Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:05:58 -0400 (Fri, 17 Sep 2021).

CHECK results for ASICS on tokay2

To the developers/maintainers of the ASICS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASICS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 92/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.8.0  (landing page)
Gaƫlle Lefort
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: RELEASE_3_13
git_last_commit: 3169aa8
git_last_commit_date: 2021-05-19 12:34:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ASICS
Version: 2.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASICS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ASICS_2.8.0.tar.gz
StartedAt: 2021-09-16 19:43:08 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 20:01:46 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 1117.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ASICS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASICS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ASICS_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ASICS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.8.0'
* 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  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    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'
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
* 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 LazyData ... 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
simulate_spectra 42.27   3.52   45.78
ASICS            36.93   3.22   40.35
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
simulate_spectra 41.84   2.94   44.82
ASICS            32.67   3.55   37.16
* 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-3.13-bioc/meat/ASICS.Rcheck/00check.log'
for details.



Installation output

ASICS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ASICS_2.8.0.tar.gz && rm -rf ASICS.buildbin-libdir && mkdir ASICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASICS.buildbin-libdir ASICS_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ASICS_2.8.0.zip && rm ASICS_2.8.0.tar.gz ASICS_2.8.0.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
 46 3260k   46 1504k    0     0  2378k      0  0:00:01 --:--:--  0:00:01 2379k
100 3260k  100 3260k    0     0  2867k      0  0:00:01  0:00:01 --:--:-- 2870k

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  
    simulate_spectra                        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_2.8.0.zip
* DONE (ASICS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ASICS' successfully unpacked and MD5 sums checked

Tests output

ASICS.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
Binning 

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Normalisation method : CS 

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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 0.01 s user time, 0 s system time and 0.01 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.07 s user time, 0 s system time and 0.07 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0 s user time, 0.02 s system time and 0.01 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0 s user time, 0 s system time and 0 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.04 s user time, 0.01 s system time and 0.07 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0 s user time, 0.02 s system time and 0.01 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.22 s user time, 0.01 s system time and 0.24 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.02 s user time, 0 s system time and 0.01 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 0.42 s user time, 0.06 s system time and 0.48 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 
Align spectra 

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Import spectra from txt or csv files... 
Normalisation method : CS 
Binning 

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Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Import spectra from 1r files... 

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Normalisation method : CS 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 
Compute shifts for all maximum shift values 

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Put the median shift for extreme shift values 

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Compute correlations between buckets and quantifications 

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Shift all spectra according to the best shift 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 
Compute shifts for all maximum shift values 

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Put the median shift for extreme shift values 

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Compute correlations between buckets and quantifications 

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Shift all spectra according to the best shift 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 354.46    8.92  371.98 

ASICS.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
Binning 

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Normalisation method : CS 

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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 s system time and 0 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.04 s user time, 0 s system time and 0.04 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0 s user time, 0 s system time and 0 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0.02 s user time, 0 s system time and 0.02 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.03 s user time, 0 s system time and 0.03 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.02 s user time, 0 s system time and 0.02 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.17 s user time, 0 s system time and 0.17 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.01 s user time, 0 s system time and 0.01 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.07 s user time, 0 s system time and 0.07 s elapsed time.
End PreprocessingChain 
It lasted 0.36 s user time, 0 s system time and 0.36 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 
Align spectra 

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Import spectra from txt or csv files... 
Normalisation method : CS 
Binning 

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Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Import spectra from 1r files... 

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Normalisation method : CS 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 
Compute shifts for all maximum shift values 

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Put the median shift for extreme shift values 

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Compute correlations between buckets and quantifications 

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Shift all spectra according to the best shift 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 
Compute shifts for all maximum shift values 

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Put the median shift for extreme shift values 

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Compute correlations between buckets and quantifications 

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Shift all spectra according to the best shift 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 335.46    7.95  343.42 

Example timings

ASICS.Rcheck/examples_i386/ASICS-Ex.timings

nameusersystemelapsed
ASICS36.93 3.2240.35
ASICSUsersGuide000
accessors-methods0.060.030.09
alignSpectra1.300.021.32
binning0.190.030.22
combineAndSubset-methods0.030.000.03
createPureLibrary0.270.010.76
createSpectra0.260.000.56
formatForAnalysis1.380.031.85
importSpectra1.450.041.58
importSpectraBruker0.120.000.12
kruskalWallis0.350.000.35
normaliseSpectra0.030.000.03
oplsda0.110.000.11
pca0.330.000.33
plotAlignment0.620.030.66
simulate_spectra42.27 3.5245.78
summary-methods0.010.000.01
visualisation-methods-analyses0.880.030.91
visualisation-methods-spectra0.840.020.86

ASICS.Rcheck/examples_x64/ASICS-Ex.timings

nameusersystemelapsed
ASICS32.67 3.5537.16
ASICSUsersGuide000
accessors-methods0.090.000.11
alignSpectra1.290.001.44
binning0.180.000.22
combineAndSubset-methods0.030.000.03
createPureLibrary0.200.020.27
createSpectra0.190.010.20
formatForAnalysis1.250.021.41
importSpectra1.000.031.20
importSpectraBruker0.890.001.00
kruskalWallis0.530.000.66
normaliseSpectra0.030.000.03
oplsda0.110.000.16
pca0.390.000.48
plotAlignment0.660.030.70
simulate_spectra41.84 2.9444.82
summary-methods0.020.000.01
visualisation-methods-analyses0.820.000.83
visualisation-methods-spectra0.710.000.70