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BioC 2.12: CHECK report for annotate on petty

This page was generated on 2013-10-09 09:39:20 -0700 (Wed, 09 Oct 2013).

Package 35/671HostnameOS / ArchBUILDCHECKBUILD BIN
annotate 1.38.0
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/annotate
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ ERROR ] OK 

Summary

Package: annotate
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.38.0.tar.gz
StartedAt: 2013-10-08 21:32:40 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:38:51 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 371.9 seconds
RetCode: 1
Status:  ERROR 
CheckDir: annotate.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/annotate.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.38.0'
* 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 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 ... [19s/19s] OK
* checking installed package size ... OK
* checking package 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* 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
[[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

annotate.Rcheck/00install.out:

* installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotate)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats4.5790.0714.662
GO2heatmap0.3460.0230.372
GOmnplot0.1790.0240.203
HTMLPage-class0.0220.0020.024
LL2homology0.2450.0020.247
PMIDAmat0.3730.0180.438
PWAmat11.123 0.15811.344
UniGeneQuery0.0060.0050.011
accessionToUID0.3710.0293.287
annPkgName0.0030.0030.006
aqListGOIDs0.9210.0811.006