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CHECK report for GenomicFeatures on malbec2

This page was generated on 2019-10-16 11:57:41 -0400 (Wed, 16 Oct 2019).

Package 656/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.36.4
Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GenomicFeatures
Branch: RELEASE_3_9
Last Commit: 28082ec
Last Changed Date: 2019-07-09 04:52:32 -0400 (Tue, 09 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicFeatures
Version: 1.36.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GenomicFeatures_1.36.4.tar.gz
StartedAt: 2019-10-16 01:53:51 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:06:45 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 774.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: GenomicFeatures.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GenomicFeatures_1.36.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.36.4’
* 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
':::' calls which should be '::':
  ‘S4Vectors:::duplicatedIntegerPairs’ ‘S4Vectors:::matchIntegerPairs’
  ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
  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")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 98
2   ENSEMBL_MART_MOUSE      Mouse strains 98
3     ENSEMBL_MART_SNP  Ensembl Variation 98
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 98
> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
> 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        Anole lizard genes (AnoCar2.0)
4    acitrinellus_gene_ensembl        Midas cichlid genes (Midas_v5)
5        ahaastii_gene_ensembl    Great spotted kiwi genes (aptHaa1)
6    amelanoleuca_gene_ensembl                 Panda genes (ailMel1)
      version
1 ASM259213v1
2  fAstCal1.2
3   AnoCar2.0
4    Midas_v5
5     aptHaa1
6     ailMel1
> subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))
                 dataset                             description  version
30 celegans_gene_ensembl Caenorhabditis elegans genes (WBcel235) WBcel235
> 
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
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
> 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 98
# BioMart dataset: celegans_gene_ensembl
# BioMart dataset description: Caenorhabditis elegans genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 61451
# exon_nrow: 181057
# cds_nrow: 130870
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2019-10-16 02:03:45 -0400 (Wed, 16 Oct 2019)
# GenomicFeatures version at creation time: 1.36.4
# RSQLite version at creation time: 2.1.2
# 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")
> datasets <- listDatasets(mart)
> datasets$dataset
 [1] "aclavatus_eg_gene"          "aflavus_eg_gene"           
 [3] "afumigatus_eg_gene"         "afumigatusa1163_eg_gene"   
 [5] "agossypii_eg_gene"          "anidulans_eg_gene"         
 [7] "aniger_eg_gene"             "aoryzae_eg_gene"           
 [9] "aterreus_eg_gene"           "bbassiana_eg_gene"         
[11] "bcinerea_eg_gene"           "bgraminis_eg_gene"         
[13] "cgloeosporioides_eg_gene"   "cgraminicola_eg_gene"      
[15] "chigginsianum_eg_gene"      "cneoformans_eg_gene"       
[17] "corbiculare_eg_gene"        "dseptosporum_eg_gene"      
[19] "fculmorum_eg_gene"          "ffujikuroi_eg_gene"        
[21] "fgraminearum_eg_gene"       "foxysporum_eg_gene"        
[23] "fpseudograminearum_eg_gene" "fsolani_eg_gene"           
[25] "fverticillioides_eg_gene"   "ggraminis_eg_gene"         
[27] "kpastoris_eg_gene"          "lmaculans_eg_gene"         
[29] "mlaricipopulina_eg_gene"    "moryzae_eg_gene"           
[31] "mpoae_eg_gene"              "mviolaceum_eg_gene"        
[33] "ncrassa_eg_gene"            "nfischeri_eg_gene"         
[35] "pgraminis_eg_gene"          "pgraminisug99_eg_gene"     
[37] "pnodorum_eg_gene"           "pstriiformis_eg_gene"      
[39] "pteres_eg_gene"             "ptriticina_eg_gene"        
[41] "ptriticirepentis_eg_gene"   "scerevisiae_eg_gene"       
[43] "scryophilus_eg_gene"        "sjaponicus_eg_gene"        
[45] "soctosporus_eg_gene"        "spombe_eg_gene"            
[47] "sreilianum_eg_gene"         "ssclerotiorum_eg_gene"     
[49] "tmelanosporum_eg_gene"      "treesei_eg_gene"           
[51] "tvirens_eg_gene"            "umaydis_eg_gene"           
[53] "vdahliae_eg_gene"           "vdahliaejr2_eg_gene"       
[55] "ylipolytica_eg_gene"        "ztritici_eg_gene"          
> yeast_txdb <- makeTxDbFromBiomart(biomart="fungi_mart",
+                                   dataset="scerevisiae_eg_gene",
+                                   host="fungi.ensembl.org")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in function (type, msg, asError = TRUE)  : 
  Server denied you to change to the given directory
Calls: makeTxDbFromBiomart ... ls_ftp_url -> getURL -> curlPerform ->  -> fun
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.


Installation output

GenomicFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GenomicFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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)

Tests output

GenomicFeatures.Rcheck/tests/run_unitTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
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, 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, 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
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
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... Error in x$.self$finalize() : attempt to apply non-function
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.
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
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
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 -- Wed Oct 16 02:06:35 2019 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 
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.
> 
> proc.time()
   user  system elapsed 
142.921   1.486 163.050 

Example timings

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.0670.0000.073
TxDb-class0.7350.0360.771
as-format-methods1.3750.0361.417
coordinate-mapping-methods72.029 2.10877.194
coverageByTranscript32.632 2.17434.866
disjointExons000
exonicParts52.016 0.09852.160
extractTranscriptSeqs12.000 0.02412.055
extractUpstreamSeqs1.1840.0321.217
features0.1120.0000.139
getPromoterSeq-methods0.7050.0040.709
id2name0.2130.0000.213
makeFeatureDbFromUCSC 45.365 0.471127.017
makeTxDb0.120.000.12