GGtools 3.9.61
Vince Carey
| Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 53672 / Revision: 53825 | | Last Changed Date: 2011-03-13 19:11:00 -0700 (Sun, 13 Mar 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | ERROR | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
| petty | Mac OS X Snow Leopard (10.6.6) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '3.9.61'
* checking package name space 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 64.7Mb
sub-directories of 1Mb or more:
browserTrack 1.8Mb
data 54.6Mb
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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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'
ieqtlTests: no visible global function definition for 'mclapply'
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 ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck/00_pkg_src/GGtools/man/cisProxScores.Rd':
'scoresInRanges'
See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
makeDiagDirector
Undocumented data sets:
snpLocs20 snpLocs_21
Undocumented S4 methods:
generic '[' and siglist 'multffManager,missing,probeId,ANY'
generic '[' and siglist 'multffManager,rsid,missing,ANY'
generic '[' and siglist 'multffManager,rsid,probeId,ANY'
generic 'show' and siglist 'maxchisq'
generic 'show' and siglist 'multffManager'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'eqtest.R'
Running 'fftest.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 3 warnings, see
'/Users/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck/00check.log'
for details
* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from 'package:base':
det
Loading required package: RSQLite
Loading required package: DBI
Loading required package: AnnotationDbi
Attaching package: 'IRanges'
The following object(s) are masked from 'package:Biobase':
updateObject
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: RCurl
Loading required package: bitops
Loading required package: tools
Loading required package: bit
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package bit1.1-6
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: 'bit'
The following object(s) are masked from 'package:base':
xor
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package ff2.2-1
- getOption("fftempdir")=="/tmp/RtmphiVvHW"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package ff
Attaching package: 'ff'
The following object(s) are masked from 'package:utils':
write.csv, write.csv2
The following object(s) are masked from 'package:base':
is.factor, is.ordered
** 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)