gQTLstats 1.9.2
VJ Carey
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gQTLstats | | Last Changed Rev: 129375 / Revision: 131943 | | Last Changed Date: 2017-05-03 10:48:55 -0400 (Wed, 03 May 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | 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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLstats/DESCRIPTION’ ... OK
* this is package ‘gQTLstats’ version ‘1.9.2’
* 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 66.0Mb
sub-directories of 1Mb or more:
data 11.0Mb
doc 1.6Mb
registries 18.8Mb
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.
Namespace in Imports field not imported from: ‘ldblock’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TransStore: no visible binding for global variable ‘i’
TransStore : <anonymous>: no visible binding for global variable ‘i’
VcfStack2: no visible global function definition for ‘VcfFileList’
cisAssoc: no visible global function definition for ‘DNAStringSetList’
cisCount: no visible global function definition for ‘DNAStringSetList’
cisEsts: no visible global function definition for ‘DNAStringSetList’
eqBox4: no visible binding for global variable ‘gt’
eqBox4: no visible binding for global variable ‘ex’
eqBox4: no visible binding for global variable ‘id’
eqBox4: no visible global function definition for ‘geom_boxplot’
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’
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’
setFDRfunc: no visible binding for global variable ‘assoc’
storeToHist: no visible binding for global variable ‘x’
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’
tqbrowser: no visible global function definition for ‘experiments’
tqbrowser: no visible global function definition for ‘plotlyOutput’
tqbrowser : server: no visible global function definition for
‘renderPlotly’
tqbrowser : server: no visible global function definition for ‘path’
tqbrowser : server: no visible global function definition for
‘experiments’
tqbrowser : server: no visible global function definition for
‘TabixFile’
tqbrowser : server: no visible binding for global variable ‘assoc’
tqbrowser : server: no visible binding for global variable ‘stateid’
tqbrowser : server: no visible binding for global variable ‘state’
transTable: no visible binding for global variable ‘i’
tsByRank_sing: no visible binding for global variable ‘i’
tsByRank_sing : <anonymous>: no visible binding for global variable ‘i’
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’
boxswarm,SnpToGeneQTL: no visible binding for global variable ‘g1’
Undefined global functions or variables:
DNAStringSetList Homo.sapiens MAF TabixFile VcfFileList assoc calls
ch chisq criterion ex exonsBy experiments g1 geom_boxplot gt i id maf
mindist ml10fdr nperm nth path permScore_1 permScore_2 permScore_3
plotlyOutput probeid renderPlotly snp state stateid value x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘VcfStack2’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
clipPCs 40.015 0.878 42.096
cisAssoc 21.700 0.849 23.198
TransStore 14.359 0.299 15.259
tsByRank 12.941 0.354 13.671
gQTLs 8.727 1.044 10.046
eqBox2 8.000 0.227 8.451
queryVCF 7.654 0.202 8.073
* 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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.
* installing *source* package ‘gQTLstats’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (gQTLstats)