Mike Smith
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/IONiseR |
| Branch: RELEASE_3_11 |
| Last Commit: e288533 |
| Last Changed Date: 2020-04-27 14:49:42 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:53 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE IONiseR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 889/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IONiseR 2.12.0 Mike Smith
| malbec2 | Linux (Ubuntu 18.04.4 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: IONiseR |
| Version: 2.12.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IONiseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IONiseR_2.12.0.tar.gz |
| StartedAt: 2020-10-17 05:15:36 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:26:27 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 651.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IONiseR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IONiseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IONiseR_2.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IONiseR.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 'IONiseR/DESCRIPTION' ... OK
* this is package 'IONiseR' version '2.12.0'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'IONiseR' 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
.fast5status : <anonymous>: no visible binding for global variable
'group'
.fast5status : <anonymous>: no visible binding for global variable
'name'
.get2D: no visible binding for global variable 'full_2D'
.muxToXY: no visible binding for global variable 'matrixCol'
.muxToXY: no visible binding for global variable 'mux'
.muxToXY: no visible binding for global variable 'oddEven'
.muxToXY: no visible global function definition for ':='
.muxToXY: no visible binding for global variable 'matrixRow'
.processFastq: no visible binding for global variable 'readIDs'
.strandExistence: no visible binding for global variable 'name'
.strandExistence: no visible binding for global variable 'group'
channelActivityPlot: no visible binding for global variable 'channel'
channelActivityPlot: no visible binding for global variable
'start_time'
channelActivityPlot: no visible binding for global variable 'duration'
channelActivityPlot: no visible binding for global variable 'zvalue'
channelActivityPlot: no visible binding for global variable 'time_bin'
channelActivityPlot: no visible binding for global variable
'mean_value'
layoutPlot: no visible binding for global variable 'channel'
layoutPlot: no visible binding for global variable 'seq_length'
layoutPlot: no visible binding for global variable 'median_signal'
layoutPlot: no visible global function definition for 'error'
muxHeatmap: no visible binding for global variable 'channel'
muxHeatmap: no visible binding for global variable 'matrixRow'
muxHeatmap: no visible binding for global variable 'matrixCol'
muxHeatmap: no visible binding for global variable 'meanZValue'
muxHeatmap: no visible global function definition for 'rbindlist'
muxHeatmap: no visible binding for global variable 'circleFun'
muxHeatmap: no visible binding for global variable 'x'
muxHeatmap: no visible binding for global variable 'y'
plot2DYield: no visible binding for global variable 'start_time'
plot2DYield: no visible binding for global variable 'pass'
plot2DYield: no visible binding for global variable 'nbases'
plot2DYield: no visible binding for global variable 'time_group'
plot2DYield: no visible binding for global variable 'hour'
plot2DYield: no visible binding for global variable 'accumulation'
plotActiveChannels: no visible binding for global variable 'start_time'
plotActiveChannels: no visible binding for global variable 'duration'
plotActiveChannels: no visible binding for global variable 'minute'
plotBaseProductionRate: no visible binding for global variable
'start_time'
plotBaseProductionRate: no visible binding for global variable
'bases_called'
plotBaseProductionRate: no visible binding for global variable
'duration'
plotCurrentByTime: no visible binding for global variable 'start_time'
plotCurrentByTime: no visible binding for global variable
'median_signal'
plotEventRate: no visible binding for global variable 'start_time'
plotEventRate: no visible binding for global variable 'num_events'
plotEventRate: no visible binding for global variable 'duration'
plotKmerFrequencyCorrelation: no visible binding for global variable
'full_2D'
plotKmerFrequencyCorrelation: no visible binding for global variable
'start_time'
plotKmerFrequencyCorrelation: no visible binding for global variable
'AAAAA'
plotKmerFrequencyCorrelation: no visible binding for global variable
'TTTTT'
plotKmerFrequencyCorrelation: no visible binding for global variable
'time_group'
plotKmerFrequencyCorrelation: no visible binding for global variable
'freq'
plotKmerFrequencyCorrelation: no visible binding for global variable
'pentamer'
plotKmerFrequencyCorrelation: no visible binding for global variable
'x'
plotKmerFrequencyCorrelation: no visible binding for global variable
'y'
plotReadAccumulation: no visible binding for global variable
'start_time'
plotReadAccumulation: no visible binding for global variable 'minute'
plotReadAccumulation: no visible binding for global variable
'new_reads'
plotReadAccumulation: no visible binding for global variable
'accumulation'
plotReadCategoryCounts: no visible binding for global variable
'full_2D'
plotReadCategoryCounts: no visible binding for global variable 'pass'
plotReadCategoryCounts: no visible binding for global variable
'category'
plotReadTypeProduction: no visible binding for global variable
'start_time'
plotReadTypeProduction: no visible binding for global variable
'time_group'
plotReadTypeProduction: no visible binding for global variable
'full_2D'
plotReadTypeProduction: no visible binding for global variable 'pass'
plotReadTypeProduction: no visible binding for global variable 'hour'
readFast5Summary: no visible binding for global variable 'start_time'
readFast5Summary: no visible binding for global variable 'duration'
readFast5Summary: no visible binding for global variable 'num_events'
readFast5Summary.mc: no visible binding for global variable
'start_time'
readFast5Summary.mc: no visible binding for global variable 'duration'
readFast5Summary.mc: no visible binding for global variable
'num_events'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
'baseCalledTemplate'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
'baseCalledComplement'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
'component'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
'idx'
show,Fast5Summary: no visible binding for global variable 'full_2D'
show,Fast5Summary: no visible binding for global variable 'pass'
Undefined global functions or variables:
:= AAAAA TTTTT accumulation baseCalledComplement baseCalledTemplate
bases_called category channel circleFun component duration error freq
full_2D group hour idx matrixCol matrixRow meanZValue mean_value
median_signal minute mux name nbases new_reads num_events oddEven
pass pentamer rbindlist readIDs seq_length start_time time_bin
time_group x y zvalue
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotKmerFrequencyCorrelation 44.01 1.27 45.28
channelActivityPlot 2.99 0.30 17.47
Fast5Summary-class 1.89 0.03 23.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotKmerFrequencyCorrelation 42.57 0.51 43.1
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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-3.11-bioc/meat/IONiseR.Rcheck/00check.log'
for details.
IONiseR.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/IONiseR_2.12.0.tar.gz && rm -rf IONiseR.buildbin-libdir && mkdir IONiseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IONiseR.buildbin-libdir IONiseR_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IONiseR_2.12.0.zip && rm IONiseR_2.12.0.tar.gz IONiseR_2.12.0.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 1154k 100 1154k 0 0 16.4M 0 --:--:-- --:--:-- --:--:-- 18.1M
install for i386
* installing *source* package 'IONiseR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'IONiseR'
finding HTML links ... done
Fast5Summary-class html
IONiseR html
baseCalled html
channelActivityPlot html
channelHeatmap html
eventData html
fast5toFastq html
fastq html
fastq2D html
fastqComplement html
fastqTemplate html
layoutPlot html
muxHeatmap html
plotActiveChannels html
plotBaseProductionRate html
plotCurrentByTime html
plotEventRate html
plotKmerFrequencyCorrelation html
plotReadAccumulation html
plotReadCategoryCounts html
plotReadCategoryQuals html
plotReadTypeProduction html
readFast5Log html
readFast5Summary html
readInfo 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 'IONiseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IONiseR' as IONiseR_2.12.0.zip
* DONE (IONiseR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'IONiseR' successfully unpacked and MD5 sums checked
|
IONiseR.Rcheck/tests_i386/testthat.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.
> library(testthat)
> library(IONiseR)
>
> test_check("IONiseR")
== testthat results ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 18 | FAILED: 0 ]
>
> proc.time()
user system elapsed
27.79 2.18 30.31
|
IONiseR.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(testthat)
> library(IONiseR)
>
> test_check("IONiseR")
== testthat results ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 18 | FAILED: 0 ]
>
> proc.time()
user system elapsed
26.68 0.82 27.54
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IONiseR.Rcheck/examples_i386/IONiseR-Ex.timings
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IONiseR.Rcheck/examples_x64/IONiseR-Ex.timings
|