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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 398/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVPanelizer 1.38.0  (landing page)
Thomas Wolf
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CNVPanelizer
git_branch: RELEASE_3_20
git_last_commit: bff6031
git_last_commit_date: 2024-10-29 10:02:11 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CNVPanelizer on kjohnson1

To the developers/maintainers of the CNVPanelizer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVPanelizer.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.

raw results


Summary

Package: CNVPanelizer
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVPanelizer_1.38.0.tar.gz
StartedAt: 2024-12-20 15:09:46 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 15:13:04 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 198.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVPanelizer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVPanelizer_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNVPanelizer.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVPanelizer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVPanelizer’ version ‘1.38.0’
* 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 ‘CNVPanelizer’ 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 ... NOTE
Namespace in Imports field not imported from: ‘S4Vectors’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘utils:::format.object_size’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
countBamInGRanges: no visible global function definition for ‘strand<-’
Undefined global functions or variables:
  strand<-
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNVPanelizer.Rcheck/00check.log’
for details.


Installation output

CNVPanelizer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNVPanelizer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘CNVPanelizer’ ...
** using staged installation
** R
** data
** 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 (CNVPanelizer)

Tests output

CNVPanelizer.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("CNVPanelizer")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Calculating Background for s1
Calculating Background for s2
Calculating Background for s3
Calculating Background for s4
Saving plot to '/tmp/RtmpWJwJkA/s1_plot.pdf'
Saving plot to '/tmp/RtmpWJwJkA/s2_plot.pdf'
Saving plot to '/tmp/RtmpWJwJkA/s3_plot.pdf'
Saving plot to '/tmp/RtmpWJwJkA/s4_plot.pdf'
Saving plot to '/tmp/RtmpWJwJkA/sample1.pdf'
Saving plot to '/tmp/RtmpWJwJkA/sample2.pdf'
Saving plot to '/tmp/RtmpWJwJkA/sample3.pdf'
Saving plot to '/tmp/RtmpWJwJkA/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/RtmpWJwJkA/samples.xlsx'
[1] "GENE 1:  0.166666666666667"
[1] "GENE 2:  0.356348322549899"


RUNIT TEST PROTOCOL -- Fri Dec 20 15:12:54 2024 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 31.795   0.637  32.578 

Example timings

CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings

nameusersystemelapsed
Background0.2170.0110.228
BedToGenomicRanges000
BootList0.6900.0100.703
CNVPanelizerFromReadCounts0.0000.0000.001
CNVPanelizerFromReadCountsHelper000
CollectColumnFromAllReportTables0.0010.0000.000
CombinedNormalizedCounts0.0190.0060.024
IndexMultipleBams000
NormalizedCounts0.0020.0020.005
PlotBootstrapDistributions3.7000.1103.826
ReadCountsFromBam0.0000.0010.000
ReadXLSXToList0.0000.0000.001
ReportTables0.2940.0080.303
RunCNVPanelizerShiny0.0010.0000.000
SelectReferenceSetByInterquartileRange000
SelectReferenceSetByKmeans0.0010.0010.000
SelectReferenceSetByPercentil000
SelectReferenceSetFromReadCounts000
StatusHeatmap0.0000.0000.001
WriteListToXLSX000