gQTLstats 1.0.0
VJ Carey
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/gQTLstats | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | 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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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings gQTLstats_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/gQTLstats.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [19s/28s] OK
* checking installed package size ... NOTE
installed size is 16.5Mb
sub-directories of 1Mb or more:
data 9.6Mb
vcf 5.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.eqBox: no visible global function definition for
‘SnpMatrixCisToSummex’
.eqDesc: no visible global function definition for
‘SnpMatrixCisToSummex’
bag: no visible binding for global variable ‘summex’
bag: no visible binding for global variable ‘assayind’
bag: no visible binding for global variable ‘rhs’
bag: no visible binding for global variable ‘gtdata’
bag: no visible binding for global variable ‘nperm’
cisAssoc: no visible global function definition for ‘elementLengths’
cisAssoc: no visible global function definition for ‘DNAStringSetList’
gmod2: no visible binding for global variable ‘Homo.sapiens’
gmod2: no visible binding for global variable ‘exonsBy’
manhWngr: no visible binding for global variable ‘ml10fdr’
maxByProbe: no visible binding for global variable ‘snp’
maxByProbe: no visible binding for global variable ‘probeid’
maxByProbe: no visible binding for global variable ‘chisq’
maxByProbe: no visible binding for global variable ‘permScore_1’
maxByProbe: no visible binding for global variable ‘permScore_2’
maxByProbe: no visible binding for global variable ‘permScore_3’
maxBySNP: no visible binding for global variable ‘snp’
maxBySNP: no visible binding for global variable ‘probeid’
maxBySNP: no visible binding for global variable ‘MAF’
maxBySNP: no visible binding for global variable ‘chisq’
maxBySNP: no visible binding for global variable ‘permScore_1’
maxBySNP: no visible binding for global variable ‘permScore_2’
maxBySNP: no visible binding for global variable ‘permScore_3’
maxBySNP: no visible binding for global variable ‘mindist’
maxBySNP: no visible global function definition for ‘desc’
maxBySNP: no visible global function definition for ‘nth’
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
‘elementLengths’
prep.cisAssocNB: no visible global function definition for
‘DNAStringSetList’
prep.cisAssocNB: no visible global function definition for ‘colData<-’
storeToHist: no visible binding for global variable ‘x’
storeToMaxAssocBySNP: no visible binding for global variable ‘snp’
storeToMaxAssocBySNP: no visible global function definition for ‘desc’
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’
storeToMaxAssocBySNP: no visible global function definition for
‘GRanges’
storeToMaxAssocBySNP: no visible global function definition for
‘IRanges’
* 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 8 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 ... [237s/253s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeToStats 107.560 10.027 71.351
enumerateByFDR 41.319 0.309 64.380
clipPCs 28.882 0.294 45.353
manhWngr 27.754 0.176 41.708
cisAssoc 4.220 0.113 6.502
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [225s/323s]
[225s/323s] OK
* checking for unstated dependencies in vignettes ... OK
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.
* installing *source* package ‘gQTLstats’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for class “functionORNULL” in package ‘gQTLstats’ seems equivalent to one from package ‘IRanges’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (gQTLstats)