Back to Multiple platform build/check report for BioC 3.15
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-26 11:07:44 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GenomicFeatures on riesling1


To the developers/maintainers of the GenomicFeatures package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFeatures.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 748/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.47.7  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenomicFeatures
git_branch: master
git_last_commit: dd8aaa6
git_last_commit_date: 2022-01-19 22:39:14 -0500 (Wed, 19 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GenomicFeatures
Version: 1.47.7
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFeatures.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicFeatures_1.47.7.tar.gz
StartedAt: 2022-01-25 19:03:28 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 19:15:48 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 740.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenomicFeatures.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFeatures.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicFeatures_1.47.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenomicFeatures.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.47.7'
* 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 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 ... WARNING
Missing link or links in documentation object 'as-format-methods.Rd':
  '[rtracklayer]{export}'

Missing link or links in documentation object 'makeTxDbFromGFF.Rd':
  '[rtracklayer]{import}'

Missing link or links in documentation object 'makeTxDbFromGRanges.Rd':
  '[rtracklayer]{import}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 105
2   ENSEMBL_MART_MOUSE      Mouse strains 105
3     ENSEMBL_MART_SNP  Ensembl Variation 105
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 105
> 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://"
> 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  version
28 celegans_gene_ensembl Caenorhabditis elegans genes (WBcel235) 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://"
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 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: 61451
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2022-01-25 19:12:07 -0500 (Tue, 25 Jan 2022)
# GenomicFeatures version at creation time: 1.47.7
# RSQLite version at creation time: 2.2.9
# 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 52
# 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: 2022-01-25 19:12:26 -0500 (Tue, 25 Jan 2022)
# GenomicFeatures version at creation time: 1.47.7
# RSQLite version at creation time: 2.2.9
# 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://"
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
> all(transcripts(yeast_txdb0) %in% transcripts(yeast_txdb))
[1] TRUE
> all(transcripts(yeast_txdb) %in% transcripts(yeast_txdb0))
[1] TRUE
> 
> ## -----------------------
> ## --- Ensembl Metazoa ---
> 
> ## The metazoa mart is slow and at the same time it doesn't seem to
> ## support requests that take more than 1 min at the moment. So a call to
> ## biomaRt::getBM() will fail with a "Timeout was reached" error if the
> ## requested data takes more than 1 min to download. This unfortunately
> ## happens with the example below so we don't try to run it for now.
> 
> ## Not run: 
> ##D   mart <- useMart(biomart="metazoa_mart", host="metazoa.ensembl.org")
> ##D   datasets <- listDatasets(mart)
> ##D   datasets$dataset
> ##D   worm_txdb <- makeTxDbFromBiomart(biomart="metazoa_mart",
> ##D                                    dataset="celegans_eg_gene",
> ##D                                    host="metazoa.ensembl.org")
> ##D   worm_txdb
> ##D 
> ##D   ## Note that even if the dataset for Worm on Ensembl Metazoa contains
> ##D   ## the same transcript as on the main Ensembl database, the transcript
> ##D   ## type might be annotated with slightly different terms (e.g. antisense
> ##D   ## vs antisense_RNA):
> ##D   filter <- list(tx_name="Y71G12B.44")
> ##D   transcripts(worm_txdb, filter=filter, columns=c("tx_name", "tx_type"))
> ##D   transcripts(txdb1, filter=filter, columns=c("tx_name", "tx_type"))
> ## End(Not run)
> ## ----------------------
> ## --- Ensembl Plants ---
> 
> ## Like the metazoa mart (see above), the plants mart is also slow and
> ## doesn't seem to support requests that take more than 1 min either.
> ## So we don't try to run the example below for now.
> 
> ## Not run: 
> ##D mart <- useMart(biomart="plants_mart", host="plants.ensembl.org")
> ##D datasets <- listDatasets(mart)
> ##D datasets[ , 1:2]
> ##D athaliana_txdb <- makeTxDbFromBiomart(biomart="plants_mart",
> ##D                                       dataset="athaliana_eg_gene",
> ##D                                       host="plants.ensembl.org")
> ##D athaliana_txdb
> ## End(Not run)
> ## ------------------------
> ## --- Ensembl Protists ---
> 
> mart <- useMart(biomart="protists_mart", host="protists.ensembl.org")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
> datasets <- listDatasets(mart)
> datasets$dataset
 [1] "alaibachii_eg_gene"      "bnatans_eg_gene"        
 [3] "ddiscoideum_eg_gene"     "ehistolytica_eg_gene"   
 [5] "ehuxleyi_eg_gene"        "glamblia_eg_gene"       
 [7] "gtheta_eg_gene"          "harabidopsidis_eg_gene" 
 [9] "lmajor_eg_gene"          "paphanidermatum_eg_gene"
[11] "parrhenomanes_eg_gene"   "pberghei_eg_gene"       
[13] "pchabaudi_eg_gene"       "pfalciparum_eg_gene"    
[15] "pinfestans_eg_gene"      "pirregulare_eg_gene"    
[17] "piwayamai_eg_gene"       "pkernoviae_eg_gene"     
[19] "pknowlesi_eg_gene"       "plateralis_eg_gene"     
[21] "pmultistriata_eg_gene"   "pparasitica_eg_gene"    
[23] "pramorum_eg_gene"        "psojae_eg_gene"         
[25] "ptetraurelia_eg_gene"    "ptricornutum_eg_gene"   
[27] "pultimum_eg_gene"        "pvexans_eg_gene"        
[29] "pvivax_eg_gene"          "tbrucei_eg_gene"        
[31] "tgondii_eg_gene"         "tpseudonana_eg_gene"    
[33] "tthermophila_eg_gene"   
> tgondii_txdb <- makeTxDbFromBiomart(biomart="protists_mart",
+                                     dataset="tgondii_eg_gene",
+                                     host="protists.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
> tgondii_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Toxoplasma gondii
# Taxonomy ID: 5811
# Resource URL: protists.ensembl.org:80
# BioMart database: protists_mart
# BioMart database version: Ensembl Protists Genes 52
# BioMart dataset: tgondii_eg_gene
# BioMart dataset description: Toxoplasma gondii ME49 genes (TGA4)
# BioMart dataset version: TGA4
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 8920
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2022-01-25 19:13:23 -0500 (Tue, 25 Jan 2022)
# GenomicFeatures version at creation time: 1.47.7
# RSQLite version at creation time: 2.2.9
# DBSCHEMAVERSION: 1.2
> 
> ## ---------------------------------------------------------------------
> ## C. USING AN Ensembl MIRROR
> ## ---------------------------------------------------------------------
> 
> ## You can use the 'host' argument to access the "ENSEMBL_MART_ENSEMBL"
> ## BioMart database at a mirror (e.g. at uswest.ensembl.org). A gotcha
> ## when doing this is that the name of the database on the mirror might
> ## be different! We can check this with listMarts() from the biomaRt
> ## package:
> listMarts(host="useast.ensembl.org")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://useast.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
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, 1 WARNING, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.


Installation output

GenomicFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GenomicFeatures' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicFeatures'
    finding HTML links ... done
    FeatureDb-class                         html  
    finding level-2 HTML links ... done

    TxDb-class                              html  
    as-format-methods                       html  
    coordinate-mapping-methods              html  
    coverageByTranscript                    html  
    disjointExons                           html  
    exonicParts                             html  
    extractTranscriptSeqs                   html  
    extractUpstreamSeqs                     html  
    features                                html  
    getPromoterSeq-methods                  html  
    id2name                                 html  
    makeFeatureDbFromUCSC                   html  
    makeTxDb                                html  
    makeTxDbFromBiomart                     html  
    makeTxDbFromEnsembl                     html  
    makeTxDbFromGFF                         html  
    makeTxDbFromGRanges                     html  
    makeTxDbFromUCSC                        html  
    makeTxDbPackage                         html  
    mapIdsToRanges                          html  
    mapRangesToIds                          html  
    microRNAs                               html  
    nearest-methods                         html  
    select-methods                          html  
    transcriptLengths                       html  
    transcriptLocs2refLocs                  html  
    transcripts                             html  
    transcriptsBy                           html  
    transcriptsByOverlaps                   html  
** 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)
Making 'packages.html' ... done

Tests output

GenomicFeatures.Rcheck/tests/run_unitTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.

> 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

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")'.

[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 ... 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
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.
5: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
6: 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.
7: 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.
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
'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 Jan 25 19:15:35 2022 
*********************************************** 
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 73 test functions, 0 errors, 0 failures
Number of test functions: 73 
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
  stop_codon. This information was ignored.
2: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
3: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
> 
> proc.time()
   user  system elapsed 
 103.04    3.42  129.20 

Example timings

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings

nameusersystemelapsed
FeatureDb-class0.050.000.05
TxDb-class0.980.071.06
as-format-methods1.230.121.36
coordinate-mapping-methods42.78 3.1449.31
coverageByTranscript15.89 6.8422.73
exonicParts32.53 4.7737.30
extractTranscriptSeqs8.740.419.14
extractUpstreamSeqs1.010.201.22
features0.050.000.05
getPromoterSeq-methods0.550.020.56
id2name0.140.000.14
makeFeatureDbFromUCSC 69.51 6.28136.98
makeTxDb0.130.000.14