VJ Carey
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/gQTLstats |
| Branch: RELEASE_3_9 |
| Last Commit: c68a9cf |
| Last Changed Date: 2019-05-02 11:53:51 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:43 -0400 (Wed, 16 Oct 2019).
| Package 710/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gQTLstats 1.16.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: gQTLstats |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gQTLstats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gQTLstats_1.16.0.tar.gz |
| StartedAt: 2019-10-16 03:25:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:46:22 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1241.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gQTLstats.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gQTLstats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gQTLstats_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gQTLstats.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLstats/DESCRIPTION’ ... OK
* this is package ‘gQTLstats’ version ‘1.16.0’
* 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 64.7Mb
sub-directories of 1Mb or more:
data 11.0Mb
registries 18.8Mb
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
* 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
TransStore: no visible binding for global variable ‘i’
TransStore : : 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’
eqBox4: no visible binding for global variable ‘gt’
eqBox4: no visible binding for global variable ‘ex’
eqBox4: no visible binding for global variable ‘id’
eqBox4: no visible global function definition for ‘geom_boxplot’
gQTLs: no visible binding for global variable ‘ch’
gmod2: no visible binding for global variable ‘exonsBy’
gmod2: no visible global function definition for ‘TxDb’
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 : server: no visible global function definition for
‘experiments’
tqbrowser : server: no visible global function definition for
‘TabixFile’
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 : : no visible binding for global variable ‘i’
boxswarm,SnpToGeneQTL: no visible binding for global variable ‘g1’
Undefined global functions or variables:
DNAStringSetList MAF TabixFile TxDb assoc calls ch chisq criterion ex
exonsBy experiments g1 geom_boxplot gt i id maf mindist ml10fdr nth
permScore_1 permScore_2 permScore_3 probeid snp state stateid 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 ... NOTE
Output for data("bigfiltFDR", package = "gQTLstats"):
assoc
FDRmodel
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formula
data
subset
names
class
theCall
store
xprobs
filter
sessinfo
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names
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Output for data("bigrawFDR", package = "gQTLstats"):
assoc
FDRmodel
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formula
data
subset
names
class
theCall
store
xprobs
sessinfo
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names
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Output for data("filtFDR", package = "gQTLstats"):
assoc
FDRmodel
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formula
data
subset
names
class
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store
xprobs
filter
sessinfo
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names
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srcref
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Output for data("rawFDR", package = "gQTLstats"):
assoc
FDRmodel
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formula
data
subset
names
class
theCall
store
xprobs
sessinfo
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names
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class
package
Output for data("sensByProbe", package = "gQTLstats"):
assoc
FDRmodel
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formula
data
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names
class
theCall
dfr
xprobs
xfield
filter
sessinfo
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names
class
filterUsed
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class
package
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names
out.attrs
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names
row.names
class
names
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tab
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names
row.names
class
FDRfunc
assoc
FDRmodel
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formula
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names
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dfr
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filter
sessinfo
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names
class
filterUsed
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package
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names
out.attrs
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names
row.names
class
names
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tab
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names
row.names
class
FDRfunc
assoc
FDRmodel
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* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipPCs 62.864 2.095 64.963
cisAssoc 32.481 1.914 34.413
gQTLs 12.214 0.662 12.882
queryVCF 11.466 0.653 13.304
eqBox2 10.673 0.340 11.015
manhWngr 4.784 0.287 5.183
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.
gQTLstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gQTLstats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘gQTLstats’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gQTLstats)
gQTLstats.Rcheck/tests/test-all.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("gQTLstats")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: geuvPack
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
clipping PCs 1,2 from exprs
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
Loading required package: geuvStore2
Loading required package: BatchJobs
Loading required package: BBmisc
Attaching package: 'BBmisc'
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:BiocGenerics':
normalize
The following object is masked from 'package:base':
isFALSE
The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files:
1: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BatchJobs/etc/BatchJobs_global_config.R
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
measure.mem: TRUE
Loading required package: gQTLBase
NOTE: there were 41 samples not found (of 462 requested).
using assay() to extract 'expression' matrix from RangedSummarizedExperiment
counting tests...
counting #NA...
obtaining assoc quantiles...
computing perm_assoc histogram....
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
RUNIT TEST PROTOCOL -- Wed Oct 16 03:46:14 2019
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gQTLstats RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(x, ...) : non-diploid variants are set to NA
2: In col.summary(gtdata[[1]]) :
69 rows were empty - ignored when calculating call rates
3: In .local(x, ...) : non-diploid variants are set to NA
4: In col.summary(gtdata$genotypes) :
69 rows were empty - ignored when calculating call rates
5: executing %dopar% sequentially: no parallel backend registered
6: In .local(x, ...) : non-diploid variants are set to NA
7: In .local(x, ...) : non-diploid variants are set to NA
8: In col.summary(gtdata[[1]]) :
238 rows were empty - ignored when calculating call rates
9: In .local(x, ...) : non-diploid variants are set to NA
10: In col.summary(gtdata$genotypes) :
238 rows were empty - ignored when calculating call rates
>
> proc.time()
user system elapsed
394.042 29.340 438.803
gQTLstats.Rcheck/gQTLstats-Ex.timings
| name | user | system | elapsed | |
| FDRsupp-class | 0.002 | 0.001 | 0.003 | |
| TransStore-class | 0.000 | 0.000 | 0.001 | |
| TransStore | 0.000 | 0.000 | 0.001 | |
| cisAssoc | 32.481 | 1.914 | 34.413 | |
| clipPCs | 62.864 | 2.095 | 64.963 | |
| directPlot | 0.025 | 0.003 | 0.028 | |
| enumerateByFDR | 0 | 0 | 0 | |
| eqBox2 | 10.673 | 0.340 | 11.015 | |
| filtFDR | 0.032 | 0.004 | 0.036 | |
| gQTLs | 12.214 | 0.662 | 12.882 | |
| hmm878 | 1.376 | 0.167 | 1.547 | |
| manhWngr | 4.784 | 0.287 | 5.183 | |
| mixedVCFtoSnpMatrix | 0.899 | 0.037 | 0.964 | |
| pifdr | 1.099 | 0.143 | 1.407 | |
| qqStore | 0.001 | 0.001 | 0.001 | |
| queryVCF | 11.466 | 0.653 | 13.304 | |
| senstab | 2.659 | 0.139 | 2.968 | |
| setFDRfunc | 0.068 | 0.007 | 0.083 | |
| storeToStats | 0.000 | 0.000 | 0.001 | |
| tqbrowser | 0.022 | 0.002 | 0.027 | |
| transAssoc | 0.000 | 0.001 | 0.001 | |
| transBrowse | 0.001 | 0.001 | 0.001 | |
| tsByRank | 0.001 | 0.001 | 0.002 | |
| txsPlot | 0.035 | 0.005 | 0.047 | |