_rank’ plotNhoodExpressionDA: no visible binding for global variable ‘.’ plotNhoodExpressionDA: no visible binding for global variable ‘is_signif’ plotNhoodExpressionDA: no visible binding for global variable ‘feature’ plotNhoodExpressionDA: no visible binding for global variable ‘avg_expr’ plotNhoodExpressionDA: no visible binding for global variable ‘label’ plotNhoodExpressionGroups: no visible binding for global variable ‘Nhood’ plotNhoodExpressionGroups: no visible binding for global variable ‘NhoodGroup’ plotNhoodExpressionGroups: no visible binding for global variable ‘logFC’ plotNhoodExpressionGroups: no visible binding for global variable ‘feature’ plotNhoodExpressionGroups: no visible binding for global variable ‘logFC_rank’ plotNhoodExpressionGroups: no visible binding for global variable ‘avg_expr’ plotNhoodExpressionGroups: no visible binding for global variable ‘.’ plotNhoodExpressionGroups: no visible binding for global variable ‘label’ plotNhoodGraph: no visible binding for global variable ‘weight’ plotNhoodGraph: no visible binding for global variable ‘size’ plotNhoodGraphDA: no visible binding for global variable ‘layout’ plotNhoodGroups: no visible binding for global variable ‘layout’ plotNhoodMA: no visible binding for global variable ‘logCPM’ plotNhoodMA: no visible binding for global variable ‘logFC’ plotNhoodMA: no visible binding for global variable ‘Sig’ plotNhoodSizeHist: no visible binding for global variable ‘nh_size’ testNhoods: no visible global function definition for ‘type’ Undefined global functions or variables: . Nhood NhoodGroup Sig SpatialFDR avg_expr cond feature is_signif label layout logCPM logFC logFC_color logFC_rank nh_size size type values weight y Consider adding importFrom("graphics", "layout") 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 ... 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: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck/00check.log’ for details.