| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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 | ||||
|
To the developers/maintainers of the GenomicFeatures package: Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 42/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| GenomicFeatures 1.53.0 (landing page) H. Pagès
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | ERROR | ||||||||
| Package: GenomicFeatures |
| Version: 1.53.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings GenomicFeatures_1.53.0.tar.gz |
| StartedAt: 2023-06-01 13:07:44 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 13:28:48 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 1264.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicFeatures.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings GenomicFeatures_1.53.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/GenomicFeatures.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.53.0’
* 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 ... OK
* 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 loading without being on the library search path ... 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:
‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
‘AnnotationDbi:::.valid.metadata.table’
‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
‘BiocGenerics:::testPackage’ ‘GenomeInfoDb:::check_tax_id’
‘GenomeInfoDb:::getSeqlevelsReplacementMode’
‘GenomeInfoDb:::lookup_organism_by_tax_id’
‘GenomeInfoDb:::lookup_tax_id_by_organism’
‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
‘GenomeInfoDb:::normarg_new2old’
‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
‘GenomicRanges:::unsafe.transcriptWidths’
‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’
‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’
‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’
‘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 ... WARNING
checkRd: (5) FeatureDb-class.Rd:31-34: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:30-33: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:34-39: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:40-43: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:44-52: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:53-59: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:60-65: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:66-71: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:72-80: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:21-25: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:26-50: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:51-55: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:56-62: \item in \describe must have non-empty label
* 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: makeTxDbFromUCSC
> ### Title: Make a TxDb object from annotations available at the UCSC Genome
> ### Browser
> ### Aliases: supportedUCSCtables browseUCSCtrack makeTxDbFromUCSC
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
>
> ## Use ucscGenomes() from the rtracklayer package to display the list of
> ## genomes available at UCSC:
> library(rtracklayer)
> ucscGenomes()[ , "db"]
[1] "ailMel1" "allMis1" "anoCar1" "anoCar2" "anoGam1"
[6] "anoGam3" "apiMel1" "apiMel2" "aplCal1" "aptMan1"
[11] "aquChr2" "balAcu1" "bisBis1" "bosTau2" "bosTau3"
[16] "bosTau4" "bosTau6" "bosTau7" "bosTau8" "bosTau9"
[21] "braFlo1" "caeJap1" "caePb1" "caePb2" "caeRem2"
[26] "caeRem3" "calJac1" "calJac3" "calJac4" "calMil1"
[31] "canFam1" "canFam2" "canFam3" "canFam4" "canFam5"
[36] "canFam6" "cavPor3" "cb1" "cb3" "ce10"
[41] "ce11" "ce2" "ce4" "ce6" "cerSim1"
[46] "chlSab2" "choHof1" "chrPic1" "ci1" "ci2"
[51] "ci3" "criGri1" "criGriChoV1" "criGriChoV2" "danRer10"
[56] "danRer11" "danRer3" "danRer4" "danRer5" "danRer6"
[61] "danRer7" "dasNov3" "dipOrd1" "dm1" "dm2"
[66] "dm3" "dm6" "dp2" "dp3" "droAna1"
[71] "droAna2" "droEre1" "droGri1" "droMoj1" "droMoj2"
[76] "droPer1" "droSec1" "droSim1" "droVir1" "droVir2"
[81] "droYak1" "droYak2" "eboVir3" "echTel1" "echTel2"
[86] "enhLutNer1" "equCab1" "equCab2" "equCab3" "eriEur1"
[91] "eriEur2" "felCat3" "felCat4" "felCat5" "felCat8"
[96] "felCat9" "fr1" "fr2" "fr3" "gadMor1"
[101] "galGal2" "galGal3" "galGal4" "galGal5" "galGal6"
[106] "galVar1" "gasAcu1" "geoFor1" "gorGor3" "gorGor4"
[111] "gorGor5" "gorGor6" "hetGla1" "hetGla2" "hg16"
[116] "hg17" "hg18" "hg19" "hg38" "hs1"
[121] "latCha1" "loxAfr3" "macEug2" "macFas5" "manPen1"
[126] "melGal1" "melGal5" "melUnd1" "micMur1" "micMur2"
[131] "mm10" "mm39" "mm7" "mm8" "mm9"
[136] "monDom1" "monDom4" "monDom5" "mpxvRivers" "musFur1"
[141] "nanPar1" "nasLar1" "neoSch1" "nomLeu1" "nomLeu2"
[146] "nomLeu3" "ochPri2" "ochPri3" "oreNil2" "ornAna1"
[151] "ornAna2" "oryCun2" "oryLat2" "otoGar3" "oviAri1"
[156] "oviAri3" "oviAri4" "panPan1" "panPan2" "panPan3"
[161] "panTro1" "panTro2" "panTro3" "panTro4" "panTro5"
[166] "panTro6" "papAnu2" "papAnu4" "papHam1" "petMar1"
[171] "petMar2" "petMar3" "ponAbe2" "ponAbe3" "priPac1"
[176] "proCap1" "pteVam1" "rheMac10" "rheMac2" "rheMac3"
[181] "rheMac8" "rhiRox1" "rn3" "rn4" "rn5"
[186] "rn6" "rn7" "sacCer1" "sacCer2" "sacCer3"
[191] "saiBol1" "sarHar1" "sorAra1" "sorAra2" "speTri2"
[196] "strPur1" "strPur2" "susScr11" "susScr2" "susScr3"
[201] "taeGut1" "taeGut2" "tarSyr1" "tarSyr2" "tetNig1"
[206] "tetNig2" "thaSir1" "triMan1" "tupBel1" "turTru2"
[211] "vicPac1" "vicPac2" "wuhCor1" "xenLae2" "xenTro1"
[216] "xenTro10" "xenTro2" "xenTro3" "xenTro7" "xenTro9"
>
> ## Display the list of tables known to work with makeTxDbFromUCSC():
> supportedUCSCtables("hg38")
tablename track subtrack
1 knownGene GENCODE V43 <NA>
2 ncbiRefSeq NCBI RefSeq RefSeq All
3 ncbiRefSeqCurated NCBI RefSeq RefSeq Curated
4 ncbiRefSeqPredicted NCBI RefSeq RefSeq Predicted
5 ncbiRefSeqOther NCBI RefSeq RefSeq Other
6 refGene NCBI RefSeq UCSC RefSeq
7 ncbiRefSeqSelect NCBI RefSeq RefSeq Select+MANE
8 ncbiRefSeqHgmd NCBI RefSeq RefSeq HGMD
9 xenoRefGene Other RefSeq <NA>
10 wgEncodeGencodeBasicV34 All GENCODE V34 Basic
11 wgEncodeGencodeCompV34 All GENCODE V34 Comprehensive
12 wgEncodeGencodePseudoGeneV34 All GENCODE V34 Pseudogenes
13 wgEncodeGencode2wayConsPseudoV34 All GENCODE V34 2-way Pseudogenes
14 wgEncodeGencodePolyaV34 All GENCODE V34 PolyA
15 wgEncodeGencodeBasicV33 All GENCODE V33 Basic
16 wgEncodeGencodeCompV33 All GENCODE V33 Comprehensive
17 wgEncodeGencodePseudoGeneV33 All GENCODE V33 Pseudogenes
18 wgEncodeGencode2wayConsPseudoV33 All GENCODE V33 2-way Pseudogenes
19 wgEncodeGencodePolyaV33 All GENCODE V33 PolyA
20 wgEncodeGencodeBasicV31 All GENCODE V31 Basic
21 wgEncodeGencodeCompV31 All GENCODE V31 Comprehensive
22 wgEncodeGencodePseudoGeneV31 All GENCODE V31 Pseudogenes
23 wgEncodeGencode2wayConsPseudoV31 All GENCODE V31 2-way Pseudogenes
24 wgEncodeGencodePolyaV31 All GENCODE V31 PolyA
25 wgEncodeGencodeBasicV29 All GENCODE V29 Basic
26 wgEncodeGencodeCompV29 All GENCODE V29 Comprehensive
27 wgEncodeGencodePseudoGeneV29 All GENCODE V29 Pseudogenes
28 wgEncodeGencode2wayConsPseudoV29 All GENCODE V29 2-way Pseudogenes
29 wgEncodeGencodePolyaV29 All GENCODE V29 PolyA
30 wgEncodeGencodeBasicV28 All GENCODE V28 Basic
31 wgEncodeGencodeCompV28 All GENCODE V28 Comprehensive
32 wgEncodeGencodePseudoGeneV28 All GENCODE V28 Pseudogenes
33 wgEncodeGencode2wayConsPseudoV28 All GENCODE V28 2-way Pseudogenes
34 wgEncodeGencodePolyaV28 All GENCODE V28 PolyA
35 wgEncodeGencodeBasicV27 All GENCODE V27 Basic
36 wgEncodeGencodeCompV27 All GENCODE V27 Comprehensive
37 wgEncodeGencodePseudoGeneV27 All GENCODE V27 Pseudogenes
38 wgEncodeGencode2wayConsPseudoV27 All GENCODE V27 2-way Pseudogenes
39 wgEncodeGencodePolyaV27 All GENCODE V27 PolyA
40 wgEncodeGencodeBasicV26 All GENCODE V26 Basic
41 wgEncodeGencodeCompV26 All GENCODE V26 Comprehensive
42 wgEncodeGencodePseudoGeneV26 All GENCODE V26 Pseudogenes
43 wgEncodeGencode2wayConsPseudoV26 All GENCODE V26 2-way Pseudogenes
44 wgEncodeGencodePolyaV26 All GENCODE V26 PolyA
45 wgEncodeGencodeBasicV25 All GENCODE V25 Basic
46 wgEncodeGencodeCompV25 All GENCODE V25 Comprehensive
47 wgEncodeGencodePseudoGeneV25 All GENCODE V25 Pseudogenes
48 wgEncodeGencode2wayConsPseudoV25 All GENCODE V25 2-way Pseudogenes
49 wgEncodeGencodePolyaV25 All GENCODE V25 PolyA
50 wgEncodeGencodeBasicV24 All GENCODE V24 Basic
51 wgEncodeGencodeCompV24 All GENCODE V24 Comprehensive
52 wgEncodeGencodePseudoGeneV24 All GENCODE V24 Pseudogenes
53 wgEncodeGencode2wayConsPseudoV24 All GENCODE V24 2-way Pseudogenes
54 wgEncodeGencodePolyaV24 All GENCODE V24 PolyA
55 wgEncodeGencodeBasicV23 All GENCODE V23 Basic
56 wgEncodeGencodeCompV23 All GENCODE V23 Comprehensive
57 wgEncodeGencodePseudoGeneV23 All GENCODE V23 Pseudogenes
58 wgEncodeGencode2wayConsPseudoV23 All GENCODE V23 2-way Pseudogenes
59 wgEncodeGencodePolyaV23 All GENCODE V23 PolyA
60 wgEncodeGencodeBasicV22 All GENCODE V22 Basic
61 wgEncodeGencodeCompV22 All GENCODE V22 Comprehensive
62 wgEncodeGencodePseudoGeneV22 All GENCODE V22 Pseudogenes
63 wgEncodeGencode2wayConsPseudoV22 All GENCODE V22 2-way Pseudogenes
64 wgEncodeGencodePolyaV22 All GENCODE V22 PolyA
65 wgEncodeGencodeBasicV20 GENCODE V20 (Ensembl 76) Basic
66 wgEncodeGencodeCompV20 GENCODE V20 (Ensembl 76) Comprehensive
67 wgEncodeGencodePseudoGeneV20 GENCODE V20 (Ensembl 76) Pseudogenes
68 wgEncodeGencode2wayConsPseudoV20 GENCODE V20 (Ensembl 76) 2-way Pseudogenes
69 wgEncodeGencodePolyaV20 GENCODE V20 (Ensembl 76) PolyA
70 augustusGene AUGUSTUS <NA>
71 ccdsGene CCDS <NA>
72 geneid Geneid Genes <NA>
73 genscan Genscan Genes <NA>
74 knownGeneOld12 Old UCSC Genes <NA>
75 sgpGene SGP Genes <NA>
76 sibGene SIB Genes <NA>
> supportedUCSCtables("hg19")
tablename track subtrack
1 knownGene UCSC Genes <NA>
2 ncbiRefSeq NCBI RefSeq RefSeq All
3 ncbiRefSeqCurated NCBI RefSeq RefSeq Curated
4 ncbiRefSeqPredicted NCBI RefSeq RefSeq Predicted
5 ncbiRefSeqOther NCBI RefSeq RefSeq Other
6 refGene NCBI RefSeq UCSC RefSeq
7 ncbiRefSeqSelect NCBI RefSeq RefSeq Select
8 ncbiRefSeqHgmd NCBI RefSeq RefSeq HGMD
9 xenoRefGene Other RefSeq <NA>
10 acembly AceView Genes <NA>
11 augustusGene AUGUSTUS <NA>
12 ccdsGene CCDS <NA>
13 ensGene Ensembl Genes <NA>
14 exoniphy Exoniphy <NA>
15 wgEncodeGencodeBasicV34lift37 GENCODE V34lift37 Basic
16 wgEncodeGencodeCompV34lift37 GENCODE V34lift37 Comprehensive
17 wgEncodeGencodePseudoGeneV34lift37 GENCODE V34lift37 Pseudogenes
18 wgEncodeGencodeBasicV33lift37 GENCODE V33lift37 Basic
19 wgEncodeGencodeCompV33lift37 GENCODE V33lift37 Comprehensive
20 wgEncodeGencodePseudoGeneV33lift37 GENCODE V33lift37 Pseudogenes
21 wgEncodeGencodeBasicV31lift37 GENCODE V31lift37 Basic
22 wgEncodeGencodeCompV31lift37 GENCODE V31lift37 Comprehensive
23 wgEncodeGencodePseudoGeneV31lift37 GENCODE V31lift37 Pseudogenes
24 wgEncodeGencodeBasicV28lift37 GENCODE V28lift37 Basic
25 wgEncodeGencodeCompV28lift37 GENCODE V28lift37 Comprehensive
26 wgEncodeGencodePseudoGeneV28lift37 GENCODE V28lift37 Pseudogenes
27 wgEncodeGencodeBasicV27lift37 GENCODE Gene V27lift37 Basic
28 wgEncodeGencodeCompV27lift37 GENCODE Gene V27lift37 Comprehensive
29 wgEncodeGencodePseudoGeneV27lift37 GENCODE Gene V27lift37 Pseudogenes
30 wgEncodeGencodeBasicV24lift37 GENCODE Gene V24lift37 Basic
31 wgEncodeGencodeCompV24lift37 GENCODE Gene V24lift37 Comprehensive
32 wgEncodeGencodePseudoGeneV24lift37 GENCODE Gene V24lift37 Pseudogenes
33 wgEncodeGencodeBasicV19 GENCODE Genes V19 Basic
34 wgEncodeGencodeCompV19 GENCODE Genes V19 Comprehensive
35 wgEncodeGencodePseudoGeneV19 GENCODE Genes V19 Pseudogenes
36 wgEncodeGencode2wayConsPseudoV19 GENCODE Genes V19 2-way Pseudogenes
37 wgEncodeGencodePolyaV19 GENCODE Genes V19 PolyA
38 wgEncodeGencodeBasicV17 GENCODE Genes V17 Basic
39 wgEncodeGencodeCompV17 GENCODE Genes V17 Comprehensive
40 wgEncodeGencodePseudoGeneV17 GENCODE Genes V17 Pseudogenes
41 wgEncodeGencode2wayConsPseudoV17 GENCODE Genes V17 2-way Pseudogenes
42 wgEncodeGencodePolyaV17 GENCODE Genes V17 PolyA
43 wgEncodeGencodeBasicV14 GENCODE Genes V14 Basic
44 wgEncodeGencodeCompV14 GENCODE Genes V14 Comprehensive
45 wgEncodeGencodePseudoGeneV14 GENCODE Genes V14 Pseudogenes
46 wgEncodeGencode2wayConsPseudoV14 GENCODE Genes V14 2-way Pseudogenes
47 wgEncodeGencodePolyaV14 GENCODE Genes V14 PolyA
48 wgEncodeGencodeBasicV7 GENCODE Genes V7 Basic
49 wgEncodeGencodeCompV7 GENCODE Genes V7 Comprehensive
50 wgEncodeGencodePseudoGeneV7 GENCODE Genes V7 Pseudogenes
51 wgEncodeGencode2wayConsPseudoV7 GENCODE Genes V7 2-way Pseudogenes
52 wgEncodeGencodePolyaV7 GENCODE Genes V7 PolyA
53 geneid Geneid Genes <NA>
54 genscan Genscan Genes <NA>
55 nscanGene N-SCAN <NA>
56 knownGeneOld6 Old UCSC Genes <NA>
57 sgpGene SGP Genes <NA>
58 sibGene SIB Genes <NA>
59 vegaGene Vega Genes Vega Protein Genes
60 vegaPseudoGene Vega Genes Vega Pseudogenes
61 pseudoYale60 Yale Pseudo60 <NA>
>
> ## Open the UCSC track page for a given organism/table:
> browseUCSCtrack("hg38", tablename="knownGene")
> browseUCSCtrack("hg19", tablename="knownGene")
>
> browseUCSCtrack("hg38", tablename="ncbiRefSeqSelect")
> browseUCSCtrack("hg19", tablename="ncbiRefSeqSelect")
>
> browseUCSCtrack("hg19", tablename="pseudoYale60")
>
> browseUCSCtrack("sacCer3", tablename="ensGene")
>
> ## Retrieve a full transcript dataset for Yeast from UCSC:
> txdb1 <- makeTxDbFromUCSC("sacCer3", tablename="ensGene")
Download the ensGene table ... Error: Failed to connect: Lost connection to MySQL server at 'waiting for initial communication packet', system error: 110
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 ...
‘GenomicFeatures.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-testing/meat/GenomicFeatures.Rcheck/00check.log’
for details.
GenomicFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL GenomicFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * 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 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow"
Copyright (C) 2023 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, aperm, 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 object is masked from 'package:utils':
findMatches
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
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: 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.
6: 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
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 -- Thu Jun 1 13:27:53 2023
***********************************************
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 hg19's seqlevels from UCSC to NCBI style
3: In (function (seqlevels, genome, new_style) :
cannot switch some hg19's seqlevels from UCSC to NCBI style
>
> proc.time()
user system elapsed
126.845 1.965 195.477
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
| name | user | system | elapsed | |
| FeatureDb-class | 0.060 | 0.012 | 0.072 | |
| TxDb-class | 0.661 | 0.080 | 0.741 | |
| as-format-methods | 1.335 | 0.036 | 1.372 | |
| coordinate-mapping-methods | 50.483 | 3.106 | 58.004 | |
| coverageByTranscript | 74.957 | 1.932 | 76.894 | |
| exonicParts | 42.686 | 0.296 | 43.010 | |
| extendExonsIntoIntrons | 3.405 | 0.012 | 3.455 | |
| extractTranscriptSeqs | 12.369 | 0.116 | 12.635 | |
| extractUpstreamSeqs | 1.521 | 0.068 | 1.623 | |
| features | 0.073 | 0.000 | 0.073 | |
| getPromoterSeq-methods | 0.835 | 0.000 | 0.845 | |
| id2name | 0.213 | 0.004 | 0.216 | |
| makeFeatureDbFromUCSC | 82.137 | 1.233 | 109.205 | |
| makeTxDb | 0.104 | 0.003 | 0.108 | |
| makeTxDbFromBiomart | 65.088 | 0.935 | 394.487 | |
| makeTxDbFromEnsembl | 0 | 0 | 0 | |
| makeTxDbFromGFF | 8.478 | 0.004 | 8.494 | |
| makeTxDbFromGRanges | 3.323 | 0.000 | 3.325 | |