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BioC 2.12: CHECK report for GGtools on moscato2

This page was generated on 2013-10-09 09:38:18 -0700 (Wed, 09 Oct 2013).

Package 280/671HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 4.8.0
VJ Carey
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GGtools
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GGtools
Version: 4.8.0
Command: rm -rf GGtools.buildbin-libdir && mkdir GGtools.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_4.8.0.tar.gz >GGtools-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_4.8.0.tar.gz && mv GGtools.buildbin-libdir/* GGtools.Rcheck/ && rmdir GGtools.buildbin-libdir
StartedAt: 2013-10-09 02:19:53 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:36:38 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1005.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GGtools.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '4.8.0'
* 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 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' ... [48s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
eqtlTests  17.24   0.61   18.69
gwSnpTests  5.34   0.24    5.87
** running examples for arch 'x64' ... [49s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
eqtlTests  18.25   0.51   18.81
gwSnpTests  5.85   0.14    5.99
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'eqvgwst.R' [32s]
  Running 'test.meqtlTests.R' [30s]
  Running 'test.meta.trans.R' [0s]
  Running 'testCisMap.R' [63s]
  Running 'testTrans.R' [70s]
 [195s] OK
** running tests for arch 'x64'
  Running 'eqvgwst.R' [35s]
  Running 'test.meqtlTests.R' [35s]
  Running 'test.meta.trans.R' [0s]
  Running 'testCisMap.R' [68s]
  Running 'testTrans.R' [79s]
 [216s] 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.

GGtools.Rcheck/00install.out:


install for i386

* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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_4.8.0.zip
* DONE (GGtools)