seqCNA 1.23.0
David Mosen-Ansorena
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqCNA | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings seqCNA_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/seqCNA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqCNA’ version ‘1.23.0’
* 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 ‘seqCNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘GLAD’ ‘adehabitatLT’ ‘doSNOW’ ‘methods’ ‘seqCNA.annot’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.autoTrim: no visible global function definition for ‘makeCluster’
.autoTrim: no visible global function definition for ‘registerDoSNOW’
.autoTrim: no visible global function definition for ‘%dopar%’
.autoTrim: no visible global function definition for ‘foreach’
.autoTrim: no visible global function definition for ‘wawotest’
.autoTrim: no visible global function definition for ‘quantile’
.autoTrim: no visible global function definition for ‘stopCluster’
.autoTrim: no visible global function definition for ‘loess’
.autoTrim: no visible global function definition for ‘tail’
.buildGenomeInfo: no visible global function definition for
‘makeCluster’
.buildGenomeInfo: no visible global function definition for
‘registerDoSNOW’
.buildGenomeInfo: no visible global function definition for ‘%dopar%’
.buildGenomeInfo: no visible global function definition for ‘foreach’
.buildGenomeInfo: no visible global function definition for
‘stopCluster’
.makeFormula: no visible global function definition for ‘as.formula’
.olBarplot: no visible global function definition for ‘par’
.olBarplot: no visible global function definition for ‘barplot’
.overLapper : <anonymous>: no visible global function definition for
‘combn’
.resample: no visible global function definition for ‘makeCluster’
.resample: no visible global function definition for ‘registerDoSNOW’
.resample: no visible global function definition for ‘%dopar%’
.resample: no visible global function definition for ‘foreach’
.resample: no visible global function definition for ‘stopCluster’
.seqnorm: no visible binding for global variable ‘head’
.seqnorm: no visible global function definition for ‘tail’
.seqnorm: no visible global function definition for ‘flush.console’
.seqnorm: no visible binding for global variable ‘tail’
.seqnorm: no visible global function definition for ‘makeCluster’
.seqnorm: no visible global function definition for ‘registerDoSNOW’
.seqnorm: no visible global function definition for ‘%dopar%’
.seqnorm: no visible global function definition for ‘foreach’
.seqnorm: no visible global function definition for ‘as.profileCGH’
.seqnorm: no visible global function definition for ‘glad’
.seqnorm : <anonymous>: no visible global function definition for
‘quantile’
.seqnorm : .getSegmLm: no visible global function definition for
‘quantile’
.seqnorm: no visible global function definition for ‘predict’
.seqnorm: no visible global function definition for ‘median’
.seqnorm : <anonymous>: no visible global function definition for
‘median’
.seqnorm: no visible global function definition for ‘stopCluster’
.seqnorm: no visible global function definition for ‘jpeg’
.seqnorm: no visible global function definition for ‘quantile’
.seqnorm: no visible global function definition for ‘layout’
.seqnorm: no visible global function definition for ‘par’
.seqnorm: no visible global function definition for ‘density’
.seqnorm: no visible global function definition for ‘plot’
.seqnorm: no visible global function definition for ‘points’
.seqnorm: no visible global function definition for ‘plot.new’
.seqnorm: no visible global function definition for ‘legend’
.seqnorm: no visible global function definition for ‘abline’
.seqnorm: no visible global function definition for ‘dev.off’
.seqnorm: no visible global function definition for ‘lines’
.seqnorm: no visible global function definition for ‘smoothScatter’
.seqnorm: no visible global function definition for ‘colorRampPalette’
.summary.SeqCNAInfo: no visible global function definition for ‘head’
.summary.SeqCNAInfo: no visible global function definition for ‘tail’
.vennPlot: no visible global function definition for ‘symbols’
.vennPlot: no visible global function definition for ‘text’
.vennPlot : plotellipse: no visible global function definition for
‘par’
.vennPlot : plotellipse: no visible global function definition for
‘plot’
.vennPlot : ellipseVenn: no visible global function definition for
‘plot.new’
.vennPlot : ellipseVenn: no visible global function definition for
‘text’
applyFilters: no visible global function definition for
‘supported.builds’
applyFilters: no visible global function definition for ‘data’
applyFilters: no visible global function definition for ‘quantile’
applyFilters: no visible global function definition for ‘flush.console’
applyFilters: no visible global function definition for ‘jpeg’
applyFilters: no visible global function definition for ‘layout’
applyFilters: no visible global function definition for ‘par’
applyFilters: no visible global function definition for ‘smoothScatter’
applyFilters: no visible global function definition for
‘colorRampPalette’
applyFilters: no visible global function definition for ‘points’
applyFilters: no visible global function definition for ‘dev.off’
applyFilters: no visible global function definition for ‘density’
applyFilters: no visible global function definition for ‘plot’
applyFilters: no visible global function definition for ‘rect’
applyFilters: no visible global function definition for ‘abline’
applyFilters: no visible global function definition for ‘lines’
applyFilters: no visible global function definition for ‘text’
plotCNProfile: no visible global function definition for ‘jpeg’
plotCNProfile: no visible global function definition for ‘par’
plotCNProfile: no visible global function definition for ‘quantile’
plotCNProfile: no visible global function definition for
‘smoothScatter’
plotCNProfile: no visible global function definition for
‘colorRampPalette’
plotCNProfile: no visible global function definition for ‘abline’
plotCNProfile: no visible global function definition for ‘tail’
plotCNProfile : <anonymous>: no visible global function definition for
‘lines’
plotCNProfile: no visible global function definition for ‘median’
plotCNProfile: no visible global function definition for ‘text’
plotCNProfile: no visible global function definition for ‘dev.off’
readSeqsumm: no visible global function definition for
‘supported.builds’
readSeqsumm: no visible global function definition for ‘flush.console’
readSeqsumm: no visible global function definition for ‘read.table’
readSeqsumm: no visible global function definition for ‘data’
readSeqsumm: no visible global function definition for ‘new’
runGLAD: no visible global function definition for ‘flush.console’
runGLAD: no visible global function definition for ‘makeCluster’
runGLAD: no visible global function definition for ‘registerDoSNOW’
runGLAD: no visible global function definition for ‘%dopar%’
runGLAD: no visible global function definition for ‘foreach’
runGLAD: no visible global function definition for ‘as.profileCGH’
runGLAD: no visible global function definition for ‘glad’
runGLAD: no visible global function definition for ‘stopCluster’
writeCNProfile: no visible global function definition for ‘write.table’
summary,SeqCNAInfo: no visible global function definition for ‘head’
summary,SeqCNAInfo: no visible global function definition for ‘tail’
Undefined global functions or variables:
%dopar% abline as.formula as.profileCGH barplot colorRampPalette
combn data density dev.off flush.console foreach glad head jpeg
layout legend lines loess makeCluster median new par plot plot.new
points predict quantile read.table rect registerDoSNOW smoothScatter
stopCluster supported.builds symbols tail text wawotest write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg")
importFrom("graphics", "abline", "barplot", "layout", "legend",
"lines", "par", "plot", "plot.new", "points", "rect",
"smoothScatter", "symbols", "text")
importFrom("methods", "new")
importFrom("stats", "as.formula", "density", "loess", "median",
"predict", "quantile")
importFrom("utils", "combn", "data", "flush.console", "head",
"read.table", "tail", "write.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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘seqCNA/libs/seqCNA.so’:
Found ‘stdout’, possibly from ‘stdout’ (C)
Object: ‘seqCNA.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCNProfile 1.036 0.052 6.601
applyThresholds 0.952 0.052 6.322
writeCNProfile 0.280 0.020 5.209
runGLAD 0.248 0.040 5.899
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/seqCNA.Rcheck/00check.log’
for details.
* installing *source* package ‘seqCNA’ ...
** libs
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c seqCNA.cpp -o seqCNA.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o seqCNA.so seqCNA.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/seqCNA.Rcheck/seqCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqCNA)