GenomicFeatures 1.24.5
Bioconductor Package Maintainer
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 119545 / Revision: 122332 | | Last Changed Date: 2016-07-22 01:16:59 -0700 (Fri, 22 Jul 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | TIMEOUT | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.24.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.24.5’
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
‘AnnotationDbi:::.valid.metadata.table’
‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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: makeFeatureDbFromUCSC
> ### Title: Making a FeatureDb object from annotations available at the UCSC
> ### Genome Browser
> ### Aliases: supportedUCSCFeatureDbTracks supportedUCSCFeatureDbTables
> ### UCSCFeatureDbTableSchema makeFeatureDbFromUCSC
>
> ### ** Examples
>
> ## Display the list of genomes available at UCSC:
> library(GenomicFeatures)
> library(rtracklayer)
> ucscGenomes()[ , "db"]
[1] "hg38" "hg19" "hg18" "hg17" "hg16" "vicPac2"
[7] "vicPac1" "dasNov3" "papHam1" "panPan1" "aptMan1" "otoGar3"
[13] "papAnu2" "felCat8" "felCat5" "felCat4" "felCat3" "panTro4"
[19] "panTro3" "panTro2" "panTro1" "criGri1" "bosTau8" "bosTau7"
[25] "bosTau6" "bosTau4" "bosTau3" "bosTau2" "macFas5" "canFam3"
[31] "canFam2" "canFam1" "turTru2" "loxAfr3" "musFur1" "nomLeu3"
[37] "nomLeu2" "nomLeu1" "gorGor4" "gorGor3" "cavPor3" "eriEur2"
[43] "eriEur1" "equCab2" "equCab1" "dipOrd1" "galVar1" "triMan1"
[49] "calJac3" "calJac1" "pteVam1" "myoLuc2" "balAcu1" "mm10"
[55] "mm9" "mm8" "mm7" "micMur2" "micMur1" "hetGla2"
[61] "hetGla1" "monDom5" "monDom4" "monDom1" "ponAbe2" "ailMel1"
[67] "susScr3" "susScr2" "ochPri3" "ochPri2" "ornAna2" "ornAna1"
[73] "oryCun2" "rn6" "rn5" "rn4" "rn3" "rheMac8"
[79] "rheMac3" "rheMac2" "proCap1" "oviAri3" "oviAri1" "sorAra2"
[85] "sorAra1" "choHof1" "speTri2" "saiBol1" "tarSyr2" "tarSyr1"
[91] "sarHar1" "echTel2" "echTel1" "tupBel1" "macEug2" "cerSim1"
[97] "allMis1" "gadMor1" "melUnd1" "galGal5" "galGal4" "galGal3"
[103] "galGal2" "latCha1" "calMil1" "fr3" "fr2" "fr1"
[109] "petMar2" "petMar1" "anoCar2" "anoCar1" "oryLat2" "geoFor1"
[115] "oreNil2" "chrPic1" "gasAcu1" "tetNig2" "tetNig1" "melGal1"
[121] "xenTro7" "xenTro3" "xenTro2" "xenTro1" "taeGut2" "taeGut1"
[127] "danRer10" "danRer7" "danRer6" "danRer5" "danRer4" "danRer3"
[133] "ci2" "ci1" "braFlo1" "strPur2" "strPur1" "apiMel2"
[139] "apiMel1" "anoGam1" "droAna2" "droAna1" "droEre1" "droGri1"
[145] "dm6" "dm3" "dm2" "dm1" "droMoj2" "droMoj1"
[151] "droPer1" "dp3" "dp2" "droSec1" "droSim1" "droVir2"
[157] "droVir1" "droYak2" "droYak1" "caePb2" "caePb1" "cb3"
[163] "cb1" "ce11" "ce10" "ce6" "ce4" "ce2"
[169] "caeJap1" "caeRem3" "caeRem2" "priPac1" "aplCal1" "sacCer3"
[175] "sacCer2" "sacCer1" "eboVir3"
>
> ## Display the list of Tracks supported by makeFeatureDbFromUCSC():
> # supportedUCSCFeatureDbTracks("mm10")
>
> ## Display the list of tables supported by your track:
> supportedUCSCFeatureDbTables(genome="mm10",
+ track="qPCR Primers")
Error in `genome<-`(`*tmp*`, value = "mm10") :
Failed to set session genome to 'mm10'
Calls: supportedUCSCFeatureDbTables -> genome<- -> genome<-
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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.