Thomas Naake
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MetCirc |
| Branch: RELEASE_3_10 |
| Last Commit: 731b255 |
| Last Changed Date: 2019-10-29 13:09:47 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:26:51 -0400 (Wed, 15 Apr 2020).
| Package 1011/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MetCirc 1.16.0 Thomas Naake
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MetCirc |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetCirc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MetCirc_1.16.0.tar.gz |
| StartedAt: 2020-04-15 04:36:44 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:43:28 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 403.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MetCirc.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetCirc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MetCirc_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MetCirc.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MetCirc/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MetCirc' version '1.16.0' * 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 '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 * 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 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 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MetCirc.Rcheck/00check.log' for details.
MetCirc.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MetCirc_1.16.0.tar.gz && rm -rf MetCirc.buildbin-libdir && mkdir MetCirc.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetCirc.buildbin-libdir MetCirc_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MetCirc_1.16.0.zip && rm MetCirc_1.16.0.tar.gz MetCirc_1.16.0.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 1574k 100 1574k 0 0 27.1M 0 --:--:-- --:--:-- --:--:-- 29.0M
install for i386
* 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
converting help for package 'MetCirc'
finding HTML links ... done
cart2Polar html
circosLegend html
compare_Spectra html
compartmentTissue html
convertExampleDF html
convertMsp2Spectra html
createLink0df html
createLinkDf html
cutLinkDf html
getLinkDfIndices html
highlight html
minFragCart2Polar html
msp2spectra html
neutralloss html
normalizeddotproduct html
orderSimilarityMatrix html
plotCircos html
plotSpectra html
printInformationSelect html
recordPlotFill_degreeFeatures html
recordPlotHighlight html
replayPlotAdd html
replayPlotOrder html
sd01_outputXCMS html
sd02_deconvoluted html
select html
shinyCircos html
similarityMat html
spectraCond html
spectra_tissue html
thresholdLinkDf html
tissue html
typeMatch_link0 html
** 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
install for x64
* installing *source* package 'MetCirc' ...
** testing if installed package can be loaded
No methods found in package 'MSnbase' for request: 'Spectra' when loading 'MetCirc'
No methods found in package 'MSnbase' for request: 'Spectrum2' when loading 'MetCirc'
* MD5 sums
packaged installation of 'MetCirc' as MetCirc_1.16.0.zip
* DONE (MetCirc)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MetCirc' successfully unpacked and MD5 sums checked
|
MetCirc.Rcheck/tests_i386/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> 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 2.12.0
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'
Note: 1 point is out of plotting region in sector 'SPL_241', track '1'.
Note: 1 point is out of plotting region in sector 'LIM_34', track '1'.
Note: 1 point is out of plotting region in sector 'ANT_16', track '1'.
Note: 1 point is out of plotting region in sector 'STY_124', track '1'.
RUNIT TEST PROTOCOL -- Wed Apr 15 04:41:43 2020
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
MetCirc RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
95.14 0.65 95.82
|
MetCirc.Rcheck/tests_x64/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> 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 2.12.0
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'
Note: 1 point is out of plotting region in sector 'SPL_241', track '1'.
Note: 1 point is out of plotting region in sector 'LIM_34', track '1'.
Note: 1 point is out of plotting region in sector 'ANT_16', track '1'.
Note: 1 point is out of plotting region in sector 'STY_124', track '1'.
RUNIT TEST PROTOCOL -- Wed Apr 15 04:43:22 2020
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
MetCirc RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
98.65 0.21 98.87
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MetCirc.Rcheck/examples_i386/MetCirc-Ex.timings
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MetCirc.Rcheck/examples_x64/MetCirc-Ex.timings
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