Federico Comoglio
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/wavClusteR |
| Branch: RELEASE_3_7 |
| Last Commit: 90945d6 |
| Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:38:44 -0400 (Wed, 17 Oct 2018).
| Package 1543/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| wavClusteR 2.14.0 Federico Comoglio
| 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: wavClusteR |
| Version: 2.14.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:wavClusteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings wavClusteR_2.14.0.tar.gz |
| StartedAt: 2018-10-17 05:25:49 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:32:01 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 371.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wavClusteR.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:wavClusteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings wavClusteR_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/wavClusteR.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 'wavClusteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wavClusteR' version '2.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'wavClusteR' 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
* 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 ... NOTE
'library' or 'require' call to 'doMC' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateClusters: no visible binding for global variable 'Percentage'
annotateClusters: no visible binding for global variable 'Compartment'
estimateFDR: no visible global function definition for 'DNAString'
estimateFDR: no visible global function definition for 'lines'
estimateFDR: no visible global function definition for 'legend'
estimateFDR: no visible global function definition for 'axis'
exportGR: no visible global function definition for 'write.table'
filterClustersCWT: no visible global function definition for
'DNAString'
filterClustersMRN: no visible global function definition for
'txtProgressBar'
filterClustersMRN: no visible global function definition for
'setTxtProgressBar'
getClustersCWT: no visible global function definition for
'registerDoMC'
getClustersCWT: no visible global function definition for 'seqlevels'
getClustersMRN: no visible global function definition for
'registerDoMC'
getComplSubst: no visible global function definition for 'DNAStringSet'
getExpInterval: no visible global function definition for 'par'
getExpInterval: no visible global function definition for 'lines'
getExpInterval: no visible global function definition for 'legend'
getExpInterval: no visible global function definition for 'polygon'
getExpInterval: no visible global function definition for 'rect'
getExpInterval: no visible global function definition for 'text'
getLogOdd: no visible global function definition for 'dbinom'
getMetaCoverage: no visible global function definition for 'axis'
getMetaGene: no visible global function definition for 'grid'
getMetaGene: no visible global function definition for 'axis'
getMetaGene: no visible global function definition for 'abline'
getMetaTSS: no visible global function definition for 'grid'
getMetaTSS: no visible global function definition for 'axis'
plotSizeDistribution: no visible global function definition for 'hist'
plotStatistics: no visible binding for global variable 'panel.smooth'
plotStatistics : panelCor: no visible global function definition for
'par'
plotStatistics : panelCor: no visible global function definition for
'strwidth'
plotStatistics : panelCor: no visible global function definition for
'text'
plotStatistics: no visible global function definition for 'pairs'
plotSubstitutions: no visible global function definition for 'par'
plotSubstitutions: no visible global function definition for 'barplot'
processChunk: no visible global function definition for 'extractAt'
processMD: no visible global function definition for 'registerDoMC'
readSortedBam: no visible global function definition for 'scanBamFlag'
readSortedBam : <anonymous>: no visible binding for global variable
'rname'
readSortedBam : <anonymous>: no visible binding for global variable
'qwidth'
Undefined global functions or variables:
Compartment DNAString DNAStringSet Percentage abline axis barplot
dbinom extractAt grid hist legend lines pairs panel.smooth par
polygon qwidth rect registerDoMC rname scanBamFlag seqlevels
setTxtProgressBar strwidth text txtProgressBar write.table
Consider adding
importFrom("graphics", "abline", "axis", "barplot", "grid", "hist",
"legend", "lines", "pairs", "panel.smooth", "par",
"polygon", "rect", "strwidth", "text")
importFrom("stats", "dbinom")
importFrom("utils", "setTxtProgressBar", "txtProgressBar",
"write.table")
to your NAMESPACE file.
* 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
annotateClusters 6.13 0.27 6.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
annotateClusters 4.39 0.38 5.66
getClusters 2.23 0.06 5.01
getExpInterval 0.10 0.02 16.49
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/wavClusteR.Rcheck/00check.log'
for details.
wavClusteR.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/wavClusteR_2.14.0.tar.gz && rm -rf wavClusteR.buildbin-libdir && mkdir wavClusteR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=wavClusteR.buildbin-libdir wavClusteR_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL wavClusteR_2.14.0.zip && rm wavClusteR_2.14.0.tar.gz wavClusteR_2.14.0.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
100 143k 100 143k 0 0 2610k 0 --:--:-- --:--:-- --:--:-- 2921k
install for i386
* installing *source* package 'wavClusteR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'wavClusteR'
finding HTML links ... done
FitMixtureModel html
annotateClusters html
estimateFDR html
exportClusters html
exportCoverage html
exportHighConfSub html
exportSequences html
filterClusters html
finding level-2 HTML links ... done
getAllSub html
getClusters html
getExpInterval html
getHighConfSub html
getMetaCoverage html
getMetaGene html
getMetaTSS html
model html
plotSizeDistribution html
plotStatistics html
plotSubstitutions html
readSortedBam html
wavClusteR-package html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'wavClusteR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'wavClusteR' as wavClusteR_2.14.0.zip
* DONE (wavClusteR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'wavClusteR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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wavClusteR.Rcheck/examples_i386/wavClusteR-Ex.timings
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wavClusteR.Rcheck/examples_x64/wavClusteR-Ex.timings
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