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BioC 2.13: CHECK report for biovizBase on perceval

This page was generated on 2014-04-05 09:52:43 -0700 (Sat, 05 Apr 2014).

Package 92/750HostnameOS / ArchBUILDCHECKBUILD BIN
biovizBase 1.10.8
Tengfei Yin
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/biovizBase
Last Changed Rev: 86925 / Revision: 88450
Last Changed Date: 2014-02-28 04:43:06 -0800 (Fri, 28 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: biovizBase
Version: 1.10.8
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.10.8.tar.gz
StartedAt: 2014-04-04 23:50:59 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:56:33 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 334.0 seconds
RetCode: 0
Status:  OK 
CheckDir: biovizBase.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/biovizBase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.10.8’
* 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 ... [30s/31s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fetch: no visible global function definition for
  ‘readBamGappedAlignments’
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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘intro.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
crunch-method 8.339  0.585   8.935
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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/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-2.13-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
GCcontent3.6240.4264.063
addStepping-method1.4490.1021.551
aes-utils0.0020.0060.008
colorBlindSafePal0.0030.0090.012
containLetters0.0020.0040.005
crc1.GeRL0.0170.0050.022
crunch-method8.3390.5858.935
darned_hg19_subset5000.0740.0050.079
flatGrl0.4770.0200.496
genesymbol0.1730.0170.190
getBioColor0.0040.0060.010
getFormalNames0.0020.0020.005
getGaps2.0060.0302.037
getIdeoGR0.5830.0220.605
getIdeogram0.0020.0030.004
hg19Ideogram0.1230.0040.128
hg19IdeogramCyto0.0910.0110.102
isIdeogram0.0070.0050.011
isMatchedWithModel0.5310.0350.566
isSimpleIdeogram0.0820.0050.086
maxGap-method0.6990.0200.719
pileupAsGRanges0.0030.0050.008
pileupGRangesAsVariantTable0.0030.0050.008
plotColorLegend0.0050.0030.008
scale0.5070.0270.534
showColor0.0020.0030.004
shrinkageFun-method0.5110.0230.534
splitByFacets-method1.3290.0271.359
strip_formula_dots0.0030.0040.007
subsetArgsByFormals0.0030.0050.008
transform3.8230.2004.031
transformGRangesForEvenSpace0.5560.0200.582