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BioC 3.2: CHECK report for Starr on zin1

This page was generated on 2015-08-24 10:47:40 -0700 (Mon, 24 Aug 2015).

Package 992/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Starr 1.25.0
Benedikt Zacher
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Starr
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Starr
Version: 1.25.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Starr_1.25.0.tar.gz
StartedAt: 2015-08-24 04:06:24 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:08:48 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 144.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Starr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Starr_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Starr.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Starr/DESCRIPTION’ ... OK
* this is package ‘Starr’ version ‘1.25.0’
* 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 ... [12s/12s] 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
cmarrt.ma: no visible global function definition for ‘exprs’
correlationPlot: no visible global function definition for ‘brewer.pal’
expressionByFeature: no visible global function definition for
  ‘featureNames’
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 global function definition for ‘exprs’
heatmapplot: no visible global function definition for ‘levelplot’
heatmapplot : <anonymous>: no visible global function definition for
  ‘panel.levelplot’
heatmapplot : <anonymous>: no visible global function definition for
  ‘panel.abline’
heatmapplot : <anonymous>: no visible global function definition for
  ‘panel.axis’
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’
plotDensity: no visible global function definition for ‘exprs’
plotImage: no visible global function definition for ‘levelplot’
plotMA: no visible global function definition for ‘exprs’
plotMA: no visible global function definition for ‘ma.plot’
plotRatioScatter: no visible global function definition for ‘exprs’
plotScatter: no visible global function definition for ‘exprs’
readCelFile: no visible global function definition for ‘preproc<-’
readCelFile: no visible global function definition for ‘featureNames<-’
writeGFF: no visible global function definition for ‘exprs’
writeWIG: no visible global function definition for ‘exprs’
* 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 10.147  0.040  10.198
plot.gcBias   7.873  0.040   7.921
plot.ma       5.381  0.044   5.453
* 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-3.2-bioc/meat/Starr.Rcheck/00check.log’
for details.


Starr.Rcheck/00install.out:

* installing *source* package ‘Starr’ ...
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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -Wall -c ahocorasick.c -o ahocorasick.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -Wall -c collect.c -o collect.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -Wall -c rm_small_peak.c -o rm_small_peak.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -Wall -c sort_by_genomic.c -o sort_by_genomic.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/Starr.Rcheck/Starr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Starr)

Starr.Rcheck/Starr-Ex.timings:

nameusersystemelapsed
bpmapToProbeAnno0.0000.0000.001
cmarrt.ma0.0000.0000.001
cmarrt.peak0.0010.0000.001
correlationPlot0.0370.0040.042
densityscatter1.5480.0311.592
filterGenes000
getMeans0.0010.0000.001
getProfiles0.0010.0000.001
getRatio0.0010.0000.001
kde2dplot0.4560.0000.457
makeSplines0.0010.0000.001
normalize.Probes0.0010.0000.000
plot.Density0.3510.0000.352
plot.boxes0.9640.0000.964
plot.cmarrt0.0010.0000.001
plot.gcBias7.8730.0407.921
plot.image000
plot.ma5.3810.0445.453
plot.posBias10.147 0.04010.198
plot.ratioScatter0.7010.0040.704
plot.scatter1.0480.0041.061
plotProfiles0.1860.0000.185
profileplot0.3640.0080.372
read.gffAnno0.0010.0000.000
readCelFile0.0000.0000.001
remap0.0010.0000.000