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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### rm -rf gQTLstats.buildbin-libdir gQTLstats.Rcheck && mkdir gQTLstats.buildbin-libdir gQTLstats.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLstats.buildbin-libdir gQTLstats_1.5.3.tar.gz >gQTLstats.Rcheck\00install.out 2>&1 && cp gQTLstats.Rcheck\00install.out gQTLstats-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gQTLstats.buildbin-libdir --install="check:gQTLstats-install.out" --force-multiarch --no-vignettes --timings gQTLstats_1.5.3.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/gQTLstats.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'gQTLstats' can be installed ... OK
* checking installed package size ... NOTE
installed size is 45.1Mb
sub-directories of 1Mb or more:
data 9.8Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
enumerateByFDR 65.74 0.28 66.02
clipPCs 46.47 0.73 47.36
cisAssoc 24.91 0.47 32.23
gQTLs 11.08 0.56 11.64
queryVCF 9.96 0.08 10.03
eqBox2 9.83 0.11 9.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
enumerateByFDR 68.98 0.52 71.32
clipPCs 41.17 1.03 42.81
cisAssoc 25.62 0.64 26.48
gQTLs 11.19 1.35 12.54
eqBox2 9.16 0.25 9.41
queryVCF 8.88 0.19 9.07
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
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
'D:/biocbld/bbs-3.4-bioc/meat/gQTLstats.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'gQTLstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLstats' as gQTLstats_1.5.3.zip
* DONE (gQTLstats)