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BioC 3.0: CHECK report for GenomicTuples on perceval

This page was generated on 2015-04-10 10:00:33 -0700 (Fri, 10 Apr 2015).

Package 371/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicTuples 1.0.0
Peter Hickey
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicTuples
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: GenomicTuples
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicTuples_1.0.0.tar.gz
StartedAt: 2015-04-10 02:04:35 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:09:52 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 317.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicTuples.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicTuples_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicTuples.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicTuples/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicTuples’ version ‘1.0.0’
* 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 ‘GenomicTuples’ can be installed ... [33s/37s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::.findOverlaps.circle’
  ‘GenomicRanges:::.strandAsSignedNumber’ ‘GenomicRanges:::clone’
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlots’
  ‘GenomicRanges:::extraColumnSlotsAsDF’ ‘GenomicRanges:::showList’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  ‘S4Vectors:::orderIntegerPairs’ ‘S4Vectors:::VH_recycle’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findEqual.GTuples: no visible global function definition for
  ‘splitRanges’
.findEqual.GTuples : <anonymous> : <anonymous>: no visible global
  function definition for ‘IRanges’
GTuples: no visible global function definition for ‘IRanges’
GTuplesList: no visible global function definition for
  ‘PartitioningByEnd’
* 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 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 ... [15s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat.R’ [101s/101s]
 [101s/101s] 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
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicTuples.Rcheck/00check.log’
for details.

GenomicTuples.Rcheck/00install.out:

* installing *source* package ‘GenomicTuples’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GenomicTuples_init.c -o GenomicTuples_init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IPD.cpp -o IPD.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c allTuplesSorted.cpp -o allTuplesSorted.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c compareGTuples.cpp -o compareGTuples.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o GenomicTuples.so GenomicTuples_init.o IPD.o RcppExports.o allTuplesSorted.o compareGTuples.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/GenomicTuples.Rcheck/GenomicTuples/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 (GenomicTuples)

GenomicTuples.Rcheck/GenomicTuples-Ex.timings:

nameusersystemelapsed
GTuples-class0.6260.0140.640
GTuples-comparison1.7460.0161.764
GTuplesList-class0.5710.0050.576
findOverlaps-methods1.9990.0172.016
illdefined-methods0.0190.0000.019
intra-tuple-methods0.1860.0020.188
nearest-methods0.9330.0030.937