gQTLstats 1.7.42
VJ Carey
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gQTLstats | | Last Changed Rev: 125036 / Revision: 127142 | | Last Changed Date: 2016-12-12 12:31:37 -0500 (Mon, 12 Dec 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | TIMEOUT | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK |  |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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_1.7.42.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gQTLstats.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.7.42’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘gQTLstats’
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘gQTLstats’
Warning: replacing previous import ‘plotly::rename’ by ‘S4Vectors::rename’ when loading ‘gQTLstats’
Warning: replacing previous import ‘plotly::slice’ by ‘IRanges::slice’ when loading ‘gQTLstats’
Warning: replacing previous import ‘plotly::select’ by ‘AnnotationDbi::select’ when loading ‘gQTLstats’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/gQTLstats.Rcheck/00install.out’ for details.
* 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
statsByRank: warning in matrix(NA, nr = length(inigr), ncol = nperm):
partial argument match of 'nr' to 'nrow'
tsByRankAccum: warning in matrix(NA, nr = length(ini), ncol = maxrank):
partial argument match of 'nr' to 'nrow'
tsByRankAccum: warning in matrix(NA_character_, nr = length(ini), ncol
= maxrank): partial argument match of 'nr' to 'nrow'
TransStore: no visible binding for global variable ‘i’
TransStore : <anonymous>: no visible binding for global variable ‘i’
cisAssoc: no visible global function definition for ‘DNAStringSetList’
cisCount: no visible global function definition for ‘DNAStringSetList’
cisEsts: no visible global function definition for ‘DNAStringSetList’
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 : server: no visible global function definition for
‘experiments’
tqbrowser : server: no visible global function definition for
‘TabixFile’
tqbrowser : server: no visible global function definition for
‘subsetByRanges’
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 assoc calls ch chisq
criterion exonsBy experiments g1 i maf mindist ml10fdr nperm nth path
permScore_1 permScore_2 permScore_3 probeid snp state stateid
subsetByRanges value x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘collapse_multiPerm’ ‘distToGene’ ‘getTransRegistries’ ‘pifdr3’
‘tsByRankAccum_sing’ ‘tsByRank_sing’
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 ... WARNING
Codoc mismatches from documentation object 'tqbrowser':
tqbrowser
Code: function(mae, felname, gelname, tiling, tsbra, annovec,
band.init = "6q12", ermaset, gwascat, ...)
Docs: function(mae, felname, gelname, tiling, tsbra, annovec,
band.init = "6q12", ...)
Argument names in code not in docs:
ermaset gwascat
Mismatches in argument names:
Position: 8 Code: ermaset Docs: ...
Codoc mismatches from documentation object 'transBrowse':
transBrowse2
Code: function(tbga, annovec, tivcf, se, title = "trans eQTL",
maxrank = 3)
Docs: function(tbg, anno, tivcf, se, title = "trans eQTL", maxrank =
3)
Argument names in code not in docs:
tbga annovec
Argument names in docs not in code:
tbg anno
Mismatches in argument names:
Position: 1 Code: tbga Docs: tbg
Position: 2 Code: annovec Docs: anno
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘gwascat’
* 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 40.837 0.866 41.714
cisAssoc 25.764 1.005 26.941
TransStore 16.059 0.358 18.638
tsByRank 13.532 0.394 14.062
gQTLs 10.200 0.783 11.001
eqBox2 9.135 0.262 9.402
queryVCF 8.897 0.208 9.110
* 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: 4 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.