annotate 1.40.1
Bioconductor Package Maintainer
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/annotate | | Last Changed Rev: 86822 / Revision: 88450 | | Last Changed Date: 2014-02-25 18:15:11 -0800 (Tue, 25 Feb 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ ERROR ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/annotate.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.40.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘annotate’ can be installed ... [15s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘AnnotationDbi’ ‘Biobase’ ‘XML’
A package should be listed in only one of these fields.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘annotate.Rnw’, ‘chromLoc.Rnw’, ‘GOusage.Rnw’, ‘prettyOutput.Rnw’,
‘query.Rnw’, ‘useDataPkgs.Rnw’, ‘useHomology.Rnw’, ‘useProbeInfo.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... ERROR
Running examples in ‘annotate-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blastSequences
> ### Title: Run a blast query to NCBI for either a string or an entrez gene
> ### ID and then return a series of MultipleAlignment objects.
> ### Aliases: blastSequences
>
> ### ** Examples
>
> ## x can be an entrez gene ID
> blastSequences(17702)
Loading required package: XML
Loading required package: Biostrings
Loading required package: IRanges
Loading required package: XVector
[[1]]
DNAMultipleAlignment with 2 rows and 161 columns
aln
[1] CCTTCGAAGGCCAAAATCGGACCAAAATGGCCTTCA...ACATGTGGCTAAATGCGCGAAACTAAGTCAAATGAG
[2] CCTTCGAAGGCCAAAATCGGACCAAAATGGCCTTCA...ACATGTGGCTAAATGCGCGAAACTAAGTCAAATGAG
[[2]]
DNAMultipleAlignment with 2 rows and 133 columns
aln
[1] GGCCTTCATTTACCCAAAATGGGTTTCAAAGCATAT...ACATGTGGCTAAATGCGGGAAATTAAGTGAAATGAG
[2] GGCCTTCATTTACCCAAAATGGGTTTCAAAGCATAT...ACATGTGGCTAAATGCGCGAAACTAAGTCAAATGAG
[[3]]
DNAMultipleAlignment with 2 rows and 140 columns
aln
[1] CCAAAATAGCCTTCATTTACCCAAAATAAGTTTCAA...ACATGTGGCTAAATGCGGGAAACTATGTGAAATGAG
[2] CCAAAATGGCCTTCATTTACCCAAAATGGGTTTCAA...ACATGTGGCTAAATGCGCGAAACTAAGTCAAATGAG
[[4]]
DNAMultipleAlignment with 2 rows and 131 columns
aln
[1] GGCCTTCATTTACCCAAAATGTGTTTCAAAGCATAT...TAACATGCGGGTAAATGCAAAAAACTAAGTGAATTG
[2] GGCCTTCATTTACCCAAAATGGGTTTCAAAGCATAT...TAACATGTGGCTAAATGCGCGAAACTAAGTCAAATG
[[5]]
DNAMultipleAlignment with 2 rows and 131 columns
aln
[1] GGCCTTCATTTACCCAAAATGTGTTTCGAAGCATAT...TAACATGCGGCTAAATGCAAAAAACTAAGTGAATTG
[2] GGCCTTCATTTACCCAAAATGGGTTTCAAAGCATAT...TAACATGTGGCTAAATGCGCGAAACTAAGTCAAATG
[[6]]
DNAMultipleAlignment with 2 rows and 155 columns
aln
[1] AAGTCTAAAATCGATCCTAAATGACCTTCATTTACC...AACATGTGGCTAAATGTGAGAATTTAGGGAAAATGA
[2] AAGGCCAAAATCGGACCAAAATGGCCTTCATTTACC...AACATGTGGCTAAATGCGCGAAACTAAGTCAAATGA
[[7]]
DNAMultipleAlignment with 2 rows and 155 columns
aln
[1] GAAAGTCTAAATCGGCCCTAAATGACCTTCATTTAC...AA-ATGTGGCTAAATGTGAGAATTTAAGGAAAATGA
[2] GAAGGCCAAAATCGGACCAAAATGGCCTTCATTTAC...AACATGTGGCTAAATGCGCGAAACTAAGTCAAATGA
[[8]]
DNAMultipleAlignment with 2 rows and 127 columns
aln
[1] AAGTCTAAAATCGGCCCTAAGTGACCTTCATTTACC...TGTAGCTATTAGTACTATATATATCTTAACATGTGG
[2] AAGGCCAAAATCGGACCAAAATGGCCTTCATTTACC...TGTACCTATTATAACTATATATGACCTAACATGTGG
[[9]]
DNAMultipleAlignment with 2 rows and 39 columns
aln
[1] ATATATGTACCTATTATATATATATATTATCAAACATGT
[2] ATATATGTACCTATTATAACTATATATGACCTAACATGT
[[10]]
DNAMultipleAlignment with 2 rows and 35 columns
aln
[1] TATAGTTATATATGTAGCTATTATTGCTACATATG
[2] TATAGTTATATATGTACCTATTATAACTATATATG
[[11]]
DNAMultipleAlignment with 2 rows and 43 columns
aln
[1] TGACTCATATAATTATATATGTATCTATTAATAACCTATGTAT
[2] TGACTCTTATAGTTATATATGTACCTATT-ATAA-CTATATAT
[[12]]
DNAMultipleAlignment with 2 rows and 39 columns
aln
[1] ATGACTGAACTTTAATTGACTCTATTCAGATATATATGT
[2] ATGAGTGAACTTTAATTGACTCT-TATAGTTATATATGT
>
> ## or x can be a sequence
> blastSequences(x = "GGCCTTCATTTACCCAAAATG")
[[1]]
DNAMultipleAlignment with 2 rows and 21 columns
aln
[1] GGCCTTCATTTACCCAAAATG
[2] GGCCTTCATTTACCCAAAATG
[[2]]
DNAMultipleAlignment with 2 rows and 21 columns
aln
[1] GGCCTTCATTTACCCAAAATG
[2] GGCCTTCATTTACCCAAAATG
[[3]]
DNAMultipleAlignment with 2 rows and 21 columns
aln
[1] GGCCTTCATTTACCCAAAATG
[2] GGCCTTCATTTACCCAAAATG
[[4]]
DNAMultipleAlignment with 2 rows and 21 columns
aln
[1] GGCCTTCATTTACCCAAAATG
[2] GGCCTTCATTTACCCAAAATG
[[5]]
DNAMultipleAlignment with 2 rows and 20 columns
aln
[1] GCCTTCATTTACCCAAAATG
[2] GCCTTCATTTACCCAAAATG
[[6]]
DNAMultipleAlignment with 2 rows and 20 columns
aln
[1] GCCTTCATTTACCCAAAATG
[2] GCCTTCATTTACCCAAAATG
[[7]]
DNAMultipleAlignment with 2 rows and 19 columns
aln
[1] GGCCTTCATTTACCCAAAA
[2] GGCCTTCATTTACCCAAAA
[[8]]
DNAMultipleAlignment with 2 rows and 19 columns
aln
[1] GGCCTTCATTTACCCAAAA
[2] GGCCTTCATTTACCCAAAA
[[9]]
DNAMultipleAlignment with 2 rows and 19 columns
aln
[1] GCCTTCATTTACCCAAAAT
[2] GCCTTCATTTACCCAAAAT
>
> ## hitListSize does not promise that you will get the number of matches you
> ## want.. It will just try to get that many.
> blastSequences(x = "GGCCTTCATTTACCCAAAATG", hitListSize="20")
Error in .tryParseResult(url1) :
no results after 5 attempts; please try again later
Calls: blastSequences -> .tryParseResult
Execution halted