##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenomicFeatures_1.46.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.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 ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.46.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicFeatures’ 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
':::' call which should be '::': ‘rtracklayer:::tableNames’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicFeatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTxDbFromBiomart
> ### Title: Make a TxDb object from annotations available on a BioMart
> ###   database
> ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
> 
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database:
> library(biomaRt)
> listMarts(host="www.ensembl.org")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
               biomart                version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 106
2   ENSEMBL_MART_MOUSE      Mouse strains 106
3     ENSEMBL_MART_SNP  Ensembl Variation 106
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 106
> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying uswest mirror
> datasets <- listDatasets(mart)
> head(datasets)
                       dataset                           description
1 abrachyrhynchus_gene_ensembl Pink-footed goose genes (ASM259213v1)
2     acalliptera_gene_ensembl      Eastern happy genes (fAstCal1.2)
3   acarolinensis_gene_ensembl       Green anole genes (AnoCar2.0v2)
4    acchrysaetos_gene_ensembl       Golden eagle genes (bAquChr1.2)
5    acitrinellus_gene_ensembl        Midas cichlid genes (Midas_v5)
6    amelanoleuca_gene_ensembl       Giant panda genes (ASM200744v2)
      version
1 ASM259213v1
2  fAstCal1.2
3 AnoCar2.0v2
4  bAquChr1.2
5    Midas_v5
6 ASM200744v2
> subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))
                 dataset                                          description
29 celegans_gene_ensembl Caenorhabditis elegans (PRJNA13758) genes (WBcel235)
    version
29 WBcel235
> 
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying asia mirror
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... Ensembl site unresponsive, trying uswest mirror
FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .infer_chrominfo_from_transcripts_and_splicings(transcripts$tx_chrom,  :
  chromosome lengths and circularity flags are not available for this
  TxDb object
OK
> txdb1
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Caenorhabditis elegans
# Taxonomy ID: 6239
# Resource URL: www.ensembl.org:80
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 105
# BioMart dataset: celegans_gene_ensembl
# BioMart dataset description: Caenorhabditis elegans genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 59897
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2022-04-12 07:47:12 -0400 (Tue, 12 Apr 2022)
# GenomicFeatures version at creation time: 1.46.5
# RSQLite version at creation time: 2.2.12
# DBSCHEMAVERSION: 1.2
> 
> ## Retrieve an incomplete transcript dataset for Human:
> transcript_ids <- c(
+     "ENST00000013894",
+     "ENST00000268655",
+     "ENST00000313243",
+     "ENST00000435657",
+     "ENST00000384428",
+     "ENST00000478783"
+ )
> 
> if (interactive()) {
+   txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
+                                transcript_ids=transcript_ids)
+   txdb2  # note that these annotations match the GRCh38 genome assembly
+ }
> 
> ## ---------------------------------------------------------------------
> ## B. ACCESSING THE EnsemblGenomes MARTS
> ## ---------------------------------------------------------------------
> 
> library(biomaRt)
> 
> ## Note that BioMart is not currently available for Ensembl Bacteria.
> 
> ## ---------------------
> ## --- Ensembl Fungi ---
> 
> mart <- useMart(biomart="fungi_mart", host="fungi.ensembl.org")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
> datasets <- listDatasets(mart)
> datasets$dataset
 [1] "aastaci_eg_gene"            "aclavatus_eg_gene"         
 [3] "aflavus_eg_gene"            "afumigatus_eg_gene"        
 [5] "afumigatusa1163_eg_gene"    "agossypii_eg_gene"         
 [7] "ainvadans_eg_gene"          "anidulans_eg_gene"         
 [9] "aniger_eg_gene"             "aoryzae_eg_gene"           
[11] "aterreus_eg_gene"           "bbassiana_eg_gene"         
[13] "bcinerea_eg_gene"           "bgraminis_eg_gene"         
[15] "calbicans_eg_gene"          "cauris_eg_gene"            
[17] "cduobushaemulonis_eg_gene"  "cglabrata_eg_gene"         
[19] "cgloeosporioides_eg_gene"   "cgraminicola_eg_gene"      
[21] "chaemuloni_eg_gene"         "chigginsianum_eg_gene"     
[23] "cneoformans_eg_gene"        "corbiculare_eg_gene"       
[25] "cparapsilosis_eg_gene"      "cpseudohaemulonis_eg_gene" 
[27] "ctropicalis_eg_gene"        "dseptosporum_eg_gene"      
[29] "fculmorum_eg_gene"          "ffujikuroi_eg_gene"        
[31] "fgraminearum_eg_gene"       "foxysporum_eg_gene"        
[33] "fpseudograminearum_eg_gene" "fsolani_eg_gene"           
[35] "fverticillioides_eg_gene"   "ggraminis_eg_gene"         
[37] "gultimum_eg_gene"           "harabidopsidis_eg_gene"    
[39] "hcapsulatum_eg_gene"        "kpastoris_eg_gene"         
[41] "lmaculans_eg_gene"          "mlaricipopulina_eg_gene"   
[43] "moryzae_eg_gene"            "mpoae_eg_gene"             
[45] "mviolaceum_eg_gene"         "ncrassa_eg_gene"           
[47] "nfischeri_eg_gene"          "pchrysosporium_eg_gene"    
[49] "pgraminis_eg_gene"          "pgraminisug99_eg_gene"     
[51] "pnodorum_eg_gene"           "poryzae_eg_gene"           
[53] "pstriiformis_eg_gene"       "pteres_eg_gene"            
[55] "ptriticina_eg_gene"         "ptriticirepentis_eg_gene"  
[57] "scerevisiae_eg_gene"        "scryophilus_eg_gene"       
[59] "sjaponicus_eg_gene"         "soctosporus_eg_gene"       
[61] "spombe_eg_gene"             "sreilianum_eg_gene"        
[63] "ssclerotiorum_eg_gene"      "tmelanosporum_eg_gene"     
[65] "treesei_eg_gene"            "tvirens_eg_gene"           
[67] "umaydis_eg_gene"            "vdahliae_eg_gene"          
[69] "vdahliaejr2_eg_gene"        "ylipolytica_eg_gene"       
[71] "ztritici_eg_gene"          
> yeast_txdb <- makeTxDbFromBiomart(biomart="fungi_mart",
+                                   dataset="scerevisiae_eg_gene",
+                                   host="fungi.ensembl.org")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> yeast_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Saccharomyces cerevisiae
# Taxonomy ID: 4932
# Resource URL: fungi.ensembl.org:80
# BioMart database: fungi_mart
# BioMart database version: Ensembl Fungi Genes 53
# BioMart dataset: scerevisiae_eg_gene
# BioMart dataset description: Saccharomyces cerevisiae genes (R64-1-1)
# BioMart dataset version: R64-1-1
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 7127
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2022-04-12 07:47:33 -0400 (Tue, 12 Apr 2022)
# GenomicFeatures version at creation time: 1.46.5
# RSQLite version at creation time: 2.2.12
# DBSCHEMAVERSION: 1.2
> 
> ## Note that the dataset for Yeast on Ensembl Fungi is not necessarily
> ## the same as on the main Ensembl database:
> yeast_txdb0 <- makeTxDbFromBiomart(dataset="scerevisiae_gene_ensembl")
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 useast mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate
Calls: makeTxDbFromBiomart ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  In addition: Warning messages:
  1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
    The "phase" metadata column contains non-NA values for features of type
    exon. This information was ignored.
  2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
    The "phase" metadata column contains non-NA values for features of type
    stop_codon. This information was ignored.
  3: In .get_cds_IDX(mcols0$type, mcols0$phase) :
    The "phase" metadata column contains non-NA values for features of type
    stop_codon. This information was ignored.
  4: In (function (seqlevels, genome, new_style)  :
    cannot switch some of hg19's seqlevels from UCSC to NCBI style
  5: In (function (seqlevels, genome, new_style)  :
    cannot switch some of hg19's seqlevels from UCSC to NCBI style
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GenomicFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GenomicFeatures’ ...
** using staged installation
** R
** 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 (GenomicFeatures)

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.

> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
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")'.

[1] TRUE
> GenomicFeatures:::.test()
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
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying asia mirror
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... Ensembl site unresponsive, trying uswest mirror
OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Ensembl site unresponsive, trying useast mirror
Timing stopped at: 3.797 0.348 135.1
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate
In addition: Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences a,
  b, and c. 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.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  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.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  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.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences 1,
  2, 3, and 4. 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.
5: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Tue Apr 12 07:52:37 2022 
*********************************************** 
Number of test functions: 73 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 73 test functions, 1 error, 0 failures
ERROR in test_makeTxDbFromBiomart: Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate

Test files with failing tests

   test_makeTxDbFromBiomart.R 
     test_makeTxDbFromBiomart 


Error in BiocGenerics:::testPackage("GenomicFeatures") : 
  unit tests failed for package GenomicFeatures
Calls: <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
3: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
4: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
5: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
Execution halted