| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:24:28 -0400 (Tue, 09 Apr 2019).
| Package 305/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNVPanelizer 1.15.0 Thomas Wolf
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: CNVPanelizer |
| Version: 1.15.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVPanelizer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNVPanelizer_1.15.0.tar.gz |
| StartedAt: 2019-04-09 01:53:10 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:58:15 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 304.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CNVPanelizer.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVPanelizer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNVPanelizer_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNVPanelizer.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.15.0'
* 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
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'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test.bootList: Error in checkEquals(resultForGENE1, 0.125, checkNames = FALSE, tolerance = tolerance) :
Mean relative difference: 0.25
Test files with failing tests
test_testing.R
test.bootList
Error in BiocGenerics:::testPackage("CNVPanelizer") :
unit tests failed for package CNVPanelizer
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test.bootList: Error in checkEquals(resultForGENE1, 0.125, checkNames = FALSE, tolerance = tolerance) :
Mean relative difference: 0.25
Test files with failing tests
test_testing.R
test.bootList
Error in BiocGenerics:::testPackage("CNVPanelizer") :
unit tests failed for package CNVPanelizer
Execution halted
* 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: 2 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNVPanelizer.Rcheck/00check.log'
for details.
CNVPanelizer.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNVPanelizer_1.15.0.tar.gz && rm -rf CNVPanelizer.buildbin-libdir && mkdir CNVPanelizer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVPanelizer.buildbin-libdir CNVPanelizer_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNVPanelizer_1.15.0.zip && rm CNVPanelizer_1.15.0.tar.gz CNVPanelizer_1.15.0.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 86486 100 86486 0 0 645k 0 --:--:-- --:--:-- --:--:-- 692k
install for i386
* installing *source* package 'CNVPanelizer' ...
** 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_1.15.0.zip
* DONE (CNVPanelizer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CNVPanelizer' successfully unpacked and MD5 sums checked
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CNVPanelizer.Rcheck/tests_i386/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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-3.9-bioc\tmpdir\RtmpOyPbAf/s1_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/s2_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/s3_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/s4_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/sample1.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/sample2.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/sample3.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpOyPbAf/samples.xlsx'
Note: zip::zip() is deprecated, please use zip::zipr() instead
[1] "GENE 1: 0.166666666666667"
[1] "GENE 2: 0.356348322549899"
Timing stopped at: 0.03 0 0.03
Error in checkEquals(resultForGENE1, 0.125, checkNames = FALSE, tolerance = tolerance) :
Mean relative difference: 0.25
RUNIT TEST PROTOCOL -- Tue Apr 09 01:57:17 2019
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 1
1 Test Suite :
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test.bootList: Error in checkEquals(resultForGENE1, 0.125, checkNames = FALSE, tolerance = tolerance) :
Mean relative difference: 0.25
Test files with failing tests
test_testing.R
test.bootList
Error in BiocGenerics:::testPackage("CNVPanelizer") :
unit tests failed for package CNVPanelizer
Execution halted
|
CNVPanelizer.Rcheck/tests_x64/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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-3.9-bioc\tmpdir\RtmpEZkaYx/s1_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/s2_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/s3_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/s4_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/sample1.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/sample2.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/sample3.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEZkaYx/samples.xlsx'
Note: zip::zip() is deprecated, please use zip::zipr() instead
[1] "GENE 1: 0.166666666666667"
[1] "GENE 2: 0.356348322549899"
Timing stopped at: 0.03 0 0.03
Error in checkEquals(resultForGENE1, 0.125, checkNames = FALSE, tolerance = tolerance) :
Mean relative difference: 0.25
RUNIT TEST PROTOCOL -- Tue Apr 09 01:58:07 2019
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 1
1 Test Suite :
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test.bootList: Error in checkEquals(resultForGENE1, 0.125, checkNames = FALSE, tolerance = tolerance) :
Mean relative difference: 0.25
Test files with failing tests
test_testing.R
test.bootList
Error in BiocGenerics:::testPackage("CNVPanelizer") :
unit tests failed for package CNVPanelizer
Execution halted
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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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