BioC 3.3: CHECK report for GenomicTuples on morelia
This page was generated on 2015-10-22 17:54:32 -0400 (Thu, 22 Oct 2015).
GenomicTuples 1.5.0 Peter Hickey
Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicTuples | Last Changed Rev: 109592 / Revision: 109826 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: GenomicTuples |
Version: 1.5.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicTuples_1.5.0.tar.gz |
StartedAt: 2015-10-22 06:31:17 -0400 (Thu, 22 Oct 2015) |
EndedAt: 2015-10-22 06:33:19 -0400 (Thu, 22 Oct 2015) |
EllapsedTime: 122.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicTuples.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicTuples_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicTuples.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.0’
* 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 ... [15s/15s] 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:::.strandAsSignedNumber’ ‘GenomicRanges:::clone’
‘GenomicRanges:::extraColumnSlotNames’
‘GenomicRanges:::extraColumnSlots’
‘GenomicRanges:::extraColumnSlotsAsDF’ ‘GenomicRanges:::showList’
‘IRanges:::findOverlaps_NCList’ ‘IRanges:::min_overlap_score’
‘S4Vectors:::VH_recycle’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
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’
tuples<-,GTuples: no visible global function definition for ‘IRanges’
Undefined global functions or variables:
IRanges PartitioningByEnd splitRanges
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [33s/33s]
[34s/34s] 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
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicTuples.Rcheck/00check.log’
for details.
GenomicTuples.Rcheck/00install.out:
* installing *source* package ‘GenomicTuples’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c GenomicTuples_init.c -o GenomicTuples_init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c IPD.cpp -o IPD.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c allTuplesSorted.cpp -o allTuplesSorted.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c compareGTuples.cpp -o compareGTuples.o
clang++ -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 -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-3.3-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:
name | user | system | elapsed
|
GTuples-class | 0.209 | 0.005 | 0.214 |
|
GTuples-comparison | 0.709 | 0.002 | 0.711 |
|
GTuplesList-class | 0.288 | 0.002 | 0.290 |
|
findOverlaps-methods | 0.486 | 0.002 | 0.487 |
|
illdefined-methods | 0.010 | 0.000 | 0.011 |
|
intra-tuple-methods | 0.089 | 0.001 | 0.090 |
|
nearest-methods | 0.428 | 0.002 | 0.429 |
|