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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenVisR_1.15.3.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenVisR.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 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.15.3'
* 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 'GenVisR' 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 ... NOTE
Namespace in Imports field not imported from: 'reshape2'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setTierTwo,data.table : a: no visible binding for global variable 'tmp'
toLolliplot,GMS: no visible binding for global variable 'missingINdex'
Undefined global functions or variables:
missingINdex tmp
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'GenVisR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Lolliplot-class
> ### Title: Class Lolliplot
> ### Aliases: Lolliplot-class Lolliplot
>
> ### ** Examples
>
> # Load a pre-existing data set
> dataset <- PIK3CA
>
> # mode 1, amino acid changes are not present
>
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
Loading required package: GenomicFeatures
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.
> library(BSgenome.Hsapiens.UCSC.hg38)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> BSgenome <- BSgenome.Hsapiens.UCSC.hg38
>
> keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
+ "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification")
> dataset.mode1 <- dataset[,keep]
> colnames(dataset.mode1) <- c("chromosome", "start", "stop", "reference", "variant",
+ "sample", "gene", "consequence")
>
>
> # mode 2, amino acid changes are present
>
> keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
+ "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification",
+ "Transcript_ID", "HGVSp")
> dataset.mode2 <- dataset[,keep]
> colnames(dataset.mode2) <- c("chromosome", "start", "stop", "reference", "variant",
+ "sample", "gene", "consequence", "transcript", "proteinCoord")
>
> # run Lolliplot
>
> object <- Lolliplot(dataset.mode1, transcript="ENST00000263967",
+ species="hsapiens", txdb=txdb, BSgenome=BSgenome)
This function is part of the new S4 feature and is under active development, did you mean to use lolliplot() with a lowercase l?
Warning in .predictCodingGRangesList(query, cache[["cdsbytx"]], seqSource, :
'varAllele' values with 'N', '.', '+' or '-' were not translated
'select()' returned many:1 mapping between keys and columns
Error in .local(object, ...) :
An ensembl transcript id could not be found for the ucsc id: uc003fjk.4, uc062qdy.1 unable to continue... This has probably occurred because of a discrepancy between the txdb object and the ensembl version queried. Please choose another transcript or alter the ensembl version queried (see the host parameter)!
Calls: Lolliplot ... annotateProteinCoord -> annotateProteinCoord -> .local
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GenVisR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Lolliplot-class
> ### Title: Class Lolliplot
> ### Aliases: Lolliplot-class Lolliplot
>
> ### ** Examples
>
> # Load a pre-existing data set
> dataset <- PIK3CA
>
> # mode 1, amino acid changes are not present
>
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
Loading required package: GenomicFeatures
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.
> library(BSgenome.Hsapiens.UCSC.hg38)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> BSgenome <- BSgenome.Hsapiens.UCSC.hg38
>
> keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
+ "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification")
> dataset.mode1 <- dataset[,keep]
> colnames(dataset.mode1) <- c("chromosome", "start", "stop", "reference", "variant",
+ "sample", "gene", "consequence")
>
>
> # mode 2, amino acid changes are present
>
> keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele",
+ "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification",
+ "Transcript_ID", "HGVSp")
> dataset.mode2 <- dataset[,keep]
> colnames(dataset.mode2) <- c("chromosome", "start", "stop", "reference", "variant",
+ "sample", "gene", "consequence", "transcript", "proteinCoord")
>
> # run Lolliplot
>
> object <- Lolliplot(dataset.mode1, transcript="ENST00000263967",
+ species="hsapiens", txdb=txdb, BSgenome=BSgenome)
This function is part of the new S4 feature and is under active development, did you mean to use lolliplot() with a lowercase l?
Warning in .predictCodingGRangesList(query, cache[["cdsbytx"]], seqSource, :
'varAllele' values with 'N', '.', '+' or '-' were not translated
'select()' returned many:1 mapping between keys and columns
Error in .local(object, ...) :
An ensembl transcript id could not be found for the ucsc id: uc003fjk.4, uc062qdy.1 unable to continue... This has probably occurred because of a discrepancy between the txdb object and the ensembl version queried. Please choose another transcript or alter the ensembl version queried (see the host parameter)!
Calls: Lolliplot ... annotateProteinCoord -> annotateProteinCoord -> .local
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:
txdb = txdb, BSgenome = BSgenome, verbose = FALSE)) at testthat/test-Lolliplot-class.R:222
2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
3: annotateProteinCoord(annotateTranscript.mode1.out, ensembl = retrieveMart.out, txdb = txdb,
BSgenome = BSgenome, verbose = FALSE)
4: annotateProteinCoord(annotateTranscript.mode1.out, ensembl = retrieveMart.out, txdb = txdb,
BSgenome = BSgenome, verbose = FALSE)
5: .local(object, ...)
6: stop(memo)
== testthat results ===========================================================
OK: 590 SKIPPED: 44 FAILED: 1
1. Error: (unknown) (@test-Lolliplot-class.R#222)
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:
txdb = txdb, BSgenome = BSgenome, verbose = FALSE)) at testthat/test-Lolliplot-class.R:222
2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
3: annotateProteinCoord(annotateTranscript.mode1.out, ensembl = retrieveMart.out, txdb = txdb,
BSgenome = BSgenome, verbose = FALSE)
4: annotateProteinCoord(annotateTranscript.mode1.out, ensembl = retrieveMart.out, txdb = txdb,
BSgenome = BSgenome, verbose = FALSE)
5: .local(object, ...)
6: stop(memo)
== testthat results ===========================================================
OK: 590 SKIPPED: 44 FAILED: 1
1. Error: (unknown) (@test-Lolliplot-class.R#222)
Error: testthat unit tests failed
Execution halted
* 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 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenVisR.Rcheck/00check.log'
for details.