BioC 2.14: CHECK report for annotate on petty

Package: annotate

Version: 1.42.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.42.1.tar.gz

StartedAt: 2014-10-07 20:40:26 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:56:14 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 948.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: annotate.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.42.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/annotate.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.42.1’
* 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 ... [19s/19s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::makeFlatBimapUsingSelect’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... 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: pm.getabst
> ### Title: Obtain the abstracts for a set PubMed list.
> ### Aliases: pm.getabst
> ### Keywords: manip
> 
> ### ** Examples
> 
>   library("hgu95av2.db")
Loading required package: org.Hs.eg.db
>   hoxa9 <- "37806_at"
>   absts <- pm.getabst(hoxa9, "hgu95av2")
Loading required package: XML
Warning in file(file, "r") : cannot open: HTTP status was '0 (null)'
Execution halted

* 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)

name	user	system	elapsed
ACCNUMStats	4.933	0.070	5.028
GO2heatmap	0.363	0.033	0.518
GOmnplot	0.208	0.020	0.232
HTMLPage-class	0.002	0.000	0.001
LL2homology	0.001	0.000	0.002
PMIDAmat	0.433	0.011	0.566
PWAmat	10.979	0.150	11.328
UniGeneQuery	0.005	0.001	0.006
accessionToUID	0.436	0.031	2.592
annPkgName	0.002	0.000	0.003
aqListGOIDs	0.998	0.105	1.204
blastSequences	2.441	0.103	584.179
buildChromLocation	4.424	0.051	5.090
buildPubMedAbst	0.141	0.003	0.561
chrCats	42.225	0.136	43.371
chromLocation-class	4.287	0.016	4.336
compatibleVersions	0.196	0.010	0.209
dropECode	0.192	0.007	0.202
entrezGeneByID	0.003	0.000	0.003
entrezGeneQuery	0.004	0.000	0.004
filterGOByOntology	0.190	0.012	0.204
findNeighbors	0.096	0.007	0.150
genbank	0.363	0.017	1.428
getAnnMap	0.184	0.027	0.641
getEvidence	0.209	0.010	0.219
getGOTerm	0.503	0.012	0.517
getOntology	0.189	0.008	0.198
getPMInfo	1.508	0.008	2.203
getSYMBOL	0.459	0.026	0.501
getSeq4Acc	0.006	0.001	0.185
hasGOannote	0.105	0.003	0.108
hgByChroms	0.023	0.005	0.029
hgCLengths	0.004	0.001	0.004
hgu95Achroloc	0.132	0.012	0.144
hgu95Achrom	0.101	0.012	0.113
hgu95All	0.116	0.013	0.128
hgu95Asym	0.120	0.013	0.132
homoData-class	0.009	0.000	0.009
htmlpage	0.066	0.002	0.085
isValidkey	0.001	0.001	0.002
makeAnchor	0.002	0.000	0.002
organism	4.543	0.019	4.604
p2LL	0.001	0.001	0.001
pm.abstGrep	2.283	0.035	3.520