* using log directory 'd:/RCompile/CRANincoming/R-devel/CatsCradle.Rcheck' * using R Under development (unstable) (2024-08-29 r87078 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'CatsCradle/DESCRIPTION' ... OK * this is package 'CatsCradle' version '0.99.10' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [12s] NOTE Maintainer: 'Michael Shapiro ' New submission License components with restrictions and base license permitting such: MIT + file LICENSE File 'LICENSE': # MIT License Copyright (c) 2023 Anna Laddach, Michael Shapiro Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Possibly misspelled words in DESCRIPTION: CatsCradle (16:227) Transcriptomics (3:9) particualr (16:359) transcriptomic (16:98) Authors@R field should be a call to person(), or combine such calls. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid file URIs: URI: doc/CatsCradle.html From: inst/doc/CatsCradleQuickStart.html URI: doc/CatsCradleSpatial.html From: inst/doc/CatsCradleQuickStart.html The Description field should not start with the package name, 'This package' or similar. * 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 whether package 'CatsCradle' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... NOTE Non-standard file/directory found at top level: 'CatsCradleLogoTransparent.png' * 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 ... [14s] OK * checking whether the package can be loaded with stated dependencies ... [13s] OK * checking whether the package can be unloaded cleanly ... [13s] OK * checking whether the namespace can be loaded with stated dependencies ... [13s] OK * checking whether the namespace can be unloaded cleanly ... [14s] OK * checking loading without being on the library search path ... [15s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [62s] NOTE edgeLengthPlot: no visible binding for global variable 'cellTypePair' edgeLengthPlot: no visible binding for global variable 'cutoff' make.getExample : getExample: no visible binding for global variable 'moransI' make.getExample : getExample: no visible binding for global variable 'moransILigandReceptor' make.getExample : getExample: no visible binding for global variable 'humanLRN' make.getExample : getExample: no visible binding for global variable 'mouseLRN' meanGeneClusterOnCellUMAP: no visible binding for global variable 'UMAP_1' meanGeneClusterOnCellUMAP: no visible binding for global variable 'UMAP_2' Undefined global functions or variables: UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI moransILigandReceptor mouseLRN * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Variables with usage in Rd file 'exSeuratObj.Rd' but not in code: 'exSeuratObj' Variables with usage in Rd file 'hallmark.Rd' but not in code: 'hallmark' Variables with usage in Rd file 'humanLRN.Rd' but not in code: 'humanLRN' Variables with usage in Rd file 'ligandReceptorResults.Rd' but not in code: 'ligandReceptorResults' Variables with usage in Rd file 'moransI.Rd' but not in code: 'moransI' Variables with usage in Rd file 'moransILigandReceptor.Rd' but not in code: 'moransILigandReceptor' Variables with usage in Rd file 'mouseLRN.Rd' but not in code: 'mouseLRN' Variables with usage in Rd file 'smallXenium.Rd' but not in code: 'smallXenium' * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [13m] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed predictAnnotationAllGenes 73.98 1.91 75.72 computeGraphEmbedding 70.30 0.36 70.73 computeNBHDVsCTObject 66.13 0.35 66.44 aggregateGeneExpression 47.73 1.78 49.36 transposeObject 29.19 0.61 29.76 randomiseNodeIndices 20.94 0.40 21.36 getObjectSubsetClusteringPValue 18.34 1.16 19.50 getObjectSubsetClusteringStatistics 17.23 1.05 18.27 medianComplementPValue 17.27 0.86 18.12 desymmetriseNN 17.52 0.45 17.96 runGeometricClusteringTrials 16.93 0.97 17.83 combinatorialSpheres 16.63 0.22 16.83 getNearbyGenes 16.43 0.33 16.79 getGeneNeighbors 16.36 0.28 16.62 runMoransI 13.81 2.83 16.50 tagRowAndColNames 16.12 0.42 16.54 predictGeneAnnotationImpl 15.89 0.53 16.41 symmetriseNN 15.80 0.37 16.17 getAverageExpressionDF 15.41 0.39 15.75 predictAnnotation 15.00 0.55 15.53 getAverageExpressionMatrix 15.12 0.38 15.48 getNearestNeighbourLists 14.85 0.23 15.07 geneSetsVsGeneClustersPValueMatrix 14.61 0.35 14.98 getClusterOrder 14.39 0.34 14.69 symmetryCheckNN 14.41 0.24 14.67 getGeneClusterAveragesPerCell 14.14 0.42 14.57 meanGeneClusterOnCellUMAP 13.89 0.30 14.17 collapseExtendedNBHDs 12.25 0.30 12.39 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13m] OK * checking PDF version of manual ... [30s] OK * checking HTML version of manual ... [12s] OK * DONE Status: 1 WARNING, 5 NOTEs