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Package 548/671HostnameOS / ArchBUILDCHECKBUILD BIN
Ringo 1.24.0
J. Toedling
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Ringo
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: Ringo
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Ringo_1.24.0.tar.gz
StartedAt: 2013-05-01 10:17:43 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 10:23:00 -0700 (Wed, 01 May 2013)
EllapsedTime: 316.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.24.0'
* 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 'Ringo' can be installed ... [29s/31s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
sigGOTable: no visible binding for global variable 'p.value'
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile', 'Ringo.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [24s/25s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck/00check.log'
for details.

Ringo.Rcheck/00install.out:

* installing *source* package 'Ringo' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mmeansd.cpp -o mmeansd.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mmedian.cpp -o mmedian.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c region_overlap.c -o region_overlap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ringo_init.c -o ringo_init.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Ringo.Rcheck/Ringo/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'ls' from package 'base' in package 'Ringo'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Ringo)

Ringo.Rcheck/Ringo-Ex.timings:

nameusersystemelapsed
arrayImage0.5940.0150.614
asExprSet0.8060.0350.842
autocorr0.3140.0090.326
cherByThreshold0.0230.0070.031
cherClass0.3390.0180.361
chipAlongChrom0.7110.0200.737
chipAlongChromOld0.0780.0090.090
computeRunningMedians0.4350.0270.462
compute_gc0.0120.0050.016
compute_sliding_t0.1110.0090.120
corrPlot0.0540.0150.087
exportCherList0.0120.0040.016
features2Probes1.7560.0881.860
findChersOnSmoothed0.1650.0210.185
ftr2xys0.0130.0090.022
newCER0.0060.0070.012
nonzero0.0300.0120.042
plotAutocorr0.0020.0040.006
plotBM0.0250.0110.042
posToProbeAnnoEnvironment0.5130.0170.532
preprocess0.4580.0340.493
probeAnnoClass0.0550.0170.072
qopS40.0020.0040.006
quantilesOverPositions1.7640.1011.878
readNimblegen0.1840.0090.194
regionoverlap0.0130.0070.020
relateCERs0.0020.0040.006
sigGOTable0.0040.0070.011
sliding_meansd0.0130.0120.024
sliding_quantile0.0250.0120.037
twoGaussiansNull0.2370.0200.284
upperBoundNull0.1200.0100.131
validProbeAnno0.0410.0150.056