Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:22:59 -0400 (Wed, 17 Oct 2018).
Package 833/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MassArray 1.32.0 Reid F. Thompson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: MassArray |
Version: 1.32.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MassArray_1.32.0.tar.gz |
StartedAt: 2018-10-16 01:41:00 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 01:41:34 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 34.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MassArray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MassArray_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MassArray.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.32.0’ * 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 ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed evaluateSNPs 9.812 0.028 9.848 * 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 ‘/home/biocbuild/bbs-3.7-bioc/meat/MassArray.Rcheck/00check.log’ for details.
MassArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MassArray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘MassArray’ ... ** 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 * DONE (MassArray)
MassArray.Rcheck/MassArray-Ex.timings
name | user | system | elapsed | |
MassArray.example.data | 0.008 | 0.004 | 0.012 | |
MassArrayData-class | 0.004 | 0.000 | 0.001 | |
MassArrayFragment-class | 0.000 | 0.000 | 0.001 | |
MassArrayPeak-class | 0.000 | 0.000 | 0.001 | |
MassArraySpectrum-class | 0.000 | 0.000 | 0.001 | |
ampliconPrediction | 0.668 | 0.000 | 0.669 | |
analyzeCpGs | 0.076 | 0.000 | 0.077 | |
bisConvert | 0.004 | 0.000 | 0.001 | |
calcMW | 0.000 | 0.000 | 0.001 | |
calcMeth | 0.008 | 0.000 | 0.009 | |
calcPercentAdduct | 0.024 | 0.000 | 0.023 | |
calcPercentConversion | 0.024 | 0.000 | 0.022 | |
combine | 0.300 | 0.000 | 0.302 | |
convControl | 0.012 | 0.000 | 0.013 | |
countCGs | 0 | 0 | 0 | |
createWiggle | 0.000 | 0.004 | 0.007 | |
estimatePrimerDimer | 0.036 | 0.000 | 0.037 | |
evaluateSNPs | 9.812 | 0.028 | 9.848 | |
expandSequence | 0.000 | 0.000 | 0.001 | |
findCollisions | 0 | 0 | 0 | |
findFragments | 0.008 | 0.000 | 0.008 | |
findPeaks | 0.000 | 0.000 | 0.001 | |
identifySNPs | 0.012 | 0.000 | 0.012 | |
inSilicoFragmentation | 0.012 | 0.000 | 0.009 | |
isAssayable | 0 | 0 | 0 | |
numCollisions | 0.000 | 0.000 | 0.001 | |
plot.MassArrayData | 0.020 | 0.000 | 0.017 | |
position | 0.004 | 0.000 | 0.006 | |
revComplement | 0.004 | 0.000 | 0.001 | |
rnaDigest | 0.004 | 0.000 | 0.004 | |
samples | 0.004 | 0.000 | 0.005 | |
sum.MassArraySpectrum | 0.108 | 0.000 | 0.106 | |