annotate 1.36.0
Bioconductor Package Maintainer
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/annotate | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/annotate.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.36.0'
* 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 whether package 'annotate' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for unstated 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'annotate-Ex.R' failed
The error most likely occurred in:
> 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
[[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 48 columns
aln
[1] TTTAATTAAATATTA-AGTTATATATATATATATATATAACTATATAT
[2] TTTAATTGACTCTTATAGTTATATATGTACCTAT-TATAACTATATAT
>
> ## 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
[[10]]
DNAMultipleAlignment with 2 rows and 18 columns
aln
[1] CTTCATTTACCCAAAATG
[2] CTTCATTTACCCAAAATG
>
> ## 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: failed to load HTTP resource
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
chrCats 23.68 0.00 23.68
probesByLL 9.39 0.02 9.42
PWAmat 7.14 0.04 7.19
pm.titles 4.49 0.01 5.61
pm.getabst 4.40 0.00 5.52
pm.abstGrep 4.37 0.00 5.73
blastSequences 1.78 0.03 114.24
install for i386
* installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GOusage.Rnw'
'annotate.Rnw'
'chromLoc.Rnw'
'prettyOutput.Rnw'
'query.Rnw'
'useDataPkgs.Rnw'
'useHomology.Rnw'
'useProbeInfo.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'annotate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotate' as annotate_1.36.0.zip
* DONE (annotate)