Jennifer Tom
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/genotypeeval |
| Branch: master |
| Last Commit: f12057d |
| Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:24:35 -0400 (Tue, 09 Apr 2019).
| Package 655/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genotypeeval 1.15.0 Jennifer Tom
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | 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: genotypeeval |
| Version: 1.15.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genotypeeval.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings genotypeeval_1.15.0.tar.gz |
| StartedAt: 2019-04-09 03:01:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:08:51 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 455.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: genotypeeval.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genotypeeval.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings genotypeeval_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/genotypeeval.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genotypeeval/DESCRIPTION' ... OK
* this is package 'genotypeeval' 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 whether package 'genotypeeval' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
Missing or unexported object: 'GenomicRanges::subset'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'genotypeeval-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ReadVCFData
> ### Title: User Constructor for class. Calls VCFData constructor:
> ### ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL
> ### chromosomes, and MULTI calls. It scans the header of the vcf file and
> ### adds in the following fields for analysis if present: AD, GT, DP, GQ.
> ### Looks for the "END" tag in the header and reads in file as gVCF if
> ### necessary.
> ### Aliases: ReadVCFData
>
> ### ** Examples
>
> vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
> mydir <- paste(dirname(vcffn), "/", sep="")
> myfile <-basename(vcffn)
> vcf <- ReadVCFData(mydir, myfile, "GRCh38")
Reading VCF ...
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error in validObject(.Object) :
invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Calls: ReadVCFData ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'genotypeeval-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ReadVCFData
> ### Title: User Constructor for class. Calls VCFData constructor:
> ### ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL
> ### chromosomes, and MULTI calls. It scans the header of the vcf file and
> ### adds in the following fields for analysis if present: AD, GT, DP, GQ.
> ### Looks for the "END" tag in the header and reads in file as gVCF if
> ### necessary.
> ### Aliases: ReadVCFData
>
> ### ** Examples
>
> vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
> mydir <- paste(dirname(vcffn), "/", sep="")
> myfile <-basename(vcffn)
> vcf <- ReadVCFData(mydir, myfile, "GRCh38")
Reading VCF ...
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error in validObject(.Object) :
invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Calls: ReadVCFData ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
6: VCFHeader(hdr$Reference, hdr$Sample, hdr$Header)
7: new("VCFHeader", reference = reference, samples = samples, header = header, ...)
8: initialize(value, ...)
9: initialize(value, ...)
10: validObject(.Object)
11: stop(msg, ": ", errors, domain = NA)
== testthat results ===========================================================
OK: 0 SKIPPED: 0 FAILED: 1
1. Error: (unknown) (@testQA.R#6)
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
6: VCFHeader(hdr$Reference, hdr$Sample, hdr$Header)
7: new("VCFHeader", reference = reference, samples = samples, header = header, ...)
8: initialize(value, ...)
9: initialize(value, ...)
10: validObject(.Object)
11: stop(msg, ": ", errors, domain = NA)
== testthat results ===========================================================
OK: 0 SKIPPED: 0 FAILED: 1
1. Error: (unknown) (@testQA.R#6)
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error: testthat unit tests failed
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 4 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/genotypeeval.Rcheck/00check.log'
for details.
genotypeeval.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/genotypeeval_1.15.0.tar.gz && rm -rf genotypeeval.buildbin-libdir && mkdir genotypeeval.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genotypeeval.buildbin-libdir genotypeeval_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL genotypeeval_1.15.0.zip && rm genotypeeval_1.15.0.tar.gz genotypeeval_1.15.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 399k 100 399k 0 0 1503k 0 --:--:-- --:--:-- --:--:-- 1541k
install for i386
* installing *source* package 'genotypeeval' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'genotypeeval'
finding HTML links ... done
GoldData-class html
GoldDataFromGRanges html
GoldDataParam-class html
GoldDataParam html
ReadGoldData html
ReadVCFData html
ReadVCFDataChunk html
VCFData-class html
VCFEvaluate html
VCFQAParam-class html
VCFQAParam html
VCFQAReport-class html
XHeterozygosity html
admixture html
callbyChrPlot html
calltypePlot html
chunkData html
computeTiTv html
didSamplePass html
didSamplePassOverall html
genotypeQualityPlot html
getCoefs html
getDescriptors html
getName html
getPlots html
getResults html
getVR html
goldCompare html
hetGap html
hetsMasked html
homrefPlot html
meanGQ html
myf html
numberCalls html
numberOfHets html
numberOfHomRefs html
numberOfHomVars html
percentHets html
percentInTarget html
rareCompare html
readDepth html
readVcfGold html
readdepthPlot html
reformatData html
titv 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 'genotypeeval' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genotypeeval' as genotypeeval_1.15.0.zip
* DONE (genotypeeval)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'genotypeeval' successfully unpacked and MD5 sums checked
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genotypeeval.Rcheck/tests_i386/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> library(genotypeeval)
Loading required package: VariantAnnotation
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: GenomeInfoDb
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: GenomicRanges
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
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
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
>
> test_check("genotypeeval")
Reading VCF ...
-- 1. Error: (unknown) (@testQA.R#6) ------------------------------------------
invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
1: ReadVCFData(mydir, myfile, "GRCh38") at testthat/testQA.R:6
2: rownames(geno(scanVcfHeader(myfn)))
3: geno(scanVcfHeader(myfn))
4: scanVcfHeader(myfn)
5: scanVcfHeader(myfn)
6: VCFHeader(hdr$Reference, hdr$Sample, hdr$Header)
7: new("VCFHeader", reference = reference, samples = samples, header = header, ...)
8: initialize(value, ...)
9: initialize(value, ...)
10: validObject(.Object)
11: stop(msg, ": ", errors, domain = NA)
== testthat results ===========================================================
OK: 0 SKIPPED: 0 FAILED: 1
1. Error: (unknown) (@testQA.R#6)
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error: testthat unit tests failed
Execution halted
|
genotypeeval.Rcheck/tests_x64/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> library(genotypeeval)
Loading required package: VariantAnnotation
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: GenomeInfoDb
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: GenomicRanges
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
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
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
>
> test_check("genotypeeval")
Reading VCF ...
-- 1. Error: (unknown) (@testQA.R#6) ------------------------------------------
invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
1: ReadVCFData(mydir, myfile, "GRCh38") at testthat/testQA.R:6
2: rownames(geno(scanVcfHeader(myfn)))
3: geno(scanVcfHeader(myfn))
4: scanVcfHeader(myfn)
5: scanVcfHeader(myfn)
6: VCFHeader(hdr$Reference, hdr$Sample, hdr$Header)
7: new("VCFHeader", reference = reference, samples = samples, header = header, ...)
8: initialize(value, ...)
9: initialize(value, ...)
10: validObject(.Object)
11: stop(msg, ": ", errors, domain = NA)
== testthat results ===========================================================
OK: 0 SKIPPED: 0 FAILED: 1
1. Error: (unknown) (@testQA.R#6)
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error: testthat unit tests failed
Execution halted
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genotypeeval.Rcheck/examples_i386/genotypeeval-Ex.timings
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genotypeeval.Rcheck/examples_x64/genotypeeval-Ex.timings
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