Reid F. Thompson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MassArray |
| Branch: RELEASE_3_9 |
| Last Commit: 85a2566 |
| Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:58:06 -0400 (Wed, 16 Oct 2019).
| Package 921/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MassArray 1.36.0 Reid F. Thompson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MassArray |
| Version: 1.36.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MassArray_1.36.0.tar.gz |
| StartedAt: 2019-10-16 02:53:24 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:54:08 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 44.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MassArray.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MassArray_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MassArray.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.36.0’
* 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 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 11.097 0.02 11.118
* 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-3.9-bioc/meat/MassArray.Rcheck/00check.log’
for details.
MassArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MassArray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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)
MassArray.Rcheck/MassArray-Ex.timings
| name | user | system | elapsed | |
| MassArray.example.data | 0.013 | 0.001 | 0.013 | |
| MassArrayData-class | 0.001 | 0.000 | 0.001 | |
| MassArrayFragment-class | 0.001 | 0.000 | 0.001 | |
| MassArrayPeak-class | 0.001 | 0.000 | 0.001 | |
| MassArraySpectrum-class | 0.001 | 0.000 | 0.001 | |
| ampliconPrediction | 0.8 | 0.0 | 0.8 | |
| analyzeCpGs | 0.084 | 0.000 | 0.085 | |
| bisConvert | 0.000 | 0.000 | 0.001 | |
| calcMW | 0.001 | 0.000 | 0.001 | |
| calcMeth | 0.006 | 0.000 | 0.007 | |
| calcPercentAdduct | 0.026 | 0.000 | 0.026 | |
| calcPercentConversion | 0.014 | 0.000 | 0.014 | |
| combine | 0.335 | 0.000 | 0.335 | |
| convControl | 0.016 | 0.000 | 0.016 | |
| countCGs | 0.000 | 0.000 | 0.001 | |
| createWiggle | 0.007 | 0.000 | 0.007 | |
| estimatePrimerDimer | 0.038 | 0.000 | 0.038 | |
| evaluateSNPs | 11.097 | 0.020 | 11.118 | |
| expandSequence | 0.000 | 0.000 | 0.001 | |
| findCollisions | 0 | 0 | 0 | |
| findFragments | 0.003 | 0.004 | 0.007 | |
| findPeaks | 0 | 0 | 0 | |
| identifySNPs | 0.010 | 0.000 | 0.011 | |
| inSilicoFragmentation | 0.011 | 0.000 | 0.010 | |
| isAssayable | 0 | 0 | 0 | |
| numCollisions | 0.000 | 0.000 | 0.001 | |
| plot.MassArrayData | 0.018 | 0.000 | 0.018 | |
| position | 0.005 | 0.000 | 0.005 | |
| revComplement | 0.001 | 0.000 | 0.000 | |
| rnaDigest | 0.004 | 0.000 | 0.004 | |
| samples | 0.002 | 0.004 | 0.006 | |
| sum.MassArraySpectrum | 0.101 | 0.000 | 0.102 | |