GGtools 5.7.0
VJ Carey
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GGtools_5.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GGtools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘5.7.0’
* 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 ... [22s/22s] OK
* checking installed package size ... NOTE
installed size is 73.0Mb
sub-directories of 1Mb or more:
data 27.0Mb
doc 1.6Mb
parts 2.0Mb
pup 2.0Mb
rdas 10.3Mb
vcf 28.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' call to ‘parallel’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Homo.sapiens’ ‘MatrixEQTL’ ‘aod’ ‘foreach’ ‘gwascat’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,gwSnpScreenResult-character: warning in axis(3, at =
genePosition(x@gene, annlib = x@annotation), col = "red", lwd = 2,
label = " "): partial argument match of 'label' to 'labels'
.summarize: no visible binding for global variable ‘npc’
.summarize: no visible binding for global variable ‘maf’
.summarize: no visible binding for global variable ‘radiusUsed’
.summarize: no visible binding for global variable ‘excl’
.transTab: no visible global function definition for ‘getSNPlocs’
SnpMatrixCisToSummex: no visible global function definition for
‘rowRanges’
add878: no visible binding for global variable ‘hmm878’
addcadd: no visible binding for global variable ‘bindcadd’
addcadd: no visible global function definition for ‘%dopar%’
addcadd: no visible global function definition for ‘foreach’
addcadd: no visible binding for global variable ‘x’
addgwhit: no visible binding for global variable ‘gwastagger’
addgwhit: no visible global function definition for ‘overlapsAny’
appraise : .redu.fdr: no visible global function definition for
‘setkey’
appraise : .redu.fdr: no visible binding for global variable ‘snp’
appraise : .redu.fdr: no visible binding for global variable ‘score’
appraise : .redu.fdr: no visible binding for global variable ‘.N’
appraise : .redu.fdr : <anonymous>: no visible global function
definition for ‘setkeyv’
appraise : .redu.fdr : <anonymous>: no visible binding for global
variable ‘.N’
appraise : .discmods: no visible global function definition for
‘%dopar%’
appraise : .discmods: no visible global function definition for
‘foreach’
bindmaf.legacy: no visible global function definition for ‘strand<-’
bindmaf.simple: no visible global function definition for ‘strand<-’
bindprops: no visible global function definition for ‘strand<-’
buildConfList : z : <anonymous>: no visible binding for global variable
‘pl’
cgff2dt: no visible global function definition for ‘%dopar%’
cgff2dt: no visible global function definition for ‘foreach’
cgff2dt: no visible global function definition for ‘as.data.table’
cgff2dt: no visible binding for global variable ‘hmm878’
cgff2dt: no visible global function definition for ‘overlapsAny’
cgff2dt: no visible binding for global variable ‘gwastagger’
cisAssoc: no visible global function definition for ‘rowRanges’
cisAssoc: no visible global function definition for ‘assays’
cisAssoc: no visible global function definition for ‘colData’
cisAssoc: no visible binding for global variable ‘chi.squared’
ciseqByCluster: no visible global function definition for
‘clusterApply’
ciseqByCluster : <anonymous>: no visible global function definition for
‘detectCores’
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 : setupSplit: no visible global function definition for
‘clusterApply’
ciseqByCluster : setupSplit : <anonymous>: no visible binding for
global variable ‘mclapply’
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 ‘ranges<-’
ciseqByCluster : <anonymous> : cr2gff: no visible global function
definition for ‘export.gff3’
ciseqByCluster: no visible global function definition for
‘clusterExport’
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: no visible global function definition for
‘clusterApplyLB’
ciseqByCluster : <anonymous>: no visible global function definition for
‘runOneSplit’
eqBox: no visible global function definition for ‘assay’
eqDesc: no visible global function definition for ‘assay’
eqsens_dt: no visible global function definition for ‘setnames’
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’
fplot: no visible global function definition for ‘forestplot’
genemodel: no visible global function definition for ‘select’
genemodel: no visible binding for global variable ‘Homo.sapiens’
getAsSlicedData: no visible binding for global variable ‘target’
getCisMap: no visible global function definition for ‘getSNPlocs’
get_probechunks: no visible global function definition for ‘select’
inflammFilter: no visible binding for global variable ‘gwrngs’
inflammFilter: no visible global function definition for ‘overlapsAny’
makeSeqinfo: no visible binding for global variable ‘hg19.si.df’
meta.bindmaf: no visible global function definition for ‘strand<-’
plotsens: no visible binding for global variable ‘mafs’
plotsens: no visible binding for global variable ‘value’
plotsens: no visible binding for global variable ‘FDR’
pullHits: no visible global function definition for ‘ranges<-’
richNull : <anonymous>: no visible global function definition for
‘bindmaf’
simpleTiling: no visible binding for global variable ‘Homo.sapiens’
simpleTiling: no visible global function definition for ‘tileGenome’
snpsCisToGenes: no visible global function definition for ‘start<-’
topKfeats: no visible binding for global variable ‘i1’
topKfeats: no visible binding for global variable ‘i2’
transeqByCluster: no visible global function definition for
‘clusterExport’
transeqByCluster: no visible global function definition for
‘clusterApplyLB’
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’
update_fdr_filt: no visible binding for global variable ‘score’
waldtests : <anonymous>: no visible global function definition for
‘wald.test’
plot,gwSnpScreenResult-character: no visible global function definition
for ‘getSNPcount’
plot,gwSnpScreenResult-character: no visible global function definition
for ‘getSNPlocs’
Undefined global functions or variables:
%dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData
as.data.table assay assays bindcadd bindmaf chi.squared clusterApply
clusterApplyLB clusterExport colData curp detectCores excl
export.gff3 firstHalf firstThird foreach forestplot getSNPcount
getSNPlocs gwastagger gwrngs hg19.si.df hmm878 i i1 i2 lastThird maf
mafs mclapply midThird modelLINEAR npc overlapsAny pl radiusUsed
ranges<- rowRanges runOneSplit score select setkey setkeyv setnames
snp start<- strand<- target tileGenome value wald.test x
* checking Rd files ... OK
* 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 ... [67s/67s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
cisAssoc 35.498 0.886 36.391
eqtlTests 7.645 0.185 7.830
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘cis.R’ [88s/76s]
Running ‘eqvgwst.R’ [16s/16s]
Running ‘test.meqtlTests.R’ [17s/17s]
Running ‘test.meta.trans.R’ [0s/0s]
Running ‘testCisMap.R’ [35s/35s]
Running ‘testTrans.R’ [60s/60s]
[216s/203s] 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
* DONE
Status: 6 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/GGtools.Rcheck/00check.log’
for details.
* installing *source* package ‘GGtools’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: aggregate
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: aggregate
* DONE (GGtools)