Gabriela Merino
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TarSeqQC |
| Branch: RELEASE_3_11 |
| Last Commit: f0f86ab |
| Last Changed Date: 2020-04-27 14:51:30 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:55 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TarSeqQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1781/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TarSeqQC 1.18.0 Gabriela Merino
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ TIMEOUT ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: TarSeqQC |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TarSeqQC_1.18.0.tar.gz |
| StartedAt: 2020-10-17 08:47:45 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 09:27:45 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: TarSeqQC.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TarSeqQC_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TarSeqQC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TarSeqQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TarSeqQC' version '1.18.0'
* 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 'TarSeqQC' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotNtdPercentage,TargetExperiment: no visible global function
definition for 'path'
plotRegion,TargetExperiment: no visible global function definition for
'path'
readFrequencies,TargetExperiment: no visible global function definition
for 'path'
Undefined global functions or variables:
path
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TargetExperiment-class 19.86 0.58 493.97
TargetExperiment-plotRegion 3.67 0.19 151.71
TargetExperiment-plotFeature 2.76 0.19 146.21
pileupCounts 1.89 0.13 82.24
TargetExperiment-plotNtdPercentage 1.89 0.08 103.79
TargetExperiment-constructor 1.85 0.08 26.67
TargetExperiment-readFrequencies 1.11 0.01 17.48
plotInOutFeatures 1.12 0.00 18.22
TargetExperiment-summarizePanel 0.79 0.03 17.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TargetExperiment-class 20.67 0.50 526.38
TargetExperiment-plotRegion 3.31 0.14 111.27
TargetExperiment-plotFeature 3.23 0.09 117.16
TargetExperiment-constructor 2.38 0.08 45.48
TargetExperiment-plotNtdPercentage 1.97 0.09 78.36
pileupCounts 1.86 0.08 68.27
TargetExperiment-readFrequencies 1.28 0.02 16.61
plotInOutFeatures 1.25 0.04 16.66
TargetExperiment-summarizePanel 0.82 0.02 16.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
TarSeqQC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TarSeqQC_1.18.0.tar.gz && rm -rf TarSeqQC.buildbin-libdir && mkdir TarSeqQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TarSeqQC.buildbin-libdir TarSeqQC_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TarSeqQC_1.18.0.zip && rm TarSeqQC_1.18.0.tar.gz TarSeqQC_1.18.0.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 1792k 100 1792k 0 0 21.9M 0 --:--:-- --:--:-- --:--:-- 23.9M
install for i386
* installing *source* package 'TarSeqQC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TarSeqQC'
finding HTML links ... done
TEList html
TarSeqQC-package html
TargetExperiment-biasExploration html
TargetExperiment-buildFeaturePanel html
TargetExperiment-buildReport html
TargetExperiment-class html
TargetExperiment-constructor html
TargetExperiment-getters html
TargetExperiment-initialize html
TargetExperiment-plot html
TargetExperiment-plotAttrExpl html
TargetExperiment-plotAttrPerform html
TargetExperiment-plotFeatPerform html
TargetExperiment-plotFeature html
TargetExperiment-plotGeneAttrPerFeat html
TargetExperiment-plotMetaDataExpl html
TargetExperiment-plotNtdPercentage html
TargetExperiment-plotRegion html
TargetExperiment-print html
TargetExperiment-readFrequencies html
TargetExperiment-setters html
TargetExperiment-show html
TargetExperiment-statistics html
TargetExperiment-summarizePanel html
TargetExperimentList-class html
TargetExperimentList-constructor html
TargetExperimentList-initialize html
TargetExperimentList-plotGlobalAttrExpl
html
TargetExperimentList-plotPoolPerformance
html
ampliPanel html
ampliPanel2 html
checkBedFasta html
myCounts html
object html
pileupCounts html
plotInOutFeatures 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 'TarSeqQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TarSeqQC' as TarSeqQC_1.18.0.zip
* DONE (TarSeqQC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TarSeqQC' successfully unpacked and MD5 sums checked
TarSeqQC.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.
> BiocGenerics:::testPackage("TarSeqQC")
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
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
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
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TarSeqQC.Rcheck/examples_i386/TarSeqQC-Ex.timings
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TarSeqQC.Rcheck/examples_x64/TarSeqQC-Ex.timings
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