AnnotationDbi 1.13.14
Biocore Team c/o BioC user list
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi | | Last Changed Rev: 52015 / Revision: 53255 | | Last Changed Date: 2011-01-21 18:35:05 -0800 (Fri, 21 Jan 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | TIMEOUT | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | TIMEOUT | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | TIMEOUT | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | ERROR | OK |
* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/AnnotationDbi.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.13.14’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘AnnotationDbi’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
.getSubNodeInfo: no visible global function definition for ‘Stop’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'buildEntrezGeneDb':
getGeneStuff
Code: function(entrezGenes, dir = "files")
Docs: function(entrezGenes)
Argument names in code not in docs:
dir
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: org.Hs.eg.db
* checking examples ...sh: line 1: 27211 Bus error LANGUAGE=en '/Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R' --vanilla > 'AnnotationDbi-Ex.Rout' 2>&1 < AnnotationDbi-Ex.R
ERROR
Running examples in ‘AnnotationDbi-Ex.R’ failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildEntrezGeneDb
> ### Title: builds an Entrez Gene centric organism database
> ### Aliases: getGeneStuff buildEntrezGeneDb getEntrezGenesFromTaxId
> ### Keywords: interface
>
> ### ** Examples
>
> ## seems that some of the EGs are not from the taxid specified? (more tests)
> ## EGs <- getEntrezGenesFromTaxId(taxId)
> ## temporarily, lets use known EGs to run tests
> library(org.Hs.eg.db)
> EGs <- Lkeys(org.Hs.egCHR)
> #EGs <- EGs[c(1:10)] ## Obviously NOT a typical step.
> system.time(buildEntrezGeneDb(EGs,file=tempfile()))
Loading required package: XML
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936288 51.8 3094291 82.7 3094291 82.7
Vcells 1934075 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936276 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936285 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936294 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936303 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936312 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
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Vcells 1934052 14.8 5634721 43.0 18662514 142.4
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used (Mb) gc trigger (Mb) max used (Mb)
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Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936348 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936357 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936366 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936375 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936384 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936393 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936402 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936411 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936420 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936429 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936438 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936447 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936456 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936465 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936474 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936483 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936492 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936501 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936510 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936519 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936528 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936537 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936546 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936555 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936564 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936573 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
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Ncells 1936582 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936591 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936600 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936609 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936618 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936627 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936636 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936645 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936654 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1936663 51.8 3094291 82.7 3094291 82.7
Vcells 1934052 14.8 5634721 43.0 18662514 142.4
R(27211) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(27211) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(27211) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(27211) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
parser error : out of memory error
parser error : out of memory error
*** caught bus error ***
address 0x1c, cause 'non-existent physical address'
Traceback:
1: .Call("RS_XML_createDocFromNode", node, PACKAGE = "XML")
2: FUN(X[[211L]], ...)
3: lapply(getNodeSet(EGSet, "//Entrezgene"), xmlDoc)
4: getGeneStuff(EGChunk)
5: getDataAndAddToDb(chunk, con)
6: buildEntrezGeneDb(EGs, file = tempfile())
7: system.time(buildEntrezGeneDb(EGs, file = tempfile()))
aborting ...
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Creating a new generic function for "toString" in "AnnotationDbi"
Creating a new generic function for "rev" in "AnnotationDbi"
Creating a new generic function for "colnames" in "AnnotationDbi"
Creating a new generic function for "subset" in "AnnotationDbi"
Creating a new generic function for "head" in "AnnotationDbi"
Creating a new generic function for "tail" in "AnnotationDbi"
Creating a new generic function for "nrow" in "AnnotationDbi"
Creating a new generic function for "ncol" in "AnnotationDbi"
Creating a new generic function for "as.list" in "AnnotationDbi"
Creating a new generic function for "ls" in "AnnotationDbi"
Creating a new generic function for "mget" in "AnnotationDbi"
Creating a new generic function for "eapply" in "AnnotationDbi"
Creating a new generic function for "get" in "AnnotationDbi"
Creating a new generic function for "exists" in "AnnotationDbi"
Creating a new generic function for "sample" in "AnnotationDbi"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (AnnotationDbi)