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Package 197/467HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 3.10.2
Vince Carey
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/GGtools
Last Changed Rev: 57657 / Revision: 59457
Last Changed Date: 2011-08-24 21:00:07 -0700 (Wed, 24 Aug 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: GGtools
Version: 3.10.2
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_3.10.2.tar.gz
StartedAt: 2011-10-20 15:13:04 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 15:27:22 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 858.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GGtools.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '3.10.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GGtools' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
See '/Users/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 59.8Mb
  sub-directories of 1Mb or more:
    browserTrack   1.8Mb
    data          49.6Mb
    doc            4.0Mb
    GGEXsite       1.0Mb
    pup            2.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
bestCis: no visible binding for '<<-' assignment to 'maxgap'
bestCis: no visible global function definition for 'mclapply'
cisProxScores: no visible binding for global variable 'mclapply'
cisSnpTests: no visible global function definition for 'snpsNear'
diagffCC: no visible global function definition for 'mclapply'
diagffCC : <anonymous>: no visible binding for '<<-' assignment to 'ex'
eqtlTests: no visible binding for '<<-' assignment to 'geneindex'
eqtlTests: no visible global function definition for 'mclapply'
eqtlTests : <anonymous> : <anonymous>: no visible binding for global
  variable 'geneindex'
eqtlTests : <anonymous> : <anonymous>: no visible binding for '<<-'
  assignment to 'geneindex'
eqtlTestsMACH : <anonymous> : <anonymous>: no visible global function
  definition for 'snp.rhs.testsMACH'
eqtlTestsNofile: no visible binding for '<<-' assignment to 'geneindex'
eqtlTestsNofile : <anonymous> : <anonymous>: no visible binding for
  global variable 'geneindex'
eqtlTestsNofile : <anonymous> : <anonymous>: no visible binding for
  '<<-' assignment to 'geneindex'
fmcisRun: no visible binding for global variable 'mclapply'
fmcisRun : <anonymous>: no visible global function definition for
  'mfeqtltests'
locreport: no visible global function definition for 'snpLocs.Hs'
maxchisq: no visible global function definition for 'mclapply'
mcisProxScores: no visible binding for global variable 'mclapply'
meqtlTests: no visible global function definition for 'mclapply'
meqtlTests2: no visible binding for global variable 'listOfSmls'
meqtlTests2: no visible binding for global variable 'summfflist'
restrictProbesToChrom: no visible binding for global variable 'chr'
sumScores2ff: no visible global function definition for 'mclapply'
sumScores2ff : <anonymous>: no visible binding for '<<-' assignment to
  'ex'
* 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'GGtools_2011.pdf' from 1197Kb to 551Kb
     compacted 'lab2010.pdf' from 1426Kb to 812Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'eqtest.R'
  Running 'fftest.R'
 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, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck/00check.log'
for details

GGtools.Rcheck/00install.out:

* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
in method for 'min_p_vals' with signature '"maxchisq","character","character","numeric"': no definition for class "maxchisq"
in method for 'coerce' with signature '"multffManager","eqtlTestsManager"': no definition for class "multffManager"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (GGtools)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
X2chunk0.0000.0010.001
cisProxScores-class0.0020.0000.002
cisProxScores66.961 3.60272.594
clipPCs100.377 4.256107.328
degnerASE010.0120.0030.015
eqtlTests7.8840.6409.598
eqtlTestsManager-class0.0010.0000.002
ex60.1010.0080.117