Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 398/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVPanelizer 1.36.0  (landing page)
Thomas Wolf
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/CNVPanelizer
git_branch: RELEASE_3_19
git_last_commit: 9cd2650
git_last_commit_date: 2024-04-30 10:44:28 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CNVPanelizer on palomino3

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: 1.36.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVPanelizer.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CNVPanelizer_1.36.0.tar.gz
StartedAt: 2024-06-10 02:02:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 02:06:45 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 255.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVPanelizer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVPanelizer.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CNVPanelizer_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CNVPanelizer.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CNVPanelizer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVPanelizer' version '1.36.0'
* 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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/CNVPanelizer.Rcheck/00check.log'
for details.


Installation output

CNVPanelizer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL CNVPanelizer
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, 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


Attaching package: 'IRanges'

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

    windows

Calculating Background for s1
Calculating Background for s2
Calculating Background for s3
Calculating Background for s4
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/s1_plot.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/s2_plot.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/s3_plot.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/s4_plot.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/sample1.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/sample2.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/sample3.pdf'
Saving plot to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpqgfgS2/samples.xlsx'
[1] "GENE 1:  0.166666666666667"
[1] "GENE 2:  0.356348322549899"


RUNIT TEST PROTOCOL -- Mon Jun 10 02:06:31 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 
  41.39    3.42   45.07 

Example timings

CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings

nameusersystemelapsed
Background0.330.000.33
BedToGenomicRanges000
BootList0.090.040.13
CNVPanelizerFromReadCounts0.000.010.01
CNVPanelizerFromReadCountsHelper000
CollectColumnFromAllReportTables000
CombinedNormalizedCounts0.030.020.05
IndexMultipleBams000
NormalizedCounts0.020.000.01
PlotBootstrapDistributions3.910.094.00
ReadCountsFromBam000
ReadXLSXToList000
ReportTables0.310.050.36
RunCNVPanelizerShiny000
SelectReferenceSetByInterquartileRange000
SelectReferenceSetByKmeans000
SelectReferenceSetByPercentil000
SelectReferenceSetFromReadCounts000
StatusHeatmap000
WriteListToXLSX000