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Package 78/631HostnameOS / ArchBUILDCHECKBUILD BIN
biovizBase 1.7.5
Tengfei Yin
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biovizBase
Last Changed Rev: 72531 / Revision: 72575
Last Changed Date: 2013-01-15 01:29:35 -0800 (Tue, 15 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: biovizBase
Version: 1.7.5
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.7.5.tar.gz
StartedAt: 2013-01-16 01:01:44 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:06:05 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 261.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: biovizBase.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.7.5’
* 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 ... 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
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 ... WARNING
Codoc mismatches from documentation object 'transformToGenome':
\S4method{transformToGenome}{GRanges}
  Code: function(data, space.skip = 0.1, chr.weight = NULL)
  Docs: function(data, space.skip = 0.1)
  Argument names in code not in docs:
    chr.weight
\S4method{transformToGenome}{GRangesList}
  Code: function(data, space.skip = 0.1, chr.weight = NULL)
  Docs: function(data, space.skip = 0.1)
  Argument names in code not in docs:
    chr.weight
transformToRectInCircle
  Code: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
                 radius = 10, direction = c("clockwise",
                 "anticlockwise"), n = 100, mul = 0.05, chr.weight =
                 NULL)
  Docs: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
                 radius = 10, direction = c("clockwise",
                 "anticlockwise"), n = 100, mul = 0.05)
  Argument names in code not in docs:
    chr.weight
transformToBarInCircle
  Code: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
                 radius = 10, direction = c("clockwise",
                 "anticlockwise"), n = 100, mul = 0.05, chr.weight =
                 NULL)
  Docs: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
                 radius = 10, direction = c("clockwise",
                 "anticlockwise"), n = 100, mul = 0.05)
  Argument names in code not in docs:
    chr.weight
transformToSegInCircle
  Code: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
                 radius = 10, direction = c("clockwise",
                 "anticlockwise"), n = 100, chr.weight = NULL)
  Docs: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
                 radius = 10, direction = c("clockwise",
                 "anticlockwise"), n = 100)
  Argument names in code not in docs:
    chr.weight
transformToLinkInCircle
  Code: function(data, linked.to, space.skip = 0.1, trackWidth = 10,
                 radius = 10, link.fun = function(x, y, n = 100)
                 bezier(x, y, evaluation = n), direction =
                 c("clockwise", "anticlockwise"), chr.weight = NULL)
  Docs: function(data, linked.to, space.skip = 0.1, trackWidth = 10,
                 radius = 10, link.fun = function(x, y, n = 100)
                 bezier(x, y, evaluation = n), direction =
                 c("clockwise", "anticlockwise"))
  Argument names in code not in docs:
    chr.weight

* 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 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 examples ... 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck/00check.log’
for details.

biovizBase.Rcheck/00install.out:

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bin_offsets.c -o bin_offsets.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘intro.Rnw’ 
** testing if installed package can be loaded

* DONE (biovizBase)

biovizBase.Rcheck/biovizBase-Ex.timings:

nameusersystemelapsed
GCcontent2.2400.3242.631
addStepping-method1.2640.0561.324
aes-utils0.0000.0040.005
colorBlindSafePal0.0000.0080.010
containLetters0.0000.0040.005
crc1.GeRL0.0120.0080.017
darned_hg19_subset5000.0600.0120.071
flatGrl0.2840.0280.310
genesymbol0.1560.0000.156
getBioColor0.0040.0040.010
getFormalNames0.0000.0040.005
getGaps1.6610.0281.688
getIdeoGR0.4280.0040.431
getIdeogram0.0040.0000.003
hg19Ideogram0.0840.0000.086
hg19IdeogramCyto0.0400.0000.041
isIdeogram0.0040.0000.009
isMatchedWithModel0.3360.0240.359
isSimpleIdeogram0.0760.0040.079
maxGap-method0.5600.0080.571
pileupAsGRanges0.0040.0000.004
pileupGRangesAsVariantTable0.0040.0040.006
plotColorLegend0.0040.0000.005
scale0.3560.0120.366
showColor0.0040.0000.003
shrinkageFun-method0.3640.0080.372
splitByFacets-method0.7520.0120.769
strip_formula_dots0.0080.0000.005
subsetArgsByFormals0.0040.0000.004
transform3.4200.1003.524
transformGRangesForEvenSpace0.3000.0160.315