Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:07 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 320/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CGHnormaliter 1.56.0 (landing page) Bart P.P. van Houte
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the CGHnormaliter 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: CGHnormaliter |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CGHnormaliter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CGHnormaliter_1.56.0.tar.gz |
StartedAt: 2024-04-17 08:39:15 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 08:40:57 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 101.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CGHnormaliter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CGHnormaliter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CGHnormaliter_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/CGHnormaliter.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 ‘CGHnormaliter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CGHnormaliter’ version ‘1.56.0’ * 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 ‘CGHnormaliter’ 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. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘CGHbase’ ‘CGHcall’ A package should be listed in only one of these fields. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .plotMA: no visible global function definition for ‘pdf’ .plotMA: no visible global function definition for ‘palette’ .plotMA: no visible global function definition for ‘par’ .plotMA: no visible global function definition for ‘title’ .plotMA: no visible global function definition for ‘abline’ .plotMA: no visible global function definition for ‘dev.off’ .readCghRaw: no visible global function definition for ‘read.table’ .readCghRaw: no visible global function definition for ‘make_cghRaw’ .runCGHcall: no visible global function definition for ‘capture.output’ .runCGHcall: no visible global function definition for ‘ExpandCGHcall’ CGHnormaliter: no visible binding for global variable ‘segment’ CGHnormaliter: no visible global function definition for ‘capture.output’ CGHnormaliter: no visible global function definition for ‘normalize’ CGHnormaliter: no visible global function definition for ‘postsegnormalize’ CGHnormaliter.write.table: no visible global function definition for ‘segmented’ CGHnormaliter.write.table: no visible global function definition for ‘calls’ Undefined global functions or variables: ExpandCGHcall abline calls capture.output dev.off make_cghRaw normalize palette par pdf postsegnormalize read.table segment segmented title Consider adding importFrom("grDevices", "dev.off", "palette", "pdf") importFrom("graphics", "abline", "par", "title") importFrom("utils", "capture.output", "read.table") 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 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 CGHnormaliter 57.02 0.578 58.509 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/CGHnormaliter.Rcheck/00check.log’ for details.
CGHnormaliter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CGHnormaliter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘CGHnormaliter’ ... ** using staged installation ** R ** data ** 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 (CGHnormaliter)
CGHnormaliter.Rcheck/CGHnormaliter-Ex.timings
name | user | system | elapsed | |
CGHnormaliter | 57.020 | 0.578 | 58.509 | |
CGHnormaliter.write.table | 0.253 | 0.008 | 0.262 | |