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BioC 3.5: CHECK report for gQTLstats on malbec2

This page was generated on 2017-08-16 13:16:18 -0400 (Wed, 16 Aug 2017).

Package 587/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLstats 1.8.0
VJ Carey
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/gQTLstats
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gQTLstats
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings gQTLstats_1.8.0.tar.gz
StartedAt: 2017-08-15 23:37:14 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:49:29 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 735.4 seconds
RetCode: 0
Status:  OK 
CheckDir: gQTLstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings gQTLstats_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/gQTLstats.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLstats/DESCRIPTION’ ... OK
* this is package ‘gQTLstats’ version ‘1.8.0’
* 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 65.7Mb
  sub-directories of 1Mb or more:
    data        11.0Mb
    doc          1.1Mb
    registries  18.9Mb
    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’
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: no visible global function definition for ‘plotlyOutput’
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
  ‘renderPlotly’
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 plotlyOutput probeid renderPlotly
  snp state stateid subsetByRanges value x
* checking Rd files ... OK
* 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
clipPCs    38.088  3.212  41.336
cisAssoc   21.820  1.008  23.286
TransStore 16.924  0.104  22.810
gQTLs       9.352  7.524  16.934
tsByRank   13.288  0.116  13.554
eqBox2      8.852  0.748   9.603
queryVCF    8.524  0.540   9.074
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.


gQTLstats.Rcheck/00install.out:

* 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)

gQTLstats.Rcheck/gQTLstats-Ex.timings:

nameusersystemelapsed
FDRsupp-class0.0000.0000.002
TransStore-class0.0000.0000.001
TransStore16.924 0.10422.810
cisAssoc21.820 1.00823.286
clipPCs38.088 3.21241.336
directPlot0.0240.0000.024
enumerateByFDR0.0000.0000.001
eqBox28.8520.7489.603
filtFDR0.0160.0000.017
gQTLs 9.352 7.52416.934
hmm8781.2200.0561.277
manhWngr3.8000.0683.885
mixedVCFtoSnpMatrix0.6280.0000.630
pifdr1.3680.0081.378
qqStore0.0000.0000.001
queryVCF8.5240.5409.074
senstab2.4920.0242.519
setFDRfunc0.0400.0040.046
storeToStats0.0000.0000.002
tqbrowser0.0120.0040.014
transAssoc0.0040.0000.001
transBrowse0.0000.0000.001
tsByRank13.288 0.11613.554
txsPlot0.0200.0000.022