Gaëlle Lefort
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ASICS |
| Branch: RELEASE_3_11 |
| Last Commit: 1a78fbf |
| Last Changed Date: 2020-07-20 02:44:56 -0400 (Mon, 20 Jul 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:06 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE ASICS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 90/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ASICS 2.4.3 Gaëlle Lefort
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ASICS |
| Version: 2.4.3 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASICS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ASICS_2.4.3.tar.gz |
| StartedAt: 2020-10-17 01:37:59 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:57:24 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1164.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASICS.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASICS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ASICS_2.4.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.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 'ASICS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASICS' version '2.4.3'
* package encoding: UTF-8
* 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 'ASICS' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 3.2Mb
extdata 1.5Mb
* 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
.shift_spec: no visible binding for global variable 'pure_library'
.shift_spec: no visible global function definition for 'rnbinom'
simulate_spectra: no visible binding for global variable 'pure_library'
simulate_spectra : <anonymous>: no visible binding for global variable
'pure_library'
Undefined global functions or variables:
pure_library rnbinom
Consider adding
importFrom("stats", "rnbinom")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'simulate_spectra'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 installed files from 'inst/doc' ... 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
ASICS 31.95 2.5 34.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ASICS 30.02 2.85 32.86
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck/00check.log'
for details.
ASICS.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ASICS_2.4.3.tar.gz && rm -rf ASICS.buildbin-libdir && mkdir ASICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASICS.buildbin-libdir ASICS_2.4.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ASICS_2.4.3.zip && rm ASICS_2.4.3.tar.gz ASICS_2.4.3.zip
###
##############################################################################
##############################################################################
% 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 3615k 100 3615k 0 0 23.2M 0 --:--:-- --:--:-- --:--:-- 24.3M
install for i386
* installing *source* package 'ASICS' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ASICS'
finding HTML links ... done
ASICS html
ASICSResults-class html
ASICSUsersGuide html
AnalysisResults-class html
finding level-2 HTML links ... done
PureLibrary-class html
Spectra-class html
accessors-methods html
alignSpectra html
binning html
combineAndSubset-methods html
createPureLibrary html
createSpectra html
formatForAnalysis html
importSpectra html
importSpectraBruker html
kruskalWallis html
normaliseSpectra html
oplsda html
pca html
plotAlignment html
pure_library html
summary-methods html
visualisation-methods-analyses html
visualisation-methods-spectra html
** building package indices
** installing vignettes
'ASICS.Rmd' using 'UTF-8'
'ASICSUsersGuide.Rmd' using 'UTF-8'
** 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 'ASICS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASICS' as ASICS_2.4.3.zip
* DONE (ASICS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ASICS' successfully unpacked and MD5 sums checked
|
ASICS.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(ASICS)
>
> test_check("ASICS")
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Import spectra from txt or csv files...
Normalisation method : CS
Import spectra from fid files...
Begin PreprocessingChain
Begin ReadFids
dim Fid_data: 2 16384
IDs: AG_faq_Beck01 AG_faq_Beck051
non-unique IDs? 0
End ReadFids
It lasted 0 s user time, 0.01 s system time and 0.01 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
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Begin SolventSuppression
End SolventSuppression
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End Apodization
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Begin ZeroFilling
End ZeroFilling
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Begin FourierTransform
End FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
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Begin InternalReferencing
End InternalReferencing
It lasted 0.03 s user time, 0 s system time and 0.03 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.11 s user time, 0 s system time and 0.11 s elapsed time.
End PreprocessingChain
It lasted 0.51 s user time, 0.06 s system time and 0.58 s elapsed time.
Normalisation method : CS
Import spectra from txt or csv files...
Normalisation method : CS
Normalisation method : CS
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== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
446.06 9.17 470.87
|
ASICS.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(ASICS)
>
> test_check("ASICS")
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Import spectra from txt or csv files...
Normalisation method : CS
Import spectra from fid files...
Begin PreprocessingChain
Begin ReadFids
dim Fid_data: 2 16384
IDs: AG_faq_Beck01 AG_faq_Beck051
non-unique IDs? 0
End ReadFids
It lasted 0.05 s user time, 0 s system time and 0.04 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
It lasted 0.03 s user time, 0 s system time and 0.03 s elapsed time.
Begin SolventSuppression
End SolventSuppression
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Begin Apodization
End Apodization
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Begin ZeroFilling
End ZeroFilling
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Begin FourierTransform
End FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.16 s user time, 0 s system time and 0.15 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.02 s user time, 0 s system time and 0.02 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.06 s user time, 0 s system time and 0.06 s elapsed time.
End PreprocessingChain
It lasted 0.38 s user time, 0 s system time and 0.37 s elapsed time.
Normalisation method : CS
Import spectra from txt or csv files...
Normalisation method : CS
Normalisation method : CS
Alignment...
Peak detection
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Finding reference spectrum
Compute FFT correlations
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The reference spectrum is the number 3 : AG_faq_Beck139
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== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
366.78 6.48 373.68
|
|
ASICS.Rcheck/examples_i386/ASICS-Ex.timings
|
ASICS.Rcheck/examples_x64/ASICS-Ex.timings
|