############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:miloR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings miloR_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘miloR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miloR’ version ‘2.1.0’ * 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 ... OK * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 14.1Mb sub-directories of 1Mb or more: data 1.8Mb libs 11.6Mb * 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed testDiffExp 4.905 0.022 5.033 * 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 re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘milo_contrasts.Rmd’ using rmarkdown --- finished re-building ‘milo_contrasts.Rmd’ --- re-building ‘milo_demo.Rmd’ using rmarkdown --- finished re-building ‘milo_demo.Rmd’ --- re-building ‘milo_gastrulation.Rmd’ using rmarkdown Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘milo_gastrulation.Rmd’ --- re-building ‘milo_glmm.Rmd’ using rmarkdown Warning: call dbDisconnect() when finished working with a connection Quitting from lines 158-164 [unnamed-chunk-8] (milo_glmm.Rmd) Error: processing vignette 'milo_glmm.Rmd' failed with diagnostics: error in evaluating the argument 'x' in selecting a method for function 'rowMeans': Failed to find a colSums2() method for dgCMatrix objects. However, the following packages are likely to contain the missing method but are not installed: sparseMatrixStats, DelayedMatrixStats. Please install them (with 'BiocManager::install(...)') and try again. Alternatively, if you know where the missing method is defined, install only that package. --- failed re-building ‘milo_glmm.Rmd’ SUMMARY: processing the following file failed: ‘milo_glmm.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck/00check.log’ for details.