* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GGtools.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 ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘4.7.17’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GGtools’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 45.5Mb
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 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
unified.col.summary: warning in matrix(NA, nr = length(oksn), nc =
npacks): partial argument match of 'nr' to 'nrow'
unified.col.summary: warning in matrix(NA, nr = length(oksn), nc =
npacks): partial argument match of 'nc' to 'ncol'
vcf2sm,TabixFile-GRanges-integer: warning in matrix(as.raw(0), nr =
length(sampids), ncol = nsnp): partial argument match of 'nr' to
'nrow'
All.cis.eQTLs: possible error in best.cis.eQTLs(smpack = smpack, rhs =
rhs, folderstem = folderstem, radius = radius, shortfac = shortfac,
chrnames = chrnames, smchrpref = smchrpref, gchrpref = gchrpref,
schrpref = schrpref, geneApply = geneApply, geneannopk = geneannopk,
snpannopk = snpannopk, smFilter = smFilter4cis, nperm = nperm,
exFilter = exFilter, ssGen = ssGen): unused argument (ssGen = ssGen)
All.cis.eQTLs: no visible binding for global variable ‘ssGen’
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’
topKfeats: no visible binding for global variable ‘i1’
topKfeats: no visible binding for global variable ‘i2’
* checking Rd files ... NOTE
prepare_Rd: richNull.Rd:75-77: Dropping empty section \note
prepare_Rd: richNull.Rd:81-83: Dropping empty section \seealso
prepare_Rd: richNull.Rd:84-85: Dropping empty section \examples
prepare_Rd: sensanal.Rd:56-57: Dropping empty section \examples
prepare_Rd: sensiCisOutput-class.Rd:56-59: Dropping empty section \seealso
* 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':
best.cis.eQTLs
Code: function(smpack = "GGdata", rhs = ˜1, folderstem =
"cisScratch", radius = 50000, shortfac = 100, chrnames
= as.character(1:22), smchrpref = "", gchrpref = "",
schrpref = "ch", geneApply = lapply, geneannopk =
"illuminaHumanv1.db", snpannopk = snplocsDefault(),
smFilter = function(x) nsFilter(MAFfilter(x, lower =
0.05), var.cutoff = 0.97), nperm = 2, useME = FALSE,
excludeRadius = NULL, exFilter = function(x) x,
keepMapCache = FALSE, getDFFITS = FALSE, SSgen =
GGBase::getSS)
Docs: function(smpack = "GGdata", rhs = ˜1, folderstem =
"cisScratch", radius = 50000, shortfac = 100, chrnames
= as.character(1:22), smchrpref = "", gchrpref = "",
schrpref = "ch", geneApply = lapply, geneannopk =
"illuminaHumanv1.db", snpannopk = snplocsDefault(),
smFilter = function(x) nsFilter(MAFfilter(x, lower =
0.05), var.cutoff = 0.97), nperm = 2, useME = FALSE,
excludeRadius = NULL, exFilter = function(x) x,
keepMapCache = FALSE, getDFFITS = FALSE)
Argument names in code not in docs:
SSgen
All.cis.eQTLs
Code: function(maxfdr = 0.05, inbestcis = NULL, smpack = "GGdata",
rhs = ˜1, folderstem = "cisScratch", radius = 50000,
shortfac = 100, chrnames = as.character(1:22),
smchrpref = "", gchrpref = "", schrpref = "ch",
geneApply = lapply, geneannopk = "illuminaHumanv1.db",
snpannopk = snplocsDefault(), 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, excludeRadius = NULL, exFilter =
function(x) x, SSgen = GGBase::getSS)
Docs: function(maxfdr = 0.05, inbestcis = NULL, smpack = "GGdata",
rhs = ˜1, folderstem = "cisScratch", radius = 50000,
shortfac = 100, chrnames = as.character(1:22),
smchrpref = "", gchrpref = "", schrpref = "ch",
geneApply = lapply, geneannopk = "illuminaHumanv1.db",
snpannopk = snplocsDefault(), 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, excludeRadius = NULL, exFilter =
function(x) x)
Argument names in code not in docs:
SSgen
Codoc mismatches from documentation object 'best.trans.eQTLs':
best.trans.eQTLs
Code: function(smpack, rhs, genechrnum, snpchrnum, K = 20,
targdirpref = "tsco", batchsize = 200, radius = 2e+06,
genequeryprefix = "", snploadprefix = "chr",
snplocprefix = "chr", geneannopk, snpannopk, exFilter
= function(x) x, smFilter = function(x) x, geneApply =
lapply, SSgen = GGBase::getSS)
Docs: function(smpack, rhs, genechrnum, snpchrnum, K = 20,
targdirpref = "tsco", batchsize = 200, radius = 2e+06,
genequeryprefix = "", snploadprefix = "chr",
snplocprefix = "chr", geneannopk, snpannopk, exFilter
= function(x) x, smFilter = function(x) x, geneApply =
lapply)
Argument names in code not in docs:
SSgen
Codoc mismatches from documentation object 'bindmaf':
bindmaf
Code: function(smpack = "GGdata", smchr = "20", obj, SSgen =
GGBase::getSS)
Docs: function(smpack = "GGdata", smchr = "20", obj)
Argument names in code not in docs:
SSgen
meta.bindmaf
Code: function(smpackvec = c("GGdata", "hmyriB36"), smchr = "20",
obj, usemaxMAF = FALSE, SSgen = GGBase::getSS)
Docs: function(smpackvec = c("GGdata", "hmyriB36"), smchr = "20",
obj, usemaxMAF = FALSE)
Argument names in code not in docs:
SSgen
Codoc mismatches from documentation object 'transScores':
transScores
Code: function(smpack, snpchr = "chr1", rhs, K = 20, targdirpref =
"tsco", geneApply = lapply, chrnames = paste("chr",
as.character(1:22), sep = ""), geneRanges = NULL,
snpRanges = NULL, radius = 2e+06, renameChrs = NULL,
probesToKeep = NULL, batchsize = 200, genegran = 50,
shortfac = 10, wrapperEndo = NULL, geneannopk =
"illuminaHumanv1.db", snpannopk = snplocsDefault(),
gchrpref = "", schrpref = "ch", exFilter = function(x)
x, SSgen = GGBase::getSS)
Docs: function(smpack, snpchr = "chr1", rhs, K = 20, targdirpref =
"tsco", geneApply = lapply, chrnames = paste("chr",
as.character(1:22), sep = ""), geneRanges = NULL,
snpRanges = NULL, radius = 2e+06, renameChrs = NULL,
probesToKeep = NULL, batchsize = 200, genegran = 50,
shortfac = 10, wrapperEndo = NULL, geneannopk =
"illuminaHumanv1.db", snpannopk = snplocsDefault(),
gchrpref = "", schrpref = "ch", exFilter = function(x)
x)
Argument names in code not in docs:
SSgen
meta.transScores
Code: function(smpackvec = c("GGdata", "hmyriB36"), snpchr = "22",
rhsList = list(˜1, ˜1), K = 20, targdirpref = "mtsco",
geneApply = lapply, chrnames = as.character(21:22),
radius = 2e+06, renameChrs = NULL, probesToKeep =
NULL, batchsize = 200, genegran = 50, shortfac = 10,
wrapperEndo = NULL, geneannopk = "illuminaHumanv1.db",
snpannopk = snplocsDefault(), gchrpref = "", schrpref
= "ch", exFilterList = list(function(x) x, function(x)
x), SMFilterList = list(function(x) x, function(x) x),
SSgen = GGBase::getSS)
Docs: function(smpackvec = c("GGdata", "hmyriB36"), snpchr = "22",
rhsList = list(˜1, ˜1), K = 20, targdirpref = "mtsco",
geneApply = lapply, chrnames = as.character(21:22),
radius = 2e+06, renameChrs = NULL, probesToKeep =
NULL, batchsize = 200, genegran = 50, shortfac = 10,
wrapperEndo = NULL, geneannopk = "illuminaHumanv1.db",
snpannopk = snplocsDefault(), gchrpref = "", schrpref
= "ch", exFilterList = list(function(x) x, function(x)
x), SMFilterList = list(function(x) x, function(x) x))
Argument names in code not in docs:
SSgen
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
eqtlTests 16.665 0.384 17.188
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘eqvgwst.R’
Running ‘test.meqtlTests.R’
Running ‘test.meta.trans.R’
Running ‘testTrans.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 4 notes.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GGtools.Rcheck/00check.log’
for details.