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BioC 3.2: CHECK report for Starr on moscato1

This page was generated on 2016-04-23 10:16:59 -0700 (Sat, 23 Apr 2016).

Package 1023/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Starr 1.26.0
Benedikt Zacher
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Starr
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] 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: 1.26.0
Command: rm -rf Starr.buildbin-libdir Starr.Rcheck && mkdir Starr.buildbin-libdir Starr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Starr.buildbin-libdir Starr_1.26.0.tar.gz >Starr.Rcheck\00install.out 2>&1 && cp Starr.Rcheck\00install.out Starr-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Starr.buildbin-libdir --install="check:Starr-install.out" --force-multiarch --no-vignettes --timings Starr_1.26.0.tar.gz
StartedAt: 2016-04-23 07:57:49 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 08:04:06 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 377.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Starr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Starr.buildbin-libdir Starr.Rcheck && mkdir Starr.buildbin-libdir Starr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Starr.buildbin-libdir Starr_1.26.0.tar.gz >Starr.Rcheck\00install.out 2>&1 && cp Starr.Rcheck\00install.out Starr-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Starr.buildbin-libdir --install="check:Starr-install.out" --force-multiarch --no-vignettes --timings Starr_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/Starr.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Starr/DESCRIPTION' ... OK
* this is package 'Starr' version '1.26.0'
* 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 whether package 'Starr' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/Starr.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/Starr.buildbin-libdir/Starr/libs/i386/Starr.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/Starr.buildbin-libdir/Starr/libs/x64/Starr.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [54s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot.posBias 12.67   0.07   12.87
plot.gcBias   9.64   0.01   11.17
plot.ma       8.34   0.07    8.55
** running examples for arch 'x64' ... [60s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot.posBias 18.52   0.04   18.55
plot.gcBias  13.18   0.08   13.26
plot.ma       9.21   0.06    9.26
* 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: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/Starr.Rcheck/00check.log'
for details.


Starr.Rcheck/00install.out:


install for i386

* installing *source* package 'Starr' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ahocorasick.c -o ahocorasick.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c collect.c -o collect.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rm_small_peak.c -o rm_small_peak.o
gcc -m32 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sort_by_genomic.c -o sort_by_genomic.o
gcc -m32 -shared -s -static-libgcc -o Starr.dll tmp.def ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -LD:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/Starr.buildbin-libdir/Starr/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5

install for x64

* installing *source* package 'Starr' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ahocorasick.c -o ahocorasick.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c collect.c -o collect.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rm_small_peak.c -o rm_small_peak.o
gcc -m64 -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sort_by_genomic.c -o sort_by_genomic.o
gcc -m64 -shared -s -static-libgcc -o Starr.dll tmp.def ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -LD:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/Starr.buildbin-libdir/Starr/libs/x64
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
* MD5 sums
packaged installation of 'Starr' as Starr_1.26.0.zip
* DONE (Starr)

Starr.Rcheck/examples_i386/Starr-Ex.timings:

nameusersystemelapsed
bpmapToProbeAnno000
cmarrt.ma000
cmarrt.peak000
correlationPlot0.030.000.03
densityscatter2.850.002.85
filterGenes000
getMeans000
getProfiles0.020.000.02
getRatio000
kde2dplot0.610.020.62
makeSplines000
normalize.Probes000
plot.Density0.560.000.56
plot.boxes1.230.051.29
plot.cmarrt000
plot.gcBias 9.64 0.0111.17
plot.image000
plot.ma8.340.078.55
plot.posBias12.67 0.0712.87
plot.ratioScatter1.420.021.43
plot.scatter1.720.033.86
plotProfiles0.310.001.06
profileplot0.700.000.78
read.gffAnno000
readCelFile000
remap000

Starr.Rcheck/examples_x64/Starr-Ex.timings:

nameusersystemelapsed
bpmapToProbeAnno000
cmarrt.ma000
cmarrt.peak000
correlationPlot0.030.000.03
densityscatter2.070.022.09
filterGenes000
getMeans000
getProfiles000
getRatio000
kde2dplot0.630.030.66
makeSplines000
normalize.Probes000
plot.Density0.530.012.29
plot.boxes1.180.031.22
plot.cmarrt000
plot.gcBias13.18 0.0813.26
plot.image000
plot.ma9.210.069.26
plot.posBias18.52 0.0418.55
plot.ratioScatter1.820.011.84
plot.scatter1.390.021.41
plotProfiles0.420.000.42
profileplot0.750.000.75
read.gffAnno000
readCelFile000
remap000