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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenVisR_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GenVisR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... 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
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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

Attaching package: ‘BiocGenerics’

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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
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: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying uswest mirror
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3780 out-of-bound ranges located on sequence
  44389. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
Warning in .predictCodingGRangesList(query, cache[["cdsbytx"]], seqSource,  :
  'varAllele' values with 'N', '.', '+' or '-' were not translated
'select()' returned many:1 mapping between keys and columns
> object <- Lolliplot(dataset.mode2, transcript="ENST00000263967",
+                     species="hsapiens")
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: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying useast mirror
Error in bmRequest(request = request, httr_config = martHTTRConfig(mart),  : 
  Gateway Timeout (HTTP 504).
Calls: Lolliplot ... .getAttributes -> .getAttrFilt -> bmRequest -> stop_for_status
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5.   └─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
    6.     └─GenVisR .local(object, ...)
    7.       └─biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = host)
    8.         └─biomaRt:::.useMart(...)
    9.           └─biomaRt:::.listMarts(...)
   10.             └─biomaRt:::bmRequest(...)
   11.               └─httr::GET(request2, config = httr_config, content_type("text/plain"))
   12.                 └─httr:::request_perform(req, hu$handle$handle)
   13.                   ├─httr:::request_fetch(req$output, req$url, handle)
   14.                   └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   15.                     └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 2 | WARN 18 | SKIP 44 | PASS 629 ]
  Error: Test failures
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GenVisR
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GenVisR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (GenVisR)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
[ FAIL 2 | WARN 18 | SKIP 44 | PASS 629 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (44)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2
── Error (test-Lolliplot-class.R:555:5): (code run outside of `test_that()`) ───
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: unable to get local issuer certificate
Backtrace:
     ▆
  1. ├─base::suppressWarnings(...) at test-Lolliplot-class.R:555:4
  2. │ └─base::withCallingHandlers(...)
  3. └─GenVisR:::LolliplotData(...)
  4.   ├─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
  5.   └─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
  6.     └─GenVisR .local(object, ...)
  7.       └─biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = host)
  8.         └─biomaRt:::.useMart(...)
  9.           └─biomaRt:::.listMarts(...)
 10.             └─biomaRt:::bmRequest(...)
 11.               └─httr::GET(request2, config = httr_config, content_type("text/plain"))
 12.                 └─httr:::request_perform(req, hu$handle$handle)
 13.                   ├─httr:::request_fetch(req$output, req$url, handle)
 14.                   └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 15.                     └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 2 | WARN 18 | SKIP 44 | PASS 629 ]
Error: Test failures
Execution halted