Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 393/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNViz 1.13.0 (landing page) Rebecca Greenblatt
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CNViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNViz.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: CNViz |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNViz_1.13.0.tar.gz |
StartedAt: 2024-08-26 20:21:35 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:23:34 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 119.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNViz_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNViz.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNViz’ version ‘1.13.0’ * 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 ‘CNViz’ can be installed ... OK * checking installed package size ... OK * 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 launchCNViz: no visible global function definition for 'is' launchCNViz: no visible binding for global variable 'gene' launchCNViz: no visible binding for global variable 'mutation_id' launchCNViz: no visible binding for global variable 'ref' launchCNViz: no visible binding for global variable 'alt' launchCNViz: no visible binding for global variable 'sampleNames' launchCNViz : server: no visible binding for global variable 'gene' launchCNViz : server: no visible binding for global variable 'weight' launchCNViz : server: no visible binding for global variable 'mean_log2' launchCNViz : server: no visible binding for global variable 's' launchCNViz : server: no visible binding for global variable 'e' launchCNViz : server: no visible binding for global variable 'cn' launchCNViz : server: no visible binding for global variable 'total_weight' launchCNViz : server: no visible binding for global variable 'loh' launchCNViz : server: no visible binding for global variable 'chrom' launchCNViz : server: no visible binding for global variable 'chr1_subplot' launchCNViz : server: no visible binding for global variable 'chr2_subplot' launchCNViz : server: no visible binding for global variable 'chr3_subplot' launchCNViz : server: no visible binding for global variable 'chr4_subplot' launchCNViz : server: no visible binding for global variable 'chr5_subplot' launchCNViz : server: no visible binding for global variable 'chr6_subplot' launchCNViz : server: no visible binding for global variable 'chr7_subplot' launchCNViz : server: no visible binding for global variable 'chr8_subplot' launchCNViz : server: no visible binding for global variable 'chr9_subplot' launchCNViz : server: no visible binding for global variable 'chr10_subplot' launchCNViz : server: no visible binding for global variable 'chr11_subplot' launchCNViz : server: no visible binding for global variable 'chr12_subplot' launchCNViz : server: no visible binding for global variable 'chr13_subplot' launchCNViz : server: no visible binding for global variable 'chr14_subplot' launchCNViz : server: no visible binding for global variable 'chr15_subplot' launchCNViz : server: no visible binding for global variable 'chr16_subplot' launchCNViz : server: no visible binding for global variable 'chr17_subplot' launchCNViz : server: no visible binding for global variable 'chr18_subplot' launchCNViz : server: no visible binding for global variable 'chr19_subplot' launchCNViz : server: no visible binding for global variable 'chr20_subplot' launchCNViz : server: no visible binding for global variable 'chr21_subplot' launchCNViz : server: no visible binding for global variable 'chr22_subplot' launchCNViz : server: no visible binding for global variable 'chrX_subplot' launchCNViz : server: no visible binding for global variable 'chrY_subplot' launchCNViz : server: no visible binding for global variable 'study_name' launchCNViz : server: no visible binding for global variable 'hugoGeneSymbol' launchCNViz : server: no visible binding for global variable 'Gain' launchCNViz : server: no visible binding for global variable 'Amplification' launchCNViz : server: no visible binding for global variable 'ShallowDeletion' launchCNViz : server: no visible binding for global variable 'DeepDeletion' launchCNViz : server : <anonymous>: no visible binding for global variable 'loh' Undefined global functions or variables: Amplification DeepDeletion Gain ShallowDeletion alt chr10_subplot chr11_subplot chr12_subplot chr13_subplot chr14_subplot chr15_subplot chr16_subplot chr17_subplot chr18_subplot chr19_subplot chr1_subplot chr20_subplot chr21_subplot chr22_subplot chr2_subplot chr3_subplot chr4_subplot chr5_subplot chr6_subplot chr7_subplot chr8_subplot chr9_subplot chrX_subplot chrY_subplot chrom cn e gene hugoGeneSymbol is loh mean_log2 mutation_id ref s sampleNames study_name total_weight weight Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNViz.Rcheck/00check.log’ for details.
CNViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CNViz’ ... ** 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 (CNViz)
CNViz.Rcheck/CNViz-Ex.timings
name | user | system | elapsed | |
launchCNViz | 0.001 | 0.000 | 0.001 | |