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This page was generated on 2022-01-26 13:06:50 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MassArray on tokay2


To the developers/maintainers of the MassArray package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MassArray.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 1052/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassArray 1.46.0  (landing page)
Reid F. Thompson
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/MassArray
git_branch: RELEASE_3_14
git_last_commit: d4621b4
git_last_commit_date: 2021-10-26 11:55:28 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: MassArray
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MassArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MassArray_1.46.0.tar.gz
StartedAt: 2022-01-25 22:22:01 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 22:23:20 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 79.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MassArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MassArray_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MassArray.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MassArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassArray' version '1.46.0'
* 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 'MassArray' 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
calcMeth: warning in matrix(0, nr = 0, nc = N): partial argument match
  of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = 0, nc = N): partial argument match
  of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = num.SNRs, nc = N): partial argument
  match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = num.SNRs, nc = N): partial argument
  match of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = num.missing, nc = N): partial
  argument match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = num.missing, nc = N): partial
  argument match of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = length(na.coefs), nc = N): partial
  argument match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = length(na.coefs), nc = N): partial
  argument match of 'nc' to 'ncol'
calcMeth : optimizeCoefficients: warning in matrix(0, nr =
  num.fragments, nc = N): partial argument match of 'nr' to 'nrow'
calcMeth : optimizeCoefficients: warning in matrix(0, nr =
  num.fragments, nc = N): partial argument match of 'nc' to 'ncol'
calcMeth : optimizeCoefficients: warning in matrix(NA, nr =
  length(coefs) + 1, nc = length(coefs)): partial argument match of
  'nr' to 'nrow'
calcMeth : optimizeCoefficients: warning in matrix(NA, nr =
  length(coefs) + 1, nc = length(coefs)): partial argument match of
  'nc' to 'ncol'
$<-,MassArrayData: no visible global function definition for 'slot<-'
$<-,MassArrayFragment: no visible global function definition for
  'slot<-'
$<-,MassArrayPeak: no visible global function definition for 'slot<-'
$<-,MassArraySpectrum: no visible global function definition for
  'slot<-'
initialize,MassArrayData: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table slot<-
Consider adding
  importFrom("methods", "slot<-")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
evaluateSNPs 12.39   0.04   12.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
evaluateSNPs 12.72   0.01   12.74
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MassArray.Rcheck/00check.log'
for details.



Installation output

MassArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MassArray_1.46.0.tar.gz && rm -rf MassArray.buildbin-libdir && mkdir MassArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MassArray.buildbin-libdir MassArray_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MassArray_1.46.0.zip && rm MassArray_1.46.0.tar.gz MassArray_1.46.0.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
100  118k  100  118k    0     0   630k      0 --:--:-- --:--:-- --:--:--  632k

install for i386

* installing *source* package 'MassArray' ...
** 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 'MassArray'
    finding HTML links ... done
    MassArray.example.data                  html  
    MassArrayData-class                     html  
    MassArrayFragment-class                 html  
    MassArrayPeak-class                     html  
    MassArraySpectrum-class                 html  
    ampliconPrediction                      html  
    analyzeCpGs                             html  
    bisConvert                              html  
    calcMW                                  html  
    calcMeth                                html  
    calcPercentAdduct                       html  
    calcPercentConversion                   html  
    combine-methods                         html  
    combine                                 html  
    convControl                             html  
    countCGs                                html  
    createWiggle                            html  
    estimatePrimerDimer                     html  
    evaluateSNPs                            html  
    expandSequence                          html  
    findCollisions                          html  
    findFragments                           html  
    findPeaks                               html  
    identifySNPs                            html  
    importEpiTyperData                      html  
    importEpiTyperData.new                  html  
    inSilicoFragmentation                   html  
    isAssayable                             html  
    numCollisions                           html  
    plot.MassArrayData                      html  
    position-methods                        html  
    position                                html  
    revComplement-methods                   html  
    revComplement                           html  
    rnaDigest                               html  
    samples-methods                         html  
    samples                                 html  
    sum.MassArraySpectrum                   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 'MassArray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MassArray' as MassArray_1.46.0.zip
* DONE (MassArray)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MassArray' successfully unpacked and MD5 sums checked

Tests output


Example timings

MassArray.Rcheck/examples_i386/MassArray-Ex.timings

nameusersystemelapsed
MassArray.example.data0.010.000.02
MassArrayData-class000
MassArrayFragment-class000
MassArrayPeak-class000
MassArraySpectrum-class000
ampliconPrediction0.850.000.84
analyzeCpGs0.090.000.10
bisConvert000
calcMW000
calcMeth000
calcPercentAdduct0.030.000.03
calcPercentConversion0.010.020.03
combine0.320.000.32
convControl0.010.000.01
countCGs000
createWiggle0.020.000.02
estimatePrimerDimer0.050.000.05
evaluateSNPs12.39 0.0412.43
expandSequence000
findCollisions000
findFragments0.010.000.02
findPeaks000
identifySNPs0.020.000.01
inSilicoFragmentation000
isAssayable000
numCollisions000
plot.MassArrayData0.030.000.04
position000
revComplement000
rnaDigest0.010.000.01
samples000
sum.MassArraySpectrum0.110.020.13

MassArray.Rcheck/examples_x64/MassArray-Ex.timings

nameusersystemelapsed
MassArray.example.data0.030.000.03
MassArrayData-class000
MassArrayFragment-class000
MassArrayPeak-class000
MassArraySpectrum-class000
ampliconPrediction101
analyzeCpGs0.110.000.11
bisConvert000
calcMW000
calcMeth000
calcPercentAdduct0.020.000.01
calcPercentConversion0.020.000.01
combine0.340.000.35
convControl0.030.000.03
countCGs000
createWiggle0.020.000.01
estimatePrimerDimer0.040.000.05
evaluateSNPs12.72 0.0112.74
expandSequence000
findCollisions000
findFragments0.020.000.01
findPeaks000
identifySNPs0.010.000.02
inSilicoFragmentation0.020.000.01
isAssayable000
numCollisions000
plot.MassArrayData0.050.000.05
position0.010.000.02
revComplement000
rnaDigest0.020.000.01
samples0.010.000.02
sum.MassArraySpectrum0.190.000.18