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This page was generated on 2022-01-14 13:05:23 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 nebbiolo2


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: 2022-01-13 01:55:04 -0500 (Thu, 13 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MassArray_1.46.0.tar.gz
StartedAt: 2022-01-13 08:20:07 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 08:20:42 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 34.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MassArray_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MassArray.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
evaluateSNPs 10.117  0.036  10.153
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MassArray.Rcheck/00check.log’
for details.



Installation output

MassArray.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MassArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* 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
** 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
* DONE (MassArray)

Tests output


Example timings

MassArray.Rcheck/MassArray-Ex.timings

nameusersystemelapsed
MassArray.example.data0.0050.0080.013
MassArrayData-class0.0010.0000.001
MassArrayFragment-class0.0010.0000.000
MassArrayPeak-class000
MassArraySpectrum-class000
ampliconPrediction0.6890.0040.692
analyzeCpGs0.0880.0000.088
bisConvert000
calcMW0.0010.0000.001
calcMeth0.0070.0000.007
calcPercentAdduct0.0280.0000.028
calcPercentConversion0.0170.0000.017
combine0.2680.0000.268
convControl0.0140.0000.014
countCGs000
createWiggle0.0070.0000.007
estimatePrimerDimer0.0350.0000.035
evaluateSNPs10.117 0.03610.153
expandSequence0.0000.0000.001
findCollisions000
findFragments0.0080.0000.007
findPeaks000
identifySNPs0.0160.0000.016
inSilicoFragmentation0.0050.0000.005
isAssayable000
numCollisions0.0000.0000.001
plot.MassArrayData0.0190.0000.019
position0.0050.0000.005
revComplement000
rnaDigest0.0040.0000.003
samples0.0060.0000.006
sum.MassArraySpectrum0.0960.0000.096