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CHECK report for GenVisR on tokay1

This page was generated on 2019-04-13 11:26:15 -0400 (Sat, 13 Apr 2019).

Package 636/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.14.2
Zachary Skidmore
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GenVisR
Branch: RELEASE_3_8
Last Commit: 4b931cc
Last Changed Date: 2019-04-04 12:02:47 -0400 (Thu, 04 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: GenVisR
Version: 1.14.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenVisR_1.14.2.tar.gz
StartedAt: 2019-04-13 02:35:50 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:49:01 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 791.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GenVisR.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenVisR_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenVisR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.14.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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, 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
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, 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
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-3.8-bioc/meat/GenVisR.Rcheck/00check.log'
for details.


Installation output

GenVisR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GenVisR_1.14.2.tar.gz && rm -rf GenVisR.buildbin-libdir && mkdir GenVisR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenVisR.buildbin-libdir GenVisR_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GenVisR_1.14.2.zip && rm GenVisR_1.14.2.tar.gz GenVisR_1.14.2.zip
###
##############################################################################
##############################################################################


  % 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 2097k  100 2097k    0     0  27.0M      0 --:--:-- --:--:-- --:--:-- 28.8M

install for i386

* installing *source* package 'GenVisR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenVisR'
    finding HTML links ... done
    Clinical-class                          html  
    GMS-class                               html  
    GMS_Virtual-class                       html  
    GMS_v4-class                            html  
    GenVisR                                 html  
    HCC1395_Germline                        html  
    HCC1395_N                               html  
    HCC1395_T                               html  
    Lolliplot-class                         html  
    LucCNseg                                html  
    MutSpectra-class                        html  
    MutationAnnotationFormat-class          html  
    MutationAnnotationFormat_Virtual-class
                                            html  
    MutationAnnotationFormat_v1.0-class     html  
    MutationAnnotationFormat_v2.0-class     html  
    MutationAnnotationFormat_v2.1-class     html  
    MutationAnnotationFormat_v2.2-class     html  
    MutationAnnotationFormat_v2.3-class     html  
    MutationAnnotationFormat_v2.4-class     html  
    PIK3CA                                  html  
    Rainfall-class                          html  
    SNPloci                                 html  
    TvTi                                    html  
    VEP-class                               html  
    VEP_Virtual-class                       html  
    VEP_v88-class                           html  
    Waterfall-class                         html  
    brcaMAF                                 html  
    cnFreq                                  html  
    cnSpec                                  html  
    cnView                                  html  
    compIdent                               html  
    covBars                                 html  
    cytoGeno                                html  
    drawPlot-methods                        html  
    genCov                                  html  
    geneViz                                 html  
    getData-methods                         html  
    getDescription-methods                  html  
    getGrob-methods                         html  
    getHeader-methods                       html  
    getMeta-methods                         html  
    getMutation-methods                     html  
    getPath-methods                         html  
    getPosition-methods                     html  
    getSample-methods                       html  
    getVersion-methods                      html  
    hg19chr                                 html  
    ideoView                                html  
    lohSpec                                 html  
    lohView                                 html  
    lolliplot                               html  
    lolliplot_AA2sidechain                  html  
    lolliplot_buildMain                     html  
    waterfall                               html  
    writeData-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenVisR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenVisR' as GenVisR_1.14.2.zip
* DONE (GenVisR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GenVisR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GenVisR.Rcheck/tests_i386/testthat.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(GenVisR)
> 
> test_check("GenVisR")
-- 1. Error: (unknown) (@test-Lolliplot-class.R#222)  --------------------------
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)!
1: suppressWarnings(annotateProteinCoord(annotateTranscript.mode1.out, ensembl = retrieveMart.out, 
       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

GenVisR.Rcheck/tests_x64/testthat.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(GenVisR)
> 
> test_check("GenVisR")
-- 1. Error: (unknown) (@test-Lolliplot-class.R#222)  --------------------------
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)!
1: suppressWarnings(annotateProteinCoord(annotateTranscript.mode1.out, ensembl = retrieveMart.out, 
       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

Example timings

GenVisR.Rcheck/examples_i386/GenVisR-Ex.timings

nameusersystemelapsed

GenVisR.Rcheck/examples_x64/GenVisR-Ex.timings

nameusersystemelapsed