Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-19 12:04:47 -0400 (Tue, 19 Oct 2021).

CHECK results for ASICS on riesling1

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 88/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.9.2  (landing page)
Gaƫlle Lefort
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: master
git_last_commit: 7a52ccf
git_last_commit_date: 2021-10-08 02:42:06 -0400 (Fri, 08 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ASICS
Version: 2.9.2
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASICS.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ASICS_2.9.2.tar.gz
StartedAt: 2021-10-19 00:13:29 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 00:28:45 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 915.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ASICS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASICS.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ASICS_2.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-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 '2.9.2'
* 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  6.2Mb
  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 ... OK
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda   1010Kb    607Kb       xz
* 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 33.02   1.53   34.55
ASICS            23.42   1.97   25.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
simulate_spectra 37.64   1.76   39.41
ASICS            23.17   2.86   26.03
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/ASICS.Rcheck/00check.log'
for details.



Installation output

ASICS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ASICS_2.9.2.tar.gz && rm -rf ASICS.buildbin-libdir && mkdir ASICS.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASICS.buildbin-libdir ASICS_2.9.2.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ASICS_2.9.2.zip && rm ASICS_2.9.2.tar.gz ASICS_2.9.2.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 3601k  100 3601k    0     0  4610k      0 --:--:-- --:--:-- --:--:-- 4610k

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_2.9.2.zip
* DONE (ASICS)
* installing to library 'D:/biocbuild/bbs-3.14-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 
Normalisation method : CS 
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 0.03 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 
It lasted 0 s user time, 0 s system time and 0 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 0.03 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 0.01 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.12 s user time, 0 s system time and 0.13 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0 s user time, 0 s system time and 0 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.05 s user time, 0 s system time and 0.05 s elapsed time.
End PreprocessingChain 
It lasted 0.28 s user time, 0 s system time and 0.29 s elapsed time.
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Normalisation method : CS 
Alignment... 
Peak detection 
Finding reference spectrum 
Compute FFT correlations 
The reference spectrum is the number 3 : AG_faq_Beck139 
Align spectra 
Import spectra from txt or csv files... 
Normalisation method : CS 
Binning 
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Deform library peaks 
Compute quantifications 
Format global results... 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Deform library peaks 
Compute quantifications 
Format global results... 
Import spectra from 1r files... 
Normalisation method : CS 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Compute shifts for all maximum shift values 
Put the median shift for extreme shift values 
Compute correlations between buckets and quantifications 
Shift all spectra according to the best shift 
Deform library peaks 
Compute quantifications 
Format global results... 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Compute shifts for all maximum shift values 
Put the median shift for extreme shift values 
Compute correlations between buckets and quantifications 
Shift all spectra according to the best shift 
Deform library peaks 
Compute quantifications 
Format global results... 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 260.28    5.78  266.64 

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 
Normalisation method : CS 
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 0.03 s user time, 0 s system time and 0.03 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0 s user time, 0.01 s system time and 0.02 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 0.52 s user time, 0 s system time and 0.51 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0 s user time, 0 s system time and 0 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.08 s user time, 0 s system time and 0.08 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0 s user time, 0 s system time and 0 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.05 s user time, 0 s system time and 0.05 s elapsed time.
End PreprocessingChain 
It lasted 0.68 s user time, 0.01 s system time and 0.69 s elapsed time.
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Normalisation method : CS 
Alignment... 
Peak detection 
Finding reference spectrum 
Compute FFT correlations 
The reference spectrum is the number 3 : AG_faq_Beck139 
Align spectra 
Import spectra from txt or csv files... 
Normalisation method : CS 
Binning 
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Deform library peaks 
Compute quantifications 
Format global results... 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Deform library peaks 
Compute quantifications 
Format global results... 
Import spectra from 1r files... 
Normalisation method : CS 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Compute shifts for all maximum shift values 
Put the median shift for extreme shift values 
Compute correlations between buckets and quantifications 
Shift all spectra according to the best shift 
Deform library peaks 
Compute quantifications 
Format global results... 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Compute shifts for all maximum shift values 
Put the median shift for extreme shift values 
Compute correlations between buckets and quantifications 
Shift all spectra according to the best shift 
Deform library peaks 
Compute quantifications 
Format global results... 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 211.04    5.46  216.50 

Example timings

ASICS.Rcheck/examples_i386/ASICS-Ex.timings

nameusersystemelapsed
ASICS23.42 1.9725.39
ASICSUsersGuide000
accessors-methods0.060.030.10
alignSpectra0.770.050.81
binning0.130.020.14
combineAndSubset-methods0.010.000.02
createPureLibrary0.090.010.11
createSpectra0.070.000.06
formatForAnalysis0.620.000.64
importSpectra0.80.00.8
importSpectraBruker0.050.000.04
kruskalWallis0.200.000.21
normaliseSpectra0.010.000.01
oplsda0.080.000.08
pca0.220.000.22
plotAlignment0.420.030.45
simulate_spectra33.02 1.5334.55
summary-methods0.010.000.01
visualisation-methods-analyses0.570.020.58
visualisation-methods-spectra0.470.020.49

ASICS.Rcheck/examples_x64/ASICS-Ex.timings

nameusersystemelapsed
ASICS23.17 2.8626.03
ASICSUsersGuide000
accessors-methods0.090.000.10
alignSpectra0.710.000.70
binning0.110.010.12
combineAndSubset-methods0.030.000.03
createPureLibrary0.200.000.21
createSpectra0.080.000.08
formatForAnalysis0.660.000.65
importSpectra0.50.00.5
importSpectraBruker0.070.000.08
kruskalWallis0.220.000.22
normaliseSpectra0.030.000.03
oplsda0.080.000.08
pca0.250.000.25
plotAlignment0.390.020.40
simulate_spectra37.64 1.7639.41
summary-methods0.020.000.02
visualisation-methods-analyses0.560.000.56
visualisation-methods-spectra0.490.030.51