GGtools 4.5.16
VJ Carey
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 66380 / Revision: 66885 | | Last Changed Date: 2012-06-03 09:22:16 -0700 (Sun, 03 Jun 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GGtools.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '4.5.16'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'MatrixEQTL'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 45.3Mb
sub-directories of 1Mb or more:
data 21.5Mb
doc 1.6Mb
olddata 13.7Mb
olddoc 2.7Mb
parts 2.0Mb
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
eqtlTests.me: no visible binding for global variable 'modelLINEAR'
eqtlTests.me: no visible binding for global variable 'SlicedData'
eqtlTests.me: no visible binding for global variable
'Matrix_eQTL_engine'
eqtlTests.meText: no visible binding for global variable 'modelLINEAR'
eqtlTests.meText: no visible binding for global variable 'SlicedData'
eqtlTests.meText: no visible binding for global variable
'Matrix_eQTL_engine'
getAsSlicedData: no visible binding for global variable 'target'
meta.All.cis.eQTLs: possible error in meta.best.cis.eQTLs(smpackvec =
smpackvec, rhslist = rhslist, folderstem = folderstem, radius =
radius, shortfac = shortfac, chrnames = chrnames, smchrpref =
smchrpref, gchrpref = gchrpref, schrpref = schrpref, geneApply =
geneApply, geneannopk = geneannopk, snpannopk = snpannopk, smFilter =
smFilter4cis, nperm = nperm): unused argument(s) (smFilter =
smFilter4cis)
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
* 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 'best.cis.eQTLs':
meta.All.cis.eQTLs
Code: function(maxfdr = 0.05, inbestcis = NULL, smpackvec =
c("GGdata", "hmyriB36"), rhslist = list(˜1, ˜1),
folderstem = "cisScratch", radius = 50000, shortfac =
100, chrnames = as.character(1:22), smchrpref = "",
gchrpref = "", schrpref = "ch", geneApply = lapply,
geneannopk = "illuminaHumanv1.db", snpannopk =
"SNPlocs.Hsapiens.dbSNP.20100427", smFilter4cis =
function(x) nsFilter(MAFfilter(clipPCs(x, 1:10), lower
= 0.05), var.cutoff = 0.85), smFilter4all =
function(x) MAFfilter(clipPCs(x, 1:10), lower = 0.05),
nperm = 2, exFilter = function(x) x)
Docs: function(maxfdr = 0.05, inbestcis = NULL, smpackvec =
c("GGdata", "hmyriB36"), rhslist = list(˜1, ˜1),
folderstem = "cisScratch", radius = 50000, shortfac =
100, chrnames = as.character(1:22), smchrpref = "",
gchrpref = "", schrpref = "ch", geneApply = lapply,
geneannopk = "illuminaHumanv1.db", snpannopk =
"SNPlocs.Hsapiens.dbSNP.20100427", smFilter4cis =
function(x) nsFilter(MAFfilter(clipPCs(x, 1:10), lower
= 0.05), var.cutoff = 0.85), smFilter4all =
function(x) MAFfilter(clipPCs(x, 1:10), lower = 0.05),
nperm = 2)
Argument names in code not in docs:
exFilter
fullreport
Code: function(x, type, ...)
Docs: function(x, type)
Argument names in code not in docs:
...
* 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' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'eqvgwst.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.
NOTE: There were 3 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/GGtools.Rcheck/00check.log'
for details.