GGtools 4.7.24
VJ Carey
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 74135 / Revision: 74774 | | Last Changed Date: 2013-03-10 05:46:04 -0700 (Sun, 10 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GGtools.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '4.7.24'
* 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 whether package 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 45.4Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
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 ... 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 examples ...
** running examples for arch 'i386' ... [34s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
eqtlTests 11.41 0.36 12.1
** running examples for arch 'x64' ... [36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
eqtlTests 12.31 0.39 12.71
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'eqvgwst.R' [22s]
Running 'test.meqtlTests.R' [25s]
Running 'test.meta.trans.R' [0s]
Running 'testCisMap.R' [54s]
Running 'testTrans.R' [54s]
[155s] OK
** running tests for arch 'x64'
Running 'eqvgwst.R' [23s]
Running 'test.meqtlTests.R' [30s]
Running 'test.meta.trans.R' [0s]
Running 'testCisMap.R' [58s]
Running 'testTrans.R' [59s]
[170s] 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
NOTE: There were 4 notes.
See
'E:/biocbld/bbs-2.12-bioc/meat/GGtools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GGtools_2012.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'GGtools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGtools' as GGtools_4.7.24.zip
* DONE (GGtools)