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BioC 3.5: CHECK report for GLAD on malbec2

This page was generated on 2017-08-16 13:12:21 -0400 (Wed, 16 Aug 2017).

Package 564/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.40.0
Philippe Hupe
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GLAD
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GLAD
Version: 2.40.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GLAD_2.40.0.tar.gz
StartedAt: 2017-08-15 23:29:54 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:30:24 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 30.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GLAD_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GLAD.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 ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.40.0’
* 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 ‘GLAD’ 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 ... NOTE
'library' or 'require' calls in package code:
  ‘aws’ ‘tcltk’
  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
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nc' to 'ncol'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nc' to 'ncol'
ColorBar: no visible global function definition for ‘heat.colors’
ColorBar: no visible global function definition for ‘image’
ColorBar: no visible global function definition for ‘axis’
ColorBar: no visible global function definition for ‘par’
ColorBar: no visible global function definition for ‘box’
FDRThres: no visible global function definition for ‘pnorm’
HaarSeg: no visible global function definition for ‘median’
HaarSegGLAD: no visible global function definition for ‘median’
OptimBkpFindCluster: no visible global function definition for ‘qnorm’
OutliersGNL.profileCGH: no visible global function definition for
  ‘qnorm’
RecomputeGNL: no visible global function definition for ‘qnorm’
affectationGNL.profileCGH: no visible global function definition for
  ‘aggregate’
affectationGNL.profileCGH: no visible binding for global variable
  ‘median’
affectationGNL.profileCGH: no visible binding for global variable ‘var’
affectationGNL.profileCGH: no visible global function definition for
  ‘qnorm’
arrayPersp.arrayCGH: no visible global function definition for ‘median’
arrayPersp.arrayCGH: no visible global function definition for
  ‘na.omit’
arrayPersp.arrayCGH: no visible global function definition for ‘par’
arrayPersp.arrayCGH: no visible global function definition for ‘layout’
arrayPersp.arrayCGH: no visible global function definition for
  ‘dev.cur’
arrayPersp.arrayCGH: no visible global function definition for ‘persp’
arrayPersp.default: no visible global function definition for ‘median’
arrayPersp.default: no visible global function definition for ‘na.omit’
arrayPersp.default: no visible global function definition for ‘par’
arrayPersp.default: no visible global function definition for ‘layout’
arrayPersp.default: no visible global function definition for ‘dev.cur’
arrayPersp.default: no visible global function definition for ‘persp’
arrayPlot.arrayCGH: no visible global function definition for ‘par’
arrayPlot.arrayCGH: no visible global function definition for ‘median’
arrayPlot.arrayCGH: no visible global function definition for ‘na.omit’
arrayPlot.arrayCGH: no visible global function definition for ‘image’
arrayPlot.arrayCGH: no visible global function definition for ‘box’
arrayPlot.arrayCGH: no visible global function definition for ‘abline’
as.profileCGH.data.frame: no visible global function definition for
  ‘na.omit’
chrBreakpoints.profileCGH : IQRdiff: no visible global function
  definition for ‘IQR’
chrBreakpoints.profileCGH: no visible global function definition for
  ‘median’
chrBreakpoints.profileCGH: no visible global function definition for
  ‘laws’
chrBreakpoints.profileCGH: no visible global function definition for
  ‘aws’
clusterglad.hclust: no visible global function definition for ‘cutree’
daglad.profileCGH : IQRdiff: no visible global function definition for
  ‘IQR’
daglad.profileCGH: no visible global function definition for ‘median’
detectOutliers.profileChr: no visible global function definition for
  ‘qnorm’
dogenomestep: no visible global function definition for ‘median’
glad.profileCGH: no visible global function definition for ‘median’
glad.profileCGH : IQRdiff: no visible global function definition for
  ‘IQR’
glad.profileCGH: no visible global function definition for ‘aggregate’
glad.profileCGH: no visible binding for global variable ‘median’
hclustglad: no visible global function definition for ‘as.dist’
lawsglad: no visible global function definition for ‘qchisq’
loopRemove.profileChr: no visible global function definition for
  ‘qnorm’
myPalette: no visible global function definition for ‘col2rgb’
myPalette: no visible global function definition for ‘rgb’
plotCytoBand.default: no visible global function definition for
  ‘symbols’
plotCytoBand.default: no visible global function definition for
  ‘arrows’
plotCytoBand.default: no visible global function definition for ‘axis’
plotProfile.profileCGH: no visible global function definition for
  ‘na.omit’
plotProfile.profileCGH: no visible global function definition for
  ‘aggregate’
plotProfile.profileCGH: no visible global function definition for ‘par’
plotProfile.profileCGH: no visible global function definition for
  ‘layout’
plotProfile.profileCGH: no visible global function definition for
  ‘plot’
plotProfile.profileCGH: no visible global function definition for
  ‘lines’
plotProfile.profileCGH: no visible global function definition for
  ‘abline’
removeLevel.profileChr: no visible global function definition for
  ‘qnorm’
tkdaglad.default: no visible global function definition for
  ‘tktoplevel’
tkdaglad.default: no visible global function definition for ‘tkframe’
tkdaglad.default: no visible global function definition for
  ‘tkwm.title’
tkdaglad.default: no visible global function definition for ‘tkpack’
tkdaglad.default: no visible global function definition for ‘tklabel’
tkdaglad.default: no visible global function definition for ‘tclVar’
tkdaglad.default: no visible global function definition for
  ‘tkimage.create’
tkdaglad.default: no visible global function definition for
  ‘tkcheckbutton’
tkdaglad.default: no visible global function definition for
  ‘tkradiobutton’
tkdaglad.default: no visible global function definition for ‘tkentry’
tkdaglad.default : OnAnalysis: no visible global function definition
  for ‘tclvalue’
tkdaglad.default : OnAnalysis: no visible global function definition
  for ‘tkmessageBox’
tkdaglad.default : OnQuit: no visible global function definition for
  ‘tkdestroy’
tkdaglad.default : OnDefault: no visible global function definition for
  ‘tclvalue<-’
tkdaglad.default : OnPlot: no visible global function definition for
  ‘tclvalue’
tkdaglad.default : OnPlot: no visible global function definition for
  ‘tkget’
tkdaglad.default : OnPlot: no visible global function definition for
  ‘tkcurselection’
tkdaglad.default : OnPlot: no visible global function definition for
  ‘X11’
tkdaglad.default : OnLogo: no visible global function definition for
  ‘tkmessageBox’
tkdaglad.default: no visible global function definition for ‘tkbutton’
tkdaglad.default: no visible global function definition for
  ‘tkscrollbar’
tkdaglad.default : <anonymous>: no visible global function definition
  for ‘tkyview’
tkdaglad.default: no visible global function definition for ‘tklistbox’
tkdaglad.default : <anonymous>: no visible global function definition
  for ‘tkset’
tkdaglad.default : MakeListBox: no visible global function definition
  for ‘tkdelete’
tkdaglad.default : MakeListBox: no visible global function definition
  for ‘tksize’
tkdaglad.default : MakeListBox: no visible global function definition
  for ‘tkinsert’
tkdaglad.default : MakeListBox: no visible global function definition
  for ‘tkselection.set’
tkglad.default: no visible global function definition for ‘tktoplevel’
tkglad.default: no visible global function definition for ‘tkframe’
tkglad.default: no visible global function definition for ‘tkwm.title’
tkglad.default: no visible global function definition for ‘tkpack’
tkglad.default: no visible global function definition for ‘tklabel’
tkglad.default: no visible global function definition for ‘tclVar’
tkglad.default: no visible global function definition for
  ‘tkimage.create’
tkglad.default: no visible global function definition for
  ‘tkcheckbutton’
tkglad.default: no visible global function definition for
  ‘tkradiobutton’
tkglad.default: no visible global function definition for ‘tkentry’
tkglad.default : OnAnalysis: no visible global function definition for
  ‘tclvalue’
tkglad.default : OnAnalysis: no visible global function definition for
  ‘tkmessageBox’
tkglad.default : OnQuit: no visible global function definition for
  ‘tkdestroy’
tkglad.default : OnDefault: no visible global function definition for
  ‘tclvalue<-’
tkglad.default : OnPlot: no visible global function definition for
  ‘tclvalue’
tkglad.default : OnPlot: no visible global function definition for
  ‘tkget’
tkglad.default : OnPlot: no visible global function definition for
  ‘tkcurselection’
tkglad.default : OnPlot: no visible global function definition for
  ‘X11’
tkglad.default : OnLogo: no visible global function definition for
  ‘tkmessageBox’
tkglad.default: no visible global function definition for ‘tkbutton’
tkglad.default: no visible global function definition for ‘tkscrollbar’
tkglad.default : <anonymous>: no visible global function definition for
  ‘tkyview’
tkglad.default: no visible global function definition for ‘tklistbox’
tkglad.default : <anonymous>: no visible global function definition for
  ‘tkset’
tkglad.default : MakeListBox: no visible global function definition for
  ‘tkdelete’
tkglad.default : MakeListBox: no visible global function definition for
  ‘tksize’
tkglad.default : MakeListBox: no visible global function definition for
  ‘tkinsert’
tkglad.default : MakeListBox: no visible global function definition for
  ‘tkselection.set’
Undefined global functions or variables:
  IQR X11 abline aggregate arrows as.dist aws axis box col2rgb cutree
  dev.cur heat.colors image laws layout lines median na.omit par persp
  plot pnorm qchisq qnorm rgb symbols tclVar tclvalue tclvalue<-
  tkbutton tkcheckbutton tkcurselection tkdelete tkdestroy tkentry
  tkframe tkget tkimage.create tkinsert tklabel tklistbox tkmessageBox
  tkpack tkradiobutton tkscrollbar tkselection.set tkset tksize
  tktoplevel tkwm.title tkyview var
Consider adding
  importFrom("grDevices", "X11", "col2rgb", "dev.cur", "heat.colors",
             "rgb")
  importFrom("graphics", "abline", "arrows", "axis", "box", "image",
             "layout", "lines", "par", "persp", "plot", "symbols")
  importFrom("stats", "IQR", "aggregate", "as.dist", "cutree", "median",
             "na.omit", "pnorm", "qchisq", "qnorm", "var")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘GLAD/libs/GLAD.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘glad-utils.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘OutliersGNL.o’, ‘chrBreakpoints.o’, ‘findCluster.o’,
      ‘glad-utils.o’, ‘hclust.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
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GLAD.Rcheck/00check.log’
for details.

GLAD.Rcheck/00install.out:

* installing *source* package ‘GLAD’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Linux
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -lgsl -lgslcblas -lm
PKG_CPPFLAGS = 

** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BkpInfo.cpp -o BkpInfo.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c HaarSeg.cpp -o HaarSeg.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c MoveBkp.cpp -o MoveBkp.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c OutliersGNL.cpp -o OutliersGNL.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c chrBreakpoints.cpp -o chrBreakpoints.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cutree.cpp -o cutree.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c daglad.cpp -o daglad.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c distance.cpp -o distance.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c filterBkp.cpp -o filterBkp.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c findCluster.cpp -o findCluster.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c glad-utils.cpp -o glad-utils.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hclust.cpp -o hclust.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c laws.c -o laws.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c loopRemove.cpp -o loopRemove.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/GLAD.Rcheck/GLAD/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GLAD)

GLAD.Rcheck/GLAD-Ex.timings:

nameusersystemelapsed
ChrNumeric0.0040.0000.001
ColorBar0.060.000.06
arrayCGH0.0320.0000.030
arrayPersp000
arrayPlot0.1360.0080.144
as.data.frame.profileCGH0.3320.0000.330
as.profileCGH0.0760.0000.078
bladder0.0160.0000.017
cytoband0.0120.0000.012
daglad0.9480.0040.951
glad0.4600.0040.463
hclust0.0440.0000.056
myPalette0.0040.0000.005
plotProfile0.4120.0080.421
profileCGH0.0520.0040.056
snijders0.0560.0000.055
tkdaglad0.1000.0000.098
veltman0.0440.0200.063