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BioC 2.14: CHECK report for Ringo on zin2

This page was generated on 2014-10-08 08:48:09 -0700 (Wed, 08 Oct 2014).

Package 663/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ringo 1.28.0
J. Toedling
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Ringo
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: Ringo
Version: 1.28.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.28.0.tar.gz
StartedAt: 2014-10-08 02:23:25 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:26:11 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 166.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/Ringo.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ringo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ringo’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘RColorBrewer’ ‘limma’ ‘Matrix’ ‘grid’ ‘lattice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* 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' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘limma’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘Matrix’ ‘RColorBrewer’ ‘lattice’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘clusters’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/12s] 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/Ringo.Rcheck/00check.log’
for details.

Ringo.Rcheck/00install.out:

* installing *source* package ‘Ringo’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function ‘SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)’:
mmeansd.cpp:27:24: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c region_overlap.c -o region_overlap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ringo_init.c -o ringo_init.o
g++ -shared -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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
arrayImage0.0800.0040.083
asExprSet0.1720.0120.185
autocorr0.0960.0040.099
cherByThreshold0.0080.0000.005
cherClass0.3880.0040.391
chipAlongChrom0.1600.0000.158
chipAlongChromOld0.0360.0040.042
computeRunningMedians0.4240.0120.439
compute_gc0.0000.0000.002
compute_sliding_t0.0720.0000.072
corrPlot0.0280.0040.033
exportCherList000
features2Probes0.8480.0280.908
findChersOnSmoothed0.0880.0040.094
ftr2xys0.0040.0000.001
newCER0.0000.0000.001
nonzero0.0080.0000.012
plotAutocorr0.0000.0000.001
plotBM0.0120.0000.012
posToProbeAnnoEnvironment0.0280.0080.036
preprocess0.4520.0040.458
probeAnnoClass0.0240.0000.022
qopS4000
quantilesOverPositions0.7000.0200.719
readNimblegen0.0720.0000.072
regionoverlap0.0040.0040.007
relateCERs000
sigGOTable000
sliding_meansd0.0040.0000.003
sliding_quantile0.0120.0000.013
twoGaussiansNull0.3520.0120.368
upperBoundNull0.0640.0000.063
validProbeAnno0.0160.0040.018