Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-08-15 13:20:03 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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

CHECK results for CNViz on nebbiolo1


To the developers/maintainers of the CNViz package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 367/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNViz 1.4.0  (landing page)
Rebecca Greenblatt
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/CNViz
git_branch: RELEASE_3_15
git_last_commit: 837c711
git_last_commit_date: 2022-04-26 12:14:42 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNViz
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNViz_1.4.0.tar.gz
StartedAt: 2022-08-14 19:18:26 -0400 (Sun, 14 Aug 2022)
EndedAt: 2022-08-14 19:23:11 -0400 (Sun, 14 Aug 2022)
EllapsedTime: 284.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CNViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNViz_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CNViz.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNViz’ version ‘1.4.0’
* 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 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
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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/CNViz.Rcheck/00check.log’
for details.



Installation output

CNViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CNViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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)

Tests output


Example timings

CNViz.Rcheck/CNViz-Ex.timings

nameusersystemelapsed
launchCNViz0.0020.0000.003