Package: Starr

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Starr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Starr_1.40.0.tar.gz

StartedAt: 2019-10-16 07:11:12 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:15:27 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 254.9 seconds

RetCode: 0

Status:  OK

CheckDir: Starr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Starr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Starr_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Starr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Starr/DESCRIPTION’ ... OK
* this is package ‘Starr’ version ‘1.40.0’
* 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 ‘Starr’ 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
RGlist2ExpresionSet: no visible global function definition for ‘new’
backgd.sd: no visible global function definition for ‘density’
backgd.sd: no visible global function definition for ‘sd’
backgd.sd: no visible global function definition for ‘quantile’
backgd.sd: no visible global function definition for ‘acf’
backgd.sd: no visible global function definition for ‘na.omit’
bpmapToProbeAnno: no visible global function definition for ‘new’
cmarrt.ma: no visible global function definition for ‘exprs’
cmarrt.peak : : no visible global function definition for
  ‘new’
correlate : : no visible global function definition for
  ‘cor’
correlationPlot: no visible global function definition for
  ‘colorRampPalette’
correlationPlot: no visible global function definition for ‘brewer.pal’
correlationPlot: no visible global function definition for ‘par’
correlationPlot: no visible global function definition for ‘barplot’
correlationPlot: no visible global function definition for ‘rect’
correlationPlot: no visible global function definition for ‘text’
correlationPlot: no visible global function definition for ‘axis’
correlationPlot: no visible global function definition for ‘abline’
declare.bound: no visible global function definition for ‘p.adjust’
densityscatter: no visible global function definition for
  ‘colorRampPalette’
densityscatter: no visible global function definition for ‘points’
densityscatter: no visible global function definition for ‘abline’
expressionByFeature: no visible global function definition for
  ‘featureNames’
expressionByFeature: no visible global function definition for ‘median’
expressionByFeature: no visible global function definition for ‘exprs’
getIntensities: no visible global function definition for ‘exprs’
getProfiles: no visible global function definition for ‘exprs’
getProfilesByBase: no visible global function definition for ‘exprs’
getRatio: no visible binding for global variable ‘median’
getRatio: no visible global function definition for ‘exprs’
getRatio: no visible global function definition for ‘new’
heatmapplot: no visible binding for global variable ‘median’
heatmapplot: no visible global function definition for
  ‘colorRampPalette’
heatmapplot: no visible global function definition for ‘levelplot’
heatmapplot : : no visible global function definition for
  ‘panel.levelplot’
heatmapplot : : no visible global function definition for
  ‘panel.abline’
heatmapplot : : no visible global function definition for
  ‘panel.axis’
kde2dplot: no visible global function definition for ‘tail’
kde2dplot: no visible global function definition for ‘topo.colors’
kde2dplot: no visible global function definition for ‘par’
kde2dplot: no visible global function definition for ‘contour’
kde2dplot: no visible global function definition for ‘box’
ma.stat: no visible global function definition for ‘filter’
ma.stat: no visible global function definition for ‘pnorm’
makeProbeAnno: no visible global function definition for ‘read.table’
makeSplines : spline: no visible global function definition for
  ‘predict’
normalize.Probes: no visible binding for global variable ‘median’
normalize.Probes: no visible global function definition for ‘exprs’
normalize.Probes: no visible global function definition for
  ‘normalizeBetweenArrays’
normalize.Probes: no visible global function definition for ‘exprs<-’
normalize.Probes: no visible global function definition for
  ‘experimentData’
normalize.Probes: no visible global function definition for ‘preproc<-’
normalize.Probes: no visible global function definition for
  ‘experimentData<-’
plotBoxes: no visible global function definition for ‘exprs’
plotBoxes: no visible global function definition for ‘boxplot’
plotBoxes: no visible global function definition for ‘mtext’
plotDensity: no visible global function definition for ‘exprs’
plotDensity: no visible global function definition for ‘rainbow’
plotDensity: no visible global function definition for ‘density’
plotDensity: no visible global function definition for ‘lines’
plotDensity: no visible global function definition for ‘legend’
plotDensity: no visible global function definition for ‘par’
plotGCbias: no visible global function definition for ‘boxplot’
plotImage: no visible global function definition for ‘levelplot’
plotImage: no visible global function definition for ‘rainbow’
plotMA: no visible global function definition for ‘exprs’
plotMA: no visible global function definition for ‘par’
plotMA: no visible global function definition for ‘ma.plot’
plotPosBias: no visible global function definition for ‘points’
plotProfiles: no visible global function definition for ‘heat.colors’
plotProfiles: no visible global function definition for ‘rainbow’
plotProfiles: no visible global function definition for
  ‘colorRampPalette’
plotProfiles: no visible global function definition for ‘abline’
plotProfiles: no visible global function definition for ‘axis’
plotProfiles: no visible global function definition for ‘density’
plotProfiles: no visible global function definition for ‘lines’
plotProfiles: no visible global function definition for ‘legend’
plotRatioScatter: no visible global function definition for ‘exprs’
plotRatioScatter: no visible global function definition for ‘cor’
plotRatioScatter: no visible global function definition for ‘hclust’
plotRatioScatter: no visible global function definition for ‘pairs’
plotRatioScatter : : no visible global function definition
  for ‘text’
plotRatioScatter : : no visible global function definition
  for ‘cor’
plotRatioScatter : : no visible global function definition
  for ‘points’
plotRatioScatter : : no visible global function definition
  for ‘lines’
plotRatioScatter : : no visible global function definition
  for ‘lowess’
plotScatter: no visible global function definition for ‘exprs’
plotScatter: no visible global function definition for ‘cor’
plotScatter: no visible global function definition for ‘hclust’
plotScatter: no visible global function definition for ‘pairs’
plotScatter : : no visible global function definition for
  ‘text’
plotScatter : : no visible global function definition for
  ‘cor’
plotScatter : : no visible global function definition for
  ‘points’
plotScatter : : no visible global function definition for
  ‘lines’
plotScatter : : no visible global function definition for
  ‘lowess’
plotcmarrt: no visible global function definition for ‘par’
plotcmarrt: no visible global function definition for ‘hist’
plotcmarrt: no visible global function definition for ‘qqnorm’
plotcmarrt: no visible global function definition for ‘abline’
profileplot: no visible global function definition for ‘axis’
read.gffAnno: no visible global function definition for ‘read.table’
readCelFile: no visible global function definition for ‘new’
readCelFile: no visible global function definition for ‘preproc<-’
readCelFile: no visible global function definition for ‘featureNames<-’
singleclusterplot: no visible global function definition for ‘title’
singleclusterplot : drawline: no visible global function definition for
  ‘lines’
singleclusterplot: no visible global function definition for
  ‘heat.colors’
singleclusterplot: no visible global function definition for ‘rainbow’
singleclusterplot: no visible global function definition for
  ‘colorRampPalette’
singleclusterplot: no visible binding for global variable ‘quantile’
singleclusterplot: no visible global function definition for ‘polygon’
writeGFF: no visible global function definition for ‘exprs’
writeGFF: no visible global function definition for ‘write.table’
writePosFile: no visible global function definition for ‘write.table’
writeWIG: no visible global function definition for ‘exprs’
writeWIG: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline acf axis barplot box boxplot brewer.pal colorRampPalette
  contour cor density experimentData experimentData<- exprs exprs<-
  featureNames featureNames<- filter hclust heat.colors hist legend
  levelplot lines lowess ma.plot median mtext na.omit new
  normalizeBetweenArrays p.adjust pairs panel.abline panel.axis
  panel.levelplot par pnorm points polygon predict preproc<- qqnorm
  quantile rainbow read.table rect sd tail text title topo.colors
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "heat.colors", "rainbow",
             "topo.colors")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "contour", "hist", "legend", "lines", "mtext", "pairs",
             "par", "points", "polygon", "rect", "text", "title")
  importFrom("methods", "new")
  importFrom("stats", "acf", "cor", "density", "filter", "hclust",
             "lowess", "median", "na.omit", "p.adjust", "pnorm",
             "predict", "qqnorm", "quantile", "sd")
  importFrom("utils", "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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 19.396  0.243  19.737
plot.gcBias  16.728  0.394  17.128
plot.ma       4.758  0.324   5.087
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Starr.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Starr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Starr’ ...
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c ahocorasick.c -o ahocorasick.o
ahocorasick.c:8:1: warning: unused function 'kseq_rewind' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
./kseq.h:220:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_BASIC(type_t)                                            \
        ^
./kseq.h:152:21: note: expanded from macro '__KSEQ_BASIC'
        static inline void kseq_rewind(kseq_t *ks)                                                      \
                           ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c collect.c -o collect.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c rm_small_peak.c -o rm_small_peak.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sort_by_genomic.c -o sort_by_genomic.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Starr/00new/Starr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Starr)

name	user	system	elapsed
bpmapToProbeAnno	0.000	0.001	0.000
cmarrt.ma	0.001	0.001	0.001
cmarrt.peak	0.001	0.001	0.000
correlationPlot	0.041	0.002	0.044
densityscatter	1.119	0.056	1.176
filterGenes	0.001	0.000	0.001
getMeans	0.000	0.001	0.001
getProfiles	0.000	0.001	0.001
getRatio	0.000	0.001	0.001
kde2dplot	0.626	0.033	0.659
makeSplines	0.001	0.001	0.001
normalize.Probes	0.001	0.001	0.001
plot.Density	0.286	0.044	0.330
plot.boxes	0.937	0.050	0.987
plot.cmarrt	0.001	0.001	0.001
plot.gcBias	16.728	0.394	17.128
plot.image	0	0	0
plot.ma	4.758	0.324	5.087
plot.posBias	19.396	0.243	19.737
plot.ratioScatter	0.771	0.093	0.864
plot.scatter	0.696	0.085	0.783
plotProfiles	0.302	0.011	0.315
profileplot	0.977	0.035	1.015
read.gffAnno	0.000	0.000	0.001
readCelFile	0.000	0.000	0.001
remap	0	0	0