Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-24 11:05:32 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 CNVPanelizer on nebbiolo1


To the developers/maintainers of the CNVPanelizer package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 358/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVPanelizer 1.27.0  (landing page)
Thomas Wolf
Snapshot Date: 2022-01-23 13:55:15 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/CNVPanelizer
git_branch: master
git_last_commit: 6a20a6b
git_last_commit_date: 2021-10-26 12:21:16 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNVPanelizer
Version: 1.27.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNVPanelizer_1.27.0.tar.gz
StartedAt: 2022-01-23 19:14:30 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:17:21 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 171.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVPanelizer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNVPanelizer_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CNVPanelizer.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVPanelizer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVPanelizer’ version ‘1.27.0’
* 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 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 ... 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 ... OK
* 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 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 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/CNVPanelizer.Rcheck/00check.log’
for details.



Installation output

CNVPanelizer.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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/Rtmp0OOEUi/s1_plot.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/s2_plot.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/s3_plot.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/s4_plot.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/sample1.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/sample2.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/sample3.pdf'
Saving plot to '/tmp/Rtmp0OOEUi/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/Rtmp0OOEUi/samples.xlsx'
[1] "GENE 1:  0.166666666666667"
[1] "GENE 2:  0.356348322549899"


RUNIT TEST PROTOCOL -- Sun Jan 23 19:17:17 2022 
*********************************************** 
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 
 34.136   0.914  35.040 

Example timings

CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings

nameusersystemelapsed
Background0.2320.0040.236
BedToGenomicRanges0.0000.0000.001
BootList0.0840.0000.084
CNVPanelizerFromReadCounts000
CNVPanelizerFromReadCountsHelper0.0010.0000.000
CollectColumnFromAllReportTables000
CombinedNormalizedCounts0.0130.0040.016
IndexMultipleBams0.0010.0000.000
NormalizedCounts0.0020.0000.002
PlotBootstrapDistributions3.6080.0763.685
ReadCountsFromBam0.0000.0000.001
ReadXLSXToList000
ReportTables0.3130.0030.317
RunCNVPanelizerShiny000
SelectReferenceSetByInterquartileRange000
SelectReferenceSetByKmeans0.0000.0010.000
SelectReferenceSetByPercentil0.0000.0000.001
SelectReferenceSetFromReadCounts000
StatusHeatmap000
WriteListToXLSX000