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This page was generated on 2022-01-14 13:05:13 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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CHECK results for GenomicFeatures on nebbiolo2


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 751/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.46.3  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenomicFeatures
git_branch: RELEASE_3_14
git_last_commit: b646ba6
git_last_commit_date: 2021-12-23 11:51:00 -0500 (Thu, 23 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GenomicFeatures
Version: 1.46.3
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_1.46.3.tar.gz
StartedAt: 2022-01-13 07:43:20 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 07:57:29 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 848.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenomicFeatures.Rcheck
Warnings: NA

Command output

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###
### 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_1.46.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.46.3’
* 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 ... 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://"
Ensembl site unresponsive, trying uswest mirror
               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://"
Ensembl site unresponsive, trying asia mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate
Calls: useMart ... 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, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.


Installation output

GenomicFeatures.Rcheck/00install.out

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###
### 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)

Tests output

GenomicFeatures.Rcheck/tests/run_unitTests.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 useast mirror
Timing stopped at: 0.175 0.036 21.25
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 -- Thu Jan 13 07:57:22 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

Example timings

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings

nameusersystemelapsed
FeatureDb-class0.0540.0000.055
TxDb-class1.8770.0641.941
as-format-methods1.8840.1442.029
coordinate-mapping-methods65.038 3.98470.271
coverageByTranscript25.598 3.61229.210
exonicParts41.989 0.19242.182
extractTranscriptSeqs14.640 0.26014.901
extractUpstreamSeqs1.6660.0441.746
features0.1120.0000.112
getPromoterSeq-methods0.7030.0120.715
id2name0.260.000.26
makeFeatureDbFromUCSC 79.992 3.340203.861
makeTxDb0.0920.0000.092