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This page was generated on 2023-04-12 11:05:09 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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? 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 1099/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassArray 1.50.0  (landing page)
Reid F. Thompson
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/MassArray
git_branch: RELEASE_3_16
git_last_commit: 19928cf
git_last_commit_date: 2022-11-01 11:04:52 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MassArray
Version: 1.50.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MassArray_1.50.0.tar.gz
StartedAt: 2023-04-10 21:42:32 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:43:37 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 64.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MassArray_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MassArray.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MassArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassArray’ version ‘1.50.0’
* 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 loading without being on the library search path ... 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 10.06  0.028  10.088
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MassArray.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/MassArray.Rcheck/00check.log’
for details.



Installation output

MassArray.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MassArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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.data0.0130.0000.014
MassArrayData-class0.0010.0000.001
MassArrayFragment-class0.0010.0000.000
MassArrayPeak-class000
MassArraySpectrum-class0.0000.0000.001
ampliconPrediction0.7170.0000.717
analyzeCpGs0.0840.0000.084
bisConvert000
calcMW0.0010.0000.001
calcMeth0.0060.0000.007
calcPercentAdduct0.0240.0000.025
calcPercentConversion0.0180.0000.019
combine0.2830.0030.288
convControl0.0210.0000.021
countCGs0.0010.0000.000
createWiggle0.0070.0000.007
estimatePrimerDimer0.1030.0000.103
evaluateSNPs10.060 0.02810.088
expandSequence0.0010.0000.001
findCollisions000
findFragments0.0070.0000.007
findPeaks000
identifySNPs0.0110.0000.011
inSilicoFragmentation0.0050.0000.005
isAssayable000
numCollisions000
plot.MassArrayData0.0190.0000.019
position0.0050.0000.005
revComplement000
rnaDigest0.0040.0000.004
samples0.0120.0000.011
sum.MassArraySpectrum0.0960.0000.096