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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1123/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassArray 1.52.0  (landing page)
Reid F. Thompson
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MassArray
git_branch: RELEASE_3_17
git_last_commit: c8548f2
git_last_commit_date: 2023-04-25 09:50:16 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MassArray on kjohnson2


To the developers/maintainers of the MassArray package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MassArray
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MassArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MassArray_1.52.0.tar.gz
StartedAt: 2023-10-18 04:54:28 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 04:55:48 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 79.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MassArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MassArray_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MassArray.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MassArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassArray’ version ‘1.52.0’
* 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 ... NOTE
checkRd: (-1) MassArrayData-class.Rd:37: Escaped LaTeX specials: \$
checkRd: (-1) MassArrayData-class.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) MassArrayFragment-class.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) MassArrayFragment-class.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) MassArrayPeak-class.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) MassArrayPeak-class.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) MassArraySpectrum-class.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) MassArraySpectrum-class.Rd:29: Escaped LaTeX specials: \$
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
evaluateSNPs 14.261  0.458  21.286
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MassArray.Rcheck/00check.log’
for details.



Installation output

MassArray.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MassArray
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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.data0.0140.0040.022
MassArrayData-class0.0010.0010.002
MassArrayFragment-class0.0010.0010.002
MassArrayPeak-class0.0010.0010.001
MassArraySpectrum-class0.0010.0000.001
ampliconPrediction0.8340.0121.300
analyzeCpGs0.1080.0040.170
bisConvert0.0000.0000.003
calcMW0.0010.0010.001
calcMeth0.0080.0020.015
calcPercentAdduct0.0320.0020.050
calcPercentConversion0.0200.0020.037
combine0.3470.0040.543
convControl0.0190.0030.032
countCGs000
createWiggle0.0090.0030.017
estimatePrimerDimer0.0430.0030.068
evaluateSNPs14.261 0.45821.286
expandSequence0.0010.0000.002
findCollisions0.0010.0000.001
findFragments0.0090.0010.018
findPeaks000
identifySNPs0.0150.0010.020
inSilicoFragmentation0.0070.0020.012
isAssayable0.0000.0000.001
numCollisions000
plot.MassArrayData0.0210.0030.036
position0.0060.0010.012
revComplement000
rnaDigest0.0040.0020.011
samples0.0060.0010.011
sum.MassArraySpectrum0.1290.0020.194