GGtools 5.0.0
VJ Carey
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GGtools | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GGtools_5.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/GGtools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘5.0.0’
* 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 ... [33s/33s] OK
* checking installed package size ... NOTE
installed size is 44.7Mb
sub-directories of 1Mb or more:
data 26.8Mb
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
appraise : .discmods: warning in bigglm(discfmlas[[i]], data = train,
fam = binomial(), chunksize = 50000, maxit = inmaxit): partial
argument match of 'fam' to 'family'
add878: no visible binding for global variable ‘hmm878’
addgwhit: no visible binding for global variable ‘gwastagger’
appraise : .redu.fdr: no visible binding for global variable ‘snp’
appraise : .discmods: no visible global function definition for
‘%dopar%’
appraise : .discmods: no visible global function definition for
‘foreach’
bindmaf.simple: no visible binding for global variable ‘smchr.init’
buildConfList : z : <anonymous>: no visible binding for global variable
‘pl’
calfig.old: no visible binding for global variable ‘MOREAPPR_coeflist’
calfig.old: no visible binding for global variable ‘MOREAPPR_tabs’
cgff2dt: no visible global function definition for ‘%dopar%’
cgff2dt: no visible global function definition for ‘foreach’
cgff2dt: no visible binding for global variable ‘hmm878’
cgff2dt: no visible binding for global variable ‘gwastagger’
cisAssoc: no visible global function definition for ‘ScanVcfParam’
cisAssoc: no visible global function definition for ‘readVcf’
cisAssoc: no visible global function definition for
‘genotypeToSnpMatrix’
ciseqByCluster: no visible binding for '<<-' assignment to ‘firstHalf’
ciseqByCluster: no visible binding for '<<-' assignment to ‘secondHalf’
ciseqByCluster: no visible binding for '<<-' assignment to ‘firstThird’
ciseqByCluster: no visible binding for '<<-' assignment to ‘lastThird’
ciseqByCluster: no visible binding for '<<-' assignment to ‘midThird’
ciseqByCluster: no visible binding for '<<-' assignment to
‘runOneSplit’
ciseqByCluster : <anonymous>: no visible binding for global variable
‘firstHalf’
ciseqByCluster : <anonymous> : cr2gff: no visible global function
definition for ‘export.gff3’
ciseqByCluster: no visible binding for global variable ‘firstThird’
ciseqByCluster: no visible binding for global variable ‘midThird’
ciseqByCluster: no visible binding for global variable ‘lastThird’
ciseqByCluster : <anonymous>: no visible global function definition for
‘runOneSplit’
eqsens_dt: no visible global function definition for ‘%dopar%’
eqsens_dt: no visible global function definition for ‘foreach’
eqsens_dt: no visible binding for global variable ‘curp’
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’
eqtlscan: no visible binding for global variable ‘ex’
genemodel: no visible binding for global variable ‘Homo.sapiens’
getAsSlicedData: no visible binding for global variable ‘target’
inflammFilter: no visible binding for global variable ‘gwrngs’
makeSeqinfo: no visible binding for global variable ‘hg19.si.df’
plotsens: no visible global function definition for ‘melt’
plotsens: no visible global function definition for ‘ggplot’
plotsens: no visible global function definition for ‘geom_point’
plotsens: no visible global function definition for ‘aes’
plotsens: no visible binding for global variable ‘mafs’
plotsens: no visible binding for global variable ‘value’
plotsens: no visible binding for global variable ‘FDR’
plotsens: no visible global function definition for ‘facet_grid’
plotsens: no visible global function definition for ‘theme’
plotsens: no visible global function definition for ‘element_text’
plotsens: no visible global function definition for ‘labs’
richNull : <anonymous>: no visible global function definition for
‘bindmaf’
simpleTiling: no visible binding for global variable ‘Homo.sapiens’
snvsOnly: no visible global function definition for ‘ref’
snvsOnly: no visible global function definition for ‘alt’
topKfeats: no visible binding for global variable ‘i1’
topKfeats: no visible binding for global variable ‘i2’
tscan2df: no visible global function definition for ‘%dopar%’
tscan2df: no visible global function definition for ‘foreach’
tscan2df: no visible binding for global variable ‘i’
tscan2gr: no visible global function definition for ‘%dopar%’
tscan2gr: no visible global function definition for ‘foreach’
tscan2gr: no visible binding for global variable ‘i’
* checking Rd files ... NOTE
prepare_Rd: appraise.Rd:97-98: Dropping empty section \examples
prepare_Rd: calfig.Rd:70-71: Dropping empty section \examples
prepare_Rd: transeqByCluster.Rd:82-83: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘MatrixEQTL’
* 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 ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
eqtlTests 10.441 0.088 10.575
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘cis.R’ [100s/92s]
Running ‘eqvgwst.R’ [24s/24s]
Running ‘test.meqtlTests.R’ [26s/26s]
Running ‘test.meta.trans.R’ [0s/0s]
Running ‘testCisMap.R’ [49s/49s]
Running ‘testTrans.R’ [70s/71s]
[269s/262s] 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-2.14-bioc/meat/GGtools.Rcheck/00check.log’
for details.