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This page was generated on 2020-01-16 13:45:32 -0500 (Thu, 16 Jan 2020).
| Package 1008/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MetCirc 1.17.0 Thomas Naake
| malbec2 | Linux (Ubuntu 18.04.3 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 |
| Package: MetCirc |
| Version: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetCirc_1.17.0.tar.gz |
| StartedAt: 2020-01-16 06:18:06 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:24:36 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 389.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MetCirc.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetCirc_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MetCirc.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetCirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetCirc’ version ‘1.17.0’
* 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 ‘MetCirc’ 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
Unexported objects imported by ':::' calls:
‘MSnbase:::bin_Spectra’ ‘circlize:::get.sector.data’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘recordPlotFill_degreeFeatures’ ‘recordPlotHighlight’ ‘replayPlotAdd’
‘replayPlotOrder’ ‘select’ ‘spectraCond’ ‘typeMatch_link0’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotSpectra: no visible binding for global variable ‘mz’
plotSpectra: no visible binding for global variable ‘int’
Undefined global functions or variables:
int mz
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createLinkDf 8.088 0.186 8.275
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
1 Test Suite :
MetCirc RUnit Tests - 18 test functions, 1 error, 0 failures
ERROR in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetCirc/unitTests/test_plottingFunctions.R: Error while sourcing /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetCirc/unitTests/test_plottingFunctions.R : Error : Unknown colour name: 1
Test files with failing tests
test_plottingFunctions.R
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetCirc/unitTests/test_plottingFunctions.R
Error in BiocGenerics:::testPackage("MetCirc") :
unit tests failed for package MetCirc
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: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/MetCirc.Rcheck/00check.log’
for details.
MetCirc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetCirc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘MetCirc’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘MSnbase’ for request: ‘Spectra’ when loading ‘MetCirc’ No methods found in package ‘MSnbase’ for request: ‘Spectrum2’ when loading ‘MetCirc’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘MSnbase’ for request: ‘Spectra’ when loading ‘MetCirc’ No methods found in package ‘MSnbase’ for request: ‘Spectrum2’ when loading ‘MetCirc’ ** testing if installed package can be loaded from final location No methods found in package ‘MSnbase’ for request: ‘Spectra’ when loading ‘MetCirc’ No methods found in package ‘MSnbase’ for request: ‘Spectrum2’ when loading ‘MetCirc’ ** testing if installed package keeps a record of temporary installation path * DONE (MetCirc)
MetCirc.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> library(amap)
> library(circlize)
========================================
circlize version 0.4.8
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/
If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
in R. Bioinformatics 2014.
========================================
> library(scales)
> library(shiny)
>
> data("sd01_outputXCMS", package="MetCirc")
> data("sd02_deconvoluted", package="MetCirc")
>
> BiocGenerics:::testPackage("MetCirc")
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, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.13.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
No methods found in package 'MSnbase' for request: 'Spectra' when loading 'MetCirc'
No methods found in package 'MSnbase' for request: 'Spectrum2' when loading 'MetCirc'
Error : Unknown colour name: 1
RUNIT TEST PROTOCOL -- Thu Jan 16 06:24:26 2020
***********************************************
Number of test functions: 18
Number of errors: 1
Number of failures: 0
1 Test Suite :
MetCirc RUnit Tests - 18 test functions, 1 error, 0 failures
ERROR in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetCirc/unitTests/test_plottingFunctions.R: Error while sourcing /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetCirc/unitTests/test_plottingFunctions.R : Error : Unknown colour name: 1
Test files with failing tests
test_plottingFunctions.R
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/MetCirc/unitTests/test_plottingFunctions.R
Error in BiocGenerics:::testPackage("MetCirc") :
unit tests failed for package MetCirc
Execution halted
MetCirc.Rcheck/MetCirc-Ex.timings
| name | user | system | elapsed | |
| cart2Polar | 0.001 | 0.000 | 0.001 | |
| circosLegend | 1.614 | 0.586 | 2.202 | |
| compare_Spectra | 0.303 | 0.012 | 0.315 | |
| convertMsp2Spectra | 0.348 | 0.022 | 0.370 | |
| createLink0df | 3.664 | 0.055 | 3.718 | |
| createLinkDf | 8.088 | 0.186 | 8.275 | |
| cutLinkDf | 3.898 | 0.113 | 4.012 | |
| getLinkDfIndices | 0.001 | 0.000 | 0.000 | |
| highlight | 2.355 | 0.674 | 3.030 | |
| minFragCart2Polar | 1.208 | 0.575 | 1.784 | |
| neutralloss | 0.035 | 0.010 | 0.046 | |
| normalizeddotproduct | 0.035 | 0.015 | 0.051 | |
| orderSimilarityMatrix | 1.105 | 0.656 | 1.760 | |
| plotCircos | 1.148 | 0.524 | 1.673 | |
| plotSpectra | 0.340 | 0.011 | 0.352 | |
| printInformationSelect | 1.129 | 0.642 | 1.771 | |
| recordPlotFill_degreeFeatures | 0.205 | 0.003 | 0.209 | |
| recordPlotHighlight | 0.131 | 0.003 | 0.136 | |
| replayPlotAdd | 2.601 | 0.748 | 3.350 | |
| replayPlotOrder | 0.300 | 0.039 | 0.341 | |
| select | 0.001 | 0.000 | 0.001 | |
| spectraCond | 0.023 | 0.009 | 0.033 | |
| thresholdLinkDf | 3.462 | 0.223 | 3.685 | |
| typeMatch_link0 | 1.132 | 0.677 | 1.809 | |