mosaics 2.10.0
Dongjun Chung
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/mosaics | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings mosaics_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/mosaics.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mosaics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mosaics’ version ‘2.10.0’
* 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 ‘mosaics’ 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
.calMDZ1_2S: no visible global function definition for ‘dnbinom’
.calcPN: no visible global function definition for ‘dnbinom’
.calcPN : <anonymous>: no visible global function definition for
‘dnbinom’
.calcYbdAll: no visible global function definition for ‘dnbinom’
.exportBED: no visible global function definition for ‘write.table’
.exportEncodePeak: no visible global function definition for
‘write.table’
.exportGFF: no visible global function definition for ‘write.table’
.exportTXT: no visible global function definition for ‘write.table’
.extractPostProb: no visible global function definition for ‘mclapply’
.extread2GRanges: no visible global function definition for
‘read.table’
.getPi0: no visible global function definition for ‘dnbinom’
.getPi0: no visible global function definition for ‘density’
.getPi0: no visible global function definition for ‘loess.smooth’
.getPi0: no visible global function definition for ‘rnbinom’
.loadReadData: no visible global function definition for ‘read.table’
.loadReadData: no visible global function definition for ‘mclapply’
.loadReadData: no visible global function definition for
‘readGAlignmentPairsFromBam’
.margDistZ1_1S: no visible global function definition for ‘dnbinom’
.margDistZ1_2S: no visible global function definition for ‘dnbinom’
.margDist_1S: no visible global function definition for ‘dnbinom’
.margDist_2S: no visible global function definition for ‘dnbinom’
.mosaicsZ0: no visible global function definition for ‘mclapply’
.plotGOF: no visible global function definition for ‘rnbinom’
.plotGOFHMM: no visible global function definition for ‘rnbinom’
.plotGOFHMM: no visible global function definition for ‘mclapply’
.rlmFit_IO: no visible global function definition for ‘coef’
.rlmFit_OS: no visible global function definition for ‘coef’
.rlmFit_TS: no visible global function definition for ‘coef’
.simulateHMM_1S: no visible global function definition for ‘rnbinom’
.simulateHMM_2S: no visible global function definition for ‘rnbinom’
constructBins: no visible global function definition for ‘read.table’
constructBins: no visible global function definition for
‘readGAlignmentPairsFromBam’
constructBins: no visible binding for global variable ‘readfile’
constructBins: no visible global function definition for ‘write.table’
generateWig: no visible global function definition for ‘read.table’
generateWig: no visible global function definition for
‘readGAlignmentPairsFromBam’
generateWig: no visible binding for global variable ‘readfile’
generateWig: no visible global function definition for ‘write.table’
mosaicsRunAll: no visible global function definition for ‘mclapply’
mosaicsRunAll: no visible global function definition for ‘pdf’
mosaicsRunAll: no visible global function definition for ‘dev.off’
readBins: no visible global function definition for ‘read.table’
readBins: no visible global function definition for ‘mclapply’
adjustBoundary,MosaicsPeak: no visible global function definition for
‘mclapply’
filterPeak,MosaicsPeak: no visible global function definition for
‘mclapply’
findSummit,MosaicsPeak: no visible global function definition for
‘mclapply’
mosaicsFitHMM,MosaicsFit: no visible global function definition for
‘mclapply’
mosaicsPeakHMM,MosaicsHMM: no visible global function definition for
‘mclapply’
plot,MosaicsPeak-missing: no visible global function definition for
‘pdf’
plot,MosaicsPeak-missing: no visible global function definition for
‘dev.off’
Undefined global functions or variables:
coef density dev.off dnbinom loess.smooth mclapply pdf read.table
readGAlignmentPairsFromBam readfile rnbinom write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("stats", "coef", "density", "dnbinom", "loess.smooth",
"rnbinom")
importFrom("utils", "read.table", "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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘mosaics-example.pdf’ from 1007Kb to 895Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.3-bioc/meat/mosaics.Rcheck/00check.log’
for details.
* installing *source* package ‘mosaics’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c convolution_1S.cpp -o convolution_1S.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c convolution_2S.cpp -o convolution_2S.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c emHMM.cpp -o emHMM.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c stack.cpp -o stack.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c updatePiMat.cpp -o updatePiMat.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c viterbi.cpp -o viterbi.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o mosaics.so convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/mosaics.Rcheck/mosaics/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘mosaics’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘mosaics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mosaics)