gQTLstats 1.5.3
VJ Carey
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gQTLstats | | Last Changed Rev: 121009 / Revision: 121152 | | Last Changed Date: 2016-09-16 12:40:44 -0700 (Fri, 16 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLstats_1.5.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/gQTLstats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLstats/DESCRIPTION’ ... OK
* this is package ‘gQTLstats’ version ‘1.5.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘gQTLstats’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 45.8Mb
sub-directories of 1Mb or more:
data 9.8Mb
doc 1.6Mb
vcf 33.8Mb
* 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' call to ‘Homo.sapiens’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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
AllAssoc: no visible global function definition for ‘as.formula’
AllAssoc: no visible global function definition for ‘runif’
AllAssoc: no visible global function definition for ‘sessionInfo’
TransStore: no visible binding for global variable ‘loadRegistry’
TransStore : <anonymous>: no visible global function definition for
‘findJobs’
TransStore : <anonymous>: no visible global function definition for
‘findDone’
TransStore: no visible global function definition for ‘findDone’
TransStore: no visible binding for global variable ‘i’
TransStore : <anonymous>: no visible global function definition for
‘loadResult’
TransStore : <anonymous>: no visible binding for global variable ‘i’
TransStore : <anonymous>: no visible global function definition for
‘getJobInfo’
cisAssoc: no visible global function definition for ‘DNAStringSetList’
cisAssoc: no visible global function definition for ‘as.formula’
cisAssoc: no visible global function definition for ‘runif’
cisAssoc: no visible global function definition for ‘sessionInfo’
cisCount: no visible global function definition for ‘DNAStringSetList’
cisEsts: no visible global function definition for ‘DNAStringSetList’
cisEsts: no visible global function definition for ‘as.formula’
cisEsts: no visible global function definition for ‘runif’
cisEsts: no visible global function definition for ‘snp.rhs.estimates’
cisEsts: no visible global function definition for ‘sessionInfo’
dfrToFDR: no visible global function definition for ‘hist’
dfrToFDR: no visible global function definition for ‘sessionInfo’
directPlot: no visible global function definition for ‘plot’
directPlot: no visible global function definition for ‘abline’
enumerateByFDR: no visible global function definition for ‘sessionInfo’
gQTLs: no visible binding for global variable ‘ch’
gQTLs: no visible global function definition for ‘path’
gmod2: no visible binding for global variable ‘exonsBy’
gmod2: no visible binding for global variable ‘Homo.sapiens’
manhWngr: no visible binding for global variable ‘ml10fdr’
maxByFeature: no visible binding for global variable ‘snp’
maxByFeature: no visible binding for global variable ‘chisq’
maxByFeature: no visible binding for global variable ‘probeid’
maxByProbeOLD: no visible binding for global variable ‘snp’
maxByProbeOLD: no visible binding for global variable ‘probeid’
maxByProbeOLD: no visible binding for global variable ‘chisq’
maxByProbeOLD: no visible binding for global variable ‘permScore_1’
maxByProbeOLD: no visible binding for global variable ‘permScore_2’
maxByProbeOLD: no visible binding for global variable ‘permScore_3’
pifdr: no visible global function definition for ‘hist’
plot.senstab: no visible binding for global variable ‘MAF’
plot.senstab: no visible binding for global variable ‘value’
plot.senstab: no visible binding for global variable ‘criterion’
plot.table.sensobj: no visible binding for global variable ‘maf’
plot.table.sensobj: no visible binding for global variable ‘calls’
prep.cisAssocNB: no visible global function definition for
‘DNAStringSetList’
qqStore: no visible global function definition for ‘plot’
qqStore: no visible global function definition for ‘text’
qqStore: no visible global function definition for ‘abline’
regressOut: no visible global function definition for ‘model.matrix’
senstab : <anonymous>: no visible global function definition for
‘approx’
setFDRfunc: no visible binding for global variable ‘assoc’
setFDRfunc : <anonymous>: no visible global function definition for
‘predict’
storeToFDR: no visible global function definition for ‘sessionInfo’
storeToHist: no visible binding for global variable ‘x’
storeToHist: no visible global function definition for ‘hist’
storeToMaxAssocBySNP: no visible binding for global variable ‘snp’
storeToMaxAssocBySNP: no visible binding for global variable ‘chisq’
storeToMaxAssocBySNP: no visible binding for global variable
‘permScore_1’
storeToMaxAssocBySNP: no visible binding for global variable
‘permScore_2’
storeToMaxAssocBySNP: no visible binding for global variable
‘permScore_3’
storeToMaxAssocBySNP: no visible global function definition for ‘nth’
storeToMaxAssocBySNP: no visible binding for global variable ‘MAF’
storeToMaxAssocBySNP: no visible binding for global variable ‘probeid’
storeToMaxAssocBySNP: no visible binding for global variable ‘mindist’
table_sensobj_thresh : <anonymous>: no visible global function
definition for ‘approx’
transTable: no visible global function definition for ‘findDone’
transTable: no visible global function definition for ‘loadResult’
transTable: no visible binding for global variable ‘i’
txsPlot: no visible global function definition for ‘plot’
txsPlot: no visible global function definition for ‘lines’
txsPlot: no visible global function definition for ‘predict’
txsPlot.old: no visible global function definition for ‘plot’
txsPlot.old: no visible global function definition for ‘lines’
txsPlot.old: no visible global function definition for ‘predict’
vecToHist: no visible global function definition for ‘hist’
vecsToFDR: possible error in vecToHist(permvec, getter = getter, breaks
= c(0, xq, 1e+10), filter = filter, ids = ids): unused arguments
(getter = getter, ids = ids)
vecsToFDR: no visible binding for global variable ‘nperm’
vecsToFDR: no visible global function definition for ‘sessionInfo’
boxswarm,SnpToGeneQTL: no visible binding for global variable ‘g1’
boxswarm,SnpToGeneQTL: no visible global function definition for ‘bxp’
initialize,FDRsupp: no visible global function definition for
‘sessionInfo’
Undefined global functions or variables:
DNAStringSetList Homo.sapiens MAF abline approx as.formula assoc bxp
calls ch chisq criterion exonsBy findDone findJobs g1 getJobInfo hist
i lines loadRegistry loadResult maf mindist ml10fdr model.matrix
nperm nth path permScore_1 permScore_2 permScore_3 plot predict
probeid runif sessionInfo snp snp.rhs.estimates text value x
Consider adding
importFrom("graphics", "abline", "bxp", "hist", "lines", "plot",
"text")
importFrom("stats", "approx", "as.formula", "model.matrix", "predict",
"runif")
importFrom("utils", "sessionInfo")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: TransStore-class.Rd:36-38: Dropping empty section \references
prepare_Rd: qqStore.Rd:66-68: Dropping empty section \details
prepare_Rd: transAssoc.Rd:69-71: 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 ... NOTE
Note: found 8 marked Latin-1 strings
Note: found 12 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeToStats 157.243 28.599 46.075
enumerateByFDR 51.932 3.618 55.569
clipPCs 35.908 0.807 36.732
cisAssoc 23.140 1.096 28.114
gQTLs 9.611 0.697 10.312
eqBox2 8.415 0.254 8.673
queryVCF 8.174 0.177 8.356
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘org.Hs.eg.db’
* 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
‘/Users/biocbuild/bbs-3.4-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.