Rebecca Greenblatt
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/CNViz |
| git_branch: RELEASE_3_20 |
| git_last_commit: 0870fb9 |
| git_last_commit_date: 2024-10-29 10:58:14 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 396/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNViz 1.14.0 (landing page) Rebecca Greenblatt
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.14.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNViz.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNViz_1.14.0.tar.gz |
| StartedAt: 2024-12-20 00:12:10 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 00:18:14 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 363.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNViz.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNViz.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNViz_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CNViz.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CNViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNViz' version '1.14.0'
* 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 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
'F:/biocbuild/bbs-3.20-bioc/meat/CNViz.Rcheck/00check.log'
for details.
CNViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CNViz ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 0 | 0 | |