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BioC 3.4: CHECK report for gQTLstats on morelia

This page was generated on 2017-04-15 16:26:08 -0400 (Sat, 15 Apr 2017).

Package 554/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLstats 1.6.0
VJ Carey
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/gQTLstats
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gQTLstats
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLstats_1.6.0.tar.gz
StartedAt: 2017-04-15 03:12:12 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 03:29:06 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 1014.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gQTLstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLstats_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/gQTLstats.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.6.0’
* 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’
eqBox2: no visible global function definition for ‘bxp’
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   180.153 40.123  60.360
enumerateByFDR  64.908  3.962  71.617
clipPCs         42.003  0.872  42.906
cisAssoc        24.958  1.073  34.174
gQTLs            8.787  0.662  10.437
eqBox2           8.391  0.238   9.599
queryVCF         8.256  0.180   8.463
manhWngr         3.433  0.219  22.434
* 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.


gQTLstats.Rcheck/00install.out:

* installing *source* package ‘gQTLstats’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gQTLstats)

gQTLstats.Rcheck/gQTLstats-Ex.timings:

nameusersystemelapsed
FDRsupp-class0.0010.0000.002
TransStore-class0.0010.0010.001
TransStore0.0010.0000.008
cisAssoc24.958 1.07334.174
clipPCs42.003 0.87242.906
directPlot0.0300.0020.093
enumerateByFDR64.908 3.96271.617
eqBox28.3910.2389.599
filtFDR0.0160.0000.051
gQTLs 8.787 0.66210.437
hmm8780.8450.0541.058
manhWngr 3.433 0.21922.434
mixedVCFtoSnpMatrix0.5280.0150.616
pifdr1.4830.0452.474
qqStore0.0010.0000.001
queryVCF8.2560.1808.463
senstab1.5050.0461.839
setFDRfunc0.0450.0010.064
storeToStats180.153 40.123 60.360
transAssoc0.0000.0000.001
txsPlot0.0250.0050.042