VJ Carey
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/gQTLBase |
| Branch: master |
| Last Commit: e5fe5ca |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:40:41 -0400 (Tue, 09 Apr 2019).
| Package 698/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gQTLBase 1.15.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: gQTLBase |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gQTLBase.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gQTLBase_1.15.0.tar.gz |
| StartedAt: 2019-04-09 01:00:47 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:07:03 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 376.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gQTLBase.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gQTLBase.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gQTLBase_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gQTLBase.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLBase/DESCRIPTION’ ... OK
* this is package ‘gQTLBase’ version ‘1.15.0’
* 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 ‘gQTLBase’ can be installed ... OK
* checking installed package size ... OK
* 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
.describeStore: no visible global function definition for ‘getJobInfo’
.extractByProbes: no visible binding for global variable ‘x’
.extractByRanges: no visible global function definition for
‘subsetByOverlaps’
.extractByRanges: no visible binding for global variable ‘x’
DFstoreToFf: no visible binding for global variable ‘x’
cb2range: no visible global function definition for ‘select’
cb2range: no visible global function definition for ‘IRanges’
dendroReduce.bj: no visible global function definition for ‘batchMap’
dendroReduce.fe: no visible binding for global variable ‘i’
describeStore.old: no visible global function definition for ‘hist’
ffapp2: no visible global function definition for ‘as.ff’
ffapp2: no visible global function definition for ‘appendLevels’
ffapp2: no visible global function definition for ‘as.which’
mergeGWhits: no visible global function definition for ‘genome’
storeApply: no visible binding for global variable ‘x’
storeApply2: no visible binding for global variable ‘x’
storeToFf: no visible binding for global variable ‘x’
show,storeDescription: no visible global function definition for
‘median’
Undefined global functions or variables:
IRanges appendLevels as.ff as.which batchMap genome getJobInfo hist i
median select subsetByOverlaps x
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: ufeatByTiling.Rd:50-52: 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeApply 34.072 0.487 40.266
extractByProbes 6.895 0.083 8.007
mergeCIstates 4.810 0.208 5.135
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/gQTLBase.Rcheck/00check.log’
for details.
gQTLBase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gQTLBase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘gQTLBase’ ... ** using staged installation ** R ** 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 (gQTLBase)
gQTLBase.Rcheck/tests/test-all.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("gQTLBase")
Loading required package: digest
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: BatchJobs
Loading required package: BBmisc
Attaching package: 'BBmisc'
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: /home/biocbuild/bbs-3.9-bioc/R/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: GenomicRanges
building probe:job map...
done.
building range:job map...
done.
RUNIT TEST PROTOCOL -- Tue Apr 9 01:06:51 2019
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gQTLBase RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
174.427 38.474 44.911
gQTLBase.Rcheck/gQTLBase-Ex.timings
| name | user | system | elapsed | |
| ciseStore-class | 0.550 | 0.008 | 0.682 | |
| describeStore | 0.001 | 0.000 | 0.000 | |
| extractByProbes | 6.895 | 0.083 | 8.007 | |
| mergeCIstates | 4.810 | 0.208 | 5.135 | |
| storeApply | 34.072 | 0.487 | 40.266 | |
| storeMapResults | 0.001 | 0.000 | 0.001 | |
| storeToFf | 1.123 | 0.008 | 1.136 | |
| ufeatByTiling | 0 | 0 | 0 | |