Jesper R Gadin
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/AllelicImbalance |
| Branch: RELEASE_3_6 |
| Last Commit: 85f652a |
| Last Changed Date: 2017-10-30 12:40:08 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:24 -0400 (Thu, 12 Apr 2018).
| Package 35/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AllelicImbalance 1.16.0 Jesper R Gadin
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: AllelicImbalance |
| Version: 1.16.0 |
| Command: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.16.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz |
| StartedAt: 2018-04-11 22:09:21 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:19:17 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 596.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AllelicImbalance.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.16.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AllelicImbalance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AllelicImbalance' version '1.16.0'
* package encoding: UTF-8
* 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 'AllelicImbalance' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:186: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:333: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/cigar-utilities.Rd:53: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/getAlleleCounts.Rd:79: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/initialize-ASEset.Rd:125: missing file link 'RangedSummarizedExperiment'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
import-bam 12.81 0.02 12.83
annotation-wrappers 8.07 0.17 8.36
lva 5.50 0.00 5.53
ASEset-glocationplot 5.10 0.11 5.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getSnpIdFromLocation 19.22 0.88 25.22
import-bam 16.27 0.29 16.56
annotation-wrappers 8.89 0.28 9.18
lva 5.33 0.03 5.98
ASEset-glocationplot 5.01 0.02 5.03
makeMaskedFasta 0.61 0.02 5.88
* 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
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck/00check.log'
for details.
AllelicImbalance.Rcheck/00install.out
install for i386
* installing *source* package 'AllelicImbalance' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
** help
*** installing help indices
converting help for package 'AllelicImbalance'
finding HTML links ... done
ASEset-barplot html
ASEset-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:186: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/ASEset-class.Rd:333: missing file link 'RangedSummarizedExperiment'
ASEset-filters html
ASEset-gbarplot html
ASEset-glocationplot html
ASEset-gviztrack html
ASEset-scanForHeterozygotes html
ASEset.old html
ASEset.sim html
ASEsetFromBam html
AllelicImbalance-package html
DetectedAI-class html
DetectedAI-plot html
DetectedAI-summary html
GRvariants html
GlobalAnalysis-class html
LinkVariantAlmlof-class html
LinkVariantAlmlof-plot html
RegionSummary-class html
RiskVariant-class html
annotation-wrappers html
annotationBarplot html
barplot-lattice-support html
binom.test html
chisq.test html
cigar-utilities html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/cigar-utilities.Rd:53: missing file link 'GAlignmentsList'
countAllelesFromBam html
coverageMatrixListFromGAL html
decorateWithExons html
decorateWithGenes html
defaultMapBias html
defaultPhase html
detectAI html
fractionPlotDf html
gba html
genomatrix html
genotype2phase html
getAlleleCounts html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/getAlleleCounts.Rd:79: missing file link 'GAlignmentsList'
getAlleleQuality html
getAreaFromGeneNames html
getDefaultMapBiasExpMean html
getSnpIdFromLocation html
histplot html
implodeList-old html
import-bam-2 html
import-bam html
import-bcf html
inferAlleles html
inferAltAllele html
inferGenotypes html
initialize-ASEset html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiQmJg4/R.INSTALL52c4ed549d1/AllelicImbalance/man/initialize-ASEset.Rd:125: missing file link 'RangedSummarizedExperiment'
initialize-DetectedAI html
initialize-GlobalAnalysis html
initialize-RiskVariant html
legendBarplot html
locationplot html
lva html
lva.internal html
makeMaskedFasta html
mapBiasRef html
minCountFilt html
minFreqFilt html
multiAllelicFilt html
phase2genotype html
phaseArray2phaseMatrix html
phaseMatrix2Array html
randomRef html
reads html
refAllele html
regionSummary html
scanForHeterozygotes-old html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.16.0.zip
* DONE (AllelicImbalance)
In R CMD INSTALL
In R CMD INSTALL
|
AllelicImbalance.Rcheck/tests_i386/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> library(testthat)
> test_check("AllelicImbalance")
Loading required package: AllelicImbalance
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: GenomicAlignments
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
Loading required package: Rsamtools
== testthat results ===========================================================
OK: 96 SKIPPED: 1 FAILED: 0
>
>
>
> proc.time()
user system elapsed
12.07 0.50 12.71
|
AllelicImbalance.Rcheck/tests_x64/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> library(testthat)
> test_check("AllelicImbalance")
Loading required package: AllelicImbalance
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: GenomicAlignments
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
Loading required package: Rsamtools
== testthat results ===========================================================
OK: 96 SKIPPED: 1 FAILED: 0
>
>
>
> proc.time()
user system elapsed
15.39 0.42 15.92
|
|
AllelicImbalance.Rcheck/examples_i386/AllelicImbalance-Ex.timings
|
AllelicImbalance.Rcheck/examples_x64/AllelicImbalance-Ex.timings
|