Reid F. Thompson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MassArray |
| Branch: RELEASE_3_7 |
| Last Commit: a8908ff |
| Last Changed Date: 2018-04-30 10:35:12 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:34:36 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MassArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MassArray_1.32.0.tar.gz |
| StartedAt: 2018-10-17 03:04:47 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:05:52 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 65.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MassArray.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MassArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MassArray_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MassArray.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
evaluateSNPs 11.06 0.05 11.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
evaluateSNPs 14.16 0.01 14.17
* 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/MassArray.Rcheck/00check.log'
for details.
MassArray.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/MassArray_1.32.0.tar.gz && rm -rf MassArray.buildbin-libdir && mkdir MassArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MassArray.buildbin-libdir MassArray_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL MassArray_1.32.0.zip && rm MassArray_1.32.0.tar.gz MassArray_1.32.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 117k 100 117k 0 0 2022k 0 --:--:-- --:--:-- --:--:-- 2261k
install for i386
* installing *source* package 'MassArray' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MassArray'
finding HTML links ... done
MassArray.example.data html
MassArrayData-class html
MassArrayFragment-class html
MassArrayPeak-class html
MassArraySpectrum-class html
ampliconPrediction html
analyzeCpGs html
bisConvert html
calcMW html
calcMeth html
calcPercentAdduct html
calcPercentConversion html
combine-methods html
combine html
convControl html
countCGs html
createWiggle html
estimatePrimerDimer html
evaluateSNPs html
expandSequence html
findCollisions html
findFragments html
findPeaks html
identifySNPs html
importEpiTyperData html
importEpiTyperData.new html
inSilicoFragmentation html
isAssayable html
numCollisions html
plot.MassArrayData html
position-methods html
position html
revComplement-methods html
revComplement html
rnaDigest html
samples-methods html
samples html
sum.MassArraySpectrum html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MassArray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MassArray' as MassArray_1.32.0.zip
* DONE (MassArray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'MassArray' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
MassArray.Rcheck/examples_i386/MassArray-Ex.timings
|
MassArray.Rcheck/examples_x64/MassArray-Ex.timings
|