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BioC 3.0: CHECK report for biovizBase on perceval

This page was generated on 2015-04-10 09:56:18 -0700 (Fri, 10 Apr 2015).

Package 103/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.14.1
Tengfei Yin
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/biovizBase
Last Changed Rev: 97603 / Revision: 102249
Last Changed Date: 2014-12-12 12:30:04 -0800 (Fri, 12 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: biovizBase
Version: 1.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.14.1.tar.gz
StartedAt: 2015-04-09 23:12:55 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:20:06 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 430.8 seconds
RetCode: 0
Status:  OK 
CheckDir: biovizBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/biovizBase.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 ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.14.1’
* 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 ‘biovizBase’ can be installed ... [40s/42s] 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:
  ‘methods’
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' calls in package code:
  ‘BSgenome’ ‘rtracklayer’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
genGenesymbolTable: no visible global function definition for ‘select’
genSymbols: no visible global function definition for ‘mappedRkeys’
genSymbols: no visible global function definition for ‘revmap’
genSymbols: no visible global function definition for ‘toTable’
genSymbols: no visible binding for global variable ‘start_location’
genSymbols: no visible binding for global variable ‘end_location’
genSymbols: no visible binding for global variable ‘Chromosome’
genSymbols: no visible binding for global variable ‘symbol’
getIdeogram : <anonymous>: no visible global function definition for
  ‘browserSession’
getIdeogram : <anonymous>: no visible global function definition for
  ‘ucscGenomes’
getIdeogram : <anonymous>: no visible global function definition for
  ‘ucscTableQuery’
getIdeogram : <anonymous>: no visible global function definition for
  ‘tableName<-’
getIdeogram : <anonymous>: no visible global function definition for
  ‘getTable’
getIdeogram : <anonymous>: no visible global function definition for
  ‘GRangesForUCSCGenome’
transformToLinkInCircle: no visible binding for global variable
  ‘.circle.x’
transformToLinkInCircle: no visible binding for global variable
  ‘.circle.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘from.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘from.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘to.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘to.y’
validEven: no visible binding for global variable ‘gr’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 6.632  0.477   7.124
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

biovizBase.Rcheck/00install.out:

* installing *source* package ‘biovizBase’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_biovizBase.c -o R_init_biovizBase.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 biovizBase.so R_init_biovizBase.o bin_offsets.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/biovizBase.Rcheck/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biovizBase)

biovizBase.Rcheck/biovizBase-Ex.timings:

nameusersystemelapsed
CRC0.0070.0010.008
GCcontent1.6640.0501.726
addStepping-method1.5890.0371.627
aes-utils0.0010.0000.001
colorBlindSafePal0.0010.0000.001
containLetters0.0020.0010.002
crc1.GeRL0.0160.0010.017
crunch-method6.6320.4777.124
darned_hg19_subset5000.0650.0020.067
flatGrl0.5500.0180.568
genesymbol0.1430.0100.154
getBioColor0.0030.0010.003
getFormalNames0.0010.0000.001
getGaps1.9040.0211.928
getIdeoGR0.6040.0190.622
getIdeogram0.0000.0000.001
hg19Ideogram0.0420.0010.043
hg19IdeogramCyto0.0460.0010.046
ideo0.1680.0020.170
ideoCyto0.1740.0030.178
isIdeogram0.0040.0010.005
isMatchedWithModel0.8250.0430.870
isSimpleIdeogram0.0320.0010.033
maxGap-method0.6570.0180.675
pileupAsGRanges0.0010.0000.001
pileupGRangesAsVariantTable0.0010.0000.001
plotColorLegend0.0030.0010.004
scale0.5540.0150.568
showColor0.0010.0000.001
shrinkageFun-method0.5990.0170.616
splitByFacets-method1.1710.0181.190
strip_formula_dots0.0020.0000.002
subsetArgsByFormals0.0010.0000.001
transform3.2700.1833.457
transformGRangesForEvenSpace0.5610.0180.579