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This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 1985/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spicyR 1.17.0 (landing page) Ellis Patrick
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the spicyR 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: spicyR |
Version: 1.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.17.0.tar.gz |
StartedAt: 2024-05-20 03:50:24 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 03:56:20 -0400 (Mon, 20 May 2024) |
EllapsedTime: 355.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spicyR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/spicyR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.17.0’ * 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 ‘spicyR’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: data 5.0Mb * 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 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 ... NOTE bubblePlot: no visible global function definition for ‘setNames’ bubblePlot: no visible binding for global variable ‘condition’ convPairs: no visible binding for global variable ‘rowname’ convPairs: no visible binding for global variable ‘cellType_from’ convPairs: no visible binding for global variable ‘cellType_to’ convPairs: no visible binding for global variable ‘one’ convPairs: no visible binding for global variable ‘n_close’ convPairs: no visible binding for global variable ‘n’ convPairs: no visible binding for global variable ‘test’ convPairs: no visible binding for global variable ‘association’ inhomL: no visible binding for global variable ‘j’ inhomL: no visible binding for global variable ‘value’ inhomL: no visible binding for global variable ‘i’ inhomL: no visible binding for global variable ‘d’ inhomL: no visible binding for global variable ‘cellTypeI’ inhomL: no visible binding for global variable ‘cellTypeJ’ inhomL: no visible global function definition for ‘.’ inhomL: no visible binding for global variable ‘wt’ spicyBoxPlot: no visible binding for global variable ‘condition’ Undefined global functions or variables: . association cellTypeI cellTypeJ cellType_from cellType_to condition d i j n n_close one rowname setNames test value wt Consider adding importFrom("stats", "setNames") 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed convPairs 65.945 1.813 68.090 spicy 17.152 0.152 17.348 colTest 5.095 0.088 5.204 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/spicyR.Rcheck/00check.log’ for details.
spicyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spicyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘spicyR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (spicyR)
spicyR.Rcheck/spicyR-Ex.timings
name | user | system | elapsed | |
Accessors | 0.676 | 0.012 | 0.689 | |
SegmentedCells | 0.265 | 0.003 | 0.269 | |
bind | 0.027 | 0.005 | 0.032 | |
colTest | 5.095 | 0.088 | 5.204 | |
convPairs | 65.945 | 1.813 | 68.090 | |
getPairwise | 2.237 | 0.094 | 2.337 | |
getProp | 1.203 | 0.020 | 1.230 | |
plot-SegmentedCells | 0.344 | 0.002 | 0.348 | |
show-SegmentedCells | 0.294 | 0.002 | 0.298 | |
signifPlot | 2.747 | 0.067 | 2.820 | |
spicy | 17.152 | 0.152 | 17.348 | |
spicyBoxPlot | 0.634 | 0.007 | 0.654 | |
topPairs | 0.020 | 0.003 | 0.023 | |