Thomas Wolf
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CNVPanelizer |
| git_branch: RELEASE_3_13 |
| git_last_commit: b0dc959 |
| git_last_commit_date: 2021-05-19 12:14:20 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 352/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNVPanelizer 1.24.0 (landing page) Thomas Wolf
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CNVPanelizer |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVPanelizer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVPanelizer_1.24.0.tar.gz |
| StartedAt: 2021-10-14 21:20:47 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:25:25 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 278.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNVPanelizer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVPanelizer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVPanelizer_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVPanelizer.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CNVPanelizer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CNVPanelizer' version '1.24.0' * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVPanelizer.Rcheck/00check.log' for details.
CNVPanelizer.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CNVPanelizer_1.24.0.tar.gz && rm -rf CNVPanelizer.buildbin-libdir && mkdir CNVPanelizer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVPanelizer.buildbin-libdir CNVPanelizer_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNVPanelizer_1.24.0.zip && rm CNVPanelizer_1.24.0.tar.gz CNVPanelizer_1.24.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 87124 100 87124 0 0 550k 0 --:--:-- --:--:-- --:--:-- 552k
install for i386
* installing *source* package 'CNVPanelizer' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNVPanelizer'
finding HTML links ... done
Background html
BedToGenomicRanges html
BootList html
CNVPanelizer-package html
CNVPanelizerFromReadCounts html
CNVPanelizerFromReadCountsHelper html
CollectColumnFromAllReportTables html
CombinedNormalizedCounts html
IndexMultipleBams html
NormalizedCounts html
PlotBootstrapDistributions html
ReadCountsFromBam html
ReadXLSXToList html
ReportTables html
RunCNVPanelizerShiny html
SelectReferenceSetByInterquartileRange
html
SelectReferenceSetByKmeans html
SelectReferenceSetByPercentil html
SelectReferenceSetFromReadCounts html
StatusHeatmap html
WriteListToXLSX html
referenceReadCounts html
sampleReadCounts html
** 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
install for x64
* installing *source* package 'CNVPanelizer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVPanelizer' as CNVPanelizer_1.24.0.zip
* DONE (CNVPanelizer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CNVPanelizer' successfully unpacked and MD5 sums checked
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CNVPanelizer.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/s1_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/s2_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/s3_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/s4_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/sample1.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/sample2.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/sample3.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp21p9S1/samples.xlsx'
[1] "GENE 1: 0.166666666666667"
[1] "GENE 2: 0.356348322549899"
RUNIT TEST PROTOCOL -- Thu Oct 14 21:24:38 2021
***********************************************
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
33.95 0.96 35.01
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CNVPanelizer.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/s1_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/s2_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/s3_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/s4_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/sample1.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/sample2.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/sample3.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpkz5iCk/samples.xlsx'
[1] "GENE 1: 0.166666666666667"
[1] "GENE 2: 0.356348322549899"
RUNIT TEST PROTOCOL -- Thu Oct 14 21:25:17 2021
***********************************************
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
37.71 0.51 38.25
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CNVPanelizer.Rcheck/examples_i386/CNVPanelizer-Ex.timings
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CNVPanelizer.Rcheck/examples_x64/CNVPanelizer-Ex.timings
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