GGtools 4.10.0
VJ Carey
| 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/GGtools | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| 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 |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GGtools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘4.10.0’
* 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 ... [26s/26s] OK
* checking installed package size ... NOTE
installed size is 39.2Mb
sub-directories of 1Mb or more:
data 21.5Mb
doc 1.6Mb
parts 2.0Mb
pup 2.0Mb
rdas 10.3Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
‘GenomicRanges’ ‘IRanges’
Please remove these calls from your code.
Namespaces in Imports field not imported from:
‘methods’ ‘utils’
All declared Imports should be used.
Package in Depends field not imported from: ‘GGBase’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
‘:::’ calls which should be ‘::’:
‘IRanges:::as.data.frame’ ‘IRanges:::end’ ‘IRanges:::start’
‘Rsamtools:::close.TabixFile’ ‘Rsamtools:::isOpen’
‘Rsamtools:::open.TabixFile’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘namelist’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getFDR: warning in dir(patt = "^pop.*rda$"): partial argument match of
'patt' to 'pattern'
hns : <anonymous>: warning in dir(patt = chrtag, system.file("rdas",
package = x), full = TRUE): partial argument match of 'patt' to
'pattern'
hns : <anonymous>: warning in dir(patt = chrtag, system.file("rdas",
package = x), full = TRUE): partial argument match of 'full' to
'full.names'
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'
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’
hns : <anonymous>: possible error in convertCis(x, MAFlb = MAFlb,
radius = inradius): unused argument (MAFlb = MAFlb)
topKfeats: no visible binding for global variable ‘i1’
topKfeats: no visible binding for global variable ‘i2’
* checking Rd files ... NOTE
prepare_Rd: cisRun-class.Rd:36-38: Dropping empty section \references
prepare_Rd: cisRun-class.Rd:49-52: Dropping empty section \seealso
prepare_Rd: collectBest.Rd:69-71: Dropping empty section \seealso
prepare_Rd: pifdr.Rd:64-66: Dropping empty section \seealso
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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
eqtlTests 11.329 0.192 11.588
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘eqvgwst.R’ [22s/22s]
Running ‘test.meqtlTests.R’ [24s/24s]
Running ‘test.meta.trans.R’ [0s/0s]
Running ‘testCisMap.R’ [44s/45s]
Running ‘testTrans.R’ [46s/46s]
[137s/138s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/GGtools.Rcheck/00check.log’
for details.