| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:57:41 -0400 (Wed, 16 Oct 2019).
| Package 656/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFeatures 1.36.4 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK |  | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
| name | user | system | elapsed | |
| DEFAULT_CIRC_SEQS | 0 | 0 | 0 | |
| FeatureDb-class | 0.067 | 0.000 | 0.073 | |
| TxDb-class | 0.735 | 0.036 | 0.771 | |
| as-format-methods | 1.375 | 0.036 | 1.417 | |
| coordinate-mapping-methods | 72.029 | 2.108 | 77.194 | |
| coverageByTranscript | 32.632 | 2.174 | 34.866 | |
| disjointExons | 0 | 0 | 0 | |
| exonicParts | 52.016 | 0.098 | 52.160 | |
| extractTranscriptSeqs | 12.000 | 0.024 | 12.055 | |
| extractUpstreamSeqs | 1.184 | 0.032 | 1.217 | |
| features | 0.112 | 0.000 | 0.139 | |
| getPromoterSeq-methods | 0.705 | 0.004 | 0.709 | |
| id2name | 0.213 | 0.000 | 0.213 | |
| makeFeatureDbFromUCSC | 45.365 | 0.471 | 127.017 | |
| makeTxDb | 0.12 | 0.00 | 0.12 | |