Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:19 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 |
Package 1999/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpacePAC 1.40.0 (landing page) Gregory Ryslik
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the SpacePAC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SpacePAC |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpacePAC_1.40.0.tar.gz |
StartedAt: 2024-04-18 04:33:36 -0400 (Thu, 18 Apr 2024) |
EndedAt: 2024-04-18 04:35:40 -0400 (Thu, 18 Apr 2024) |
EllapsedTime: 124.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpacePAC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpacePAC_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SpacePAC.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpacePAC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpacePAC’ version ‘1.40.0’ * 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 ‘SpacePAC’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 dependencies in R code ... NOTE Package in Depends field not imported from: ‘iPAC’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE SpaceClust: no visible global function definition for ‘flush.console’ SpaceClust: no visible global function definition for ‘ppois’ create.Distance.Matrix: no visible global function definition for ‘dist’ create.Result.Matrix: no visible global function definition for ‘p.adjust’ get.Avg.Neighbor.Distance: no visible global function definition for ‘dist’ get.Local.Radius.Results: no visible global function definition for ‘sd’ make.3D.Sphere: no visible global function definition for ‘rgl.open’ make.3D.Sphere: no visible global function definition for ‘rgl.bg’ make.3D.Sphere: no visible global function definition for ‘plot3d’ make.3D.Sphere: no visible global function definition for ‘decorate3d’ make.3D.Sphere: no visible global function definition for ‘spheres3d’ Undefined global functions or variables: decorate3d dist flush.console p.adjust plot3d ppois rgl.bg rgl.open sd spheres3d Consider adding importFrom("stats", "dist", "p.adjust", "ppois", "sd") importFrom("utils", "flush.console") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SpaceClust 35.672 1.883 41.095 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SpacePAC.Rcheck/00check.log’ for details.
SpacePAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpacePAC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘SpacePAC’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpacePAC)
SpacePAC.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (64-bit) R 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. > BiocGenerics:::testPackage("SpacePAC") Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith Attaching package: 'BiocGenerics' The following object is masked from 'package:gdata': combine The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:gdata': first, first<- The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:gdata': trim Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25 Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50 Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75 Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25 Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50 Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75 RUNIT TEST PROTOCOL -- Thu Apr 18 04:35:30 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : SpacePAC RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 12.987 0.496 13.687
SpacePAC.Rcheck/SpacePAC-Ex.timings
name | user | system | elapsed | |
SpaceClust | 35.672 | 1.883 | 41.095 | |
SpacePAC-package | 0 | 0 | 0 | |
make.3D.Sphere | 0.000 | 0.001 | 0.000 | |