gQTLstats 1.1.2
VJ Carey
| Snapshot Date: 2015-08-20 16:24:16 -0700 (Thu, 20 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gQTLstats | | Last Changed Rev: 107269 / Revision: 107636 | | Last Changed Date: 2015-08-08 18:55:27 -0700 (Sat, 08 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / 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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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gQTLstats_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.1.2’
* 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 ... [22s/22s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘ffbase::table’ when loading ‘gQTLstats’
Warning: replacing previous import by ‘ffbase::%in%’ when loading ‘gQTLstats’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/gQTLstats.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 16.4Mb
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 ‘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 ‘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
‘DNAStringSetList’
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’
* 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 ... [298s/201s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeToStats 133.537 13.847 49.583
enumerateByFDR 41.780 0.459 42.297
clipPCs 37.513 0.611 38.187
manhWngr 29.068 0.164 29.261
cisAssoc 10.303 0.166 10.509
queryVCF 9.229 0.048 9.281
eqBox2 8.950 0.068 9.021
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [243s/245s]
[243s/245s] 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.
* installing *source* package ‘gQTLstats’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘ffbase::table’ when loading ‘gQTLstats’
Warning: replacing previous import by ‘ffbase::%in%’ when loading ‘gQTLstats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘ffbase::table’ when loading ‘gQTLstats’
Warning: replacing previous import by ‘ffbase::%in%’ when loading ‘gQTLstats’
* DONE (gQTLstats)