VJ Carey
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/gQTLBase |
| Branch: RELEASE_3_10 |
| Last Commit: b15bef8 |
| Last Changed Date: 2019-10-29 13:09:07 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:24:12 -0400 (Wed, 15 Apr 2020).
| Package 736/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gQTLBase 1.18.0 VJ Carey
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: gQTLBase |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gQTLBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings gQTLBase_1.18.0.tar.gz |
| StartedAt: 2020-04-15 03:40:00 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:07:04 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1624.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gQTLBase.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gQTLBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings gQTLBase_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/gQTLBase.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gQTLBase/DESCRIPTION' ... OK
* this is package 'gQTLBase' version '1.18.0'
* 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 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
* 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 ... 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 ... WARNING
Documented arguments not in \usage in documentation object 'extractByProbes':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeApply 29.14 0.90 64.27
extractByProbes 5.69 0.25 8.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
storeApply 34.86 0.37 35.38
extractByProbes 8.43 0.20 8.66
mergeCIstates 5.25 0.35 5.59
* 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 ... 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/gQTLBase.Rcheck/00check.log'
for details.
gQTLBase.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/gQTLBase_1.18.0.tar.gz && rm -rf gQTLBase.buildbin-libdir && mkdir gQTLBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gQTLBase.buildbin-libdir gQTLBase_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL gQTLBase_1.18.0.zip && rm gQTLBase_1.18.0.tar.gz gQTLBase_1.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 20379 100 20379 0 0 277k 0 --:--:-- --:--:-- --:--:-- 297k
install for i386
* installing *source* package 'gQTLBase' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gQTLBase'
finding HTML links ... done
ciseStore-class html
describeStore html
extractByProbes html
gqtlBase-package html
mergeCIstates html
storeApply html
storeMapResults html
storeToFf html
ufeatByTiling html
** 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
install for x64
* installing *source* package 'gQTLBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLBase' as gQTLBase_1.18.0.zip
* DONE (gQTLBase)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'gQTLBase' successfully unpacked and MD5 sums checked
|
gQTLBase.Rcheck/tests_i386/test-all.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: C:/Users/biocbuild/bbs-3.10-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 -- Wed Apr 15 03:57:06 2020
***********************************************
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
17.73 4.09 553.59
|
gQTLBase.Rcheck/tests_x64/test-all.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: C:/Users/biocbuild/bbs-3.10-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 -- Wed Apr 15 04:06:57 2020
***********************************************
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
19.29 2.84 589.85
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gQTLBase.Rcheck/examples_i386/gQTLBase-Ex.timings
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gQTLBase.Rcheck/examples_x64/gQTLBase-Ex.timings
|