annotate 1.46.1
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/annotate | | Last Changed Rev: 105987 / Revision: 109384 | | Last Changed Date: 2015-07-10 15:27:07 -0700 (Fri, 10 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.46.1.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.46.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/annotate.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.46.1'
* 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 whether package 'annotate' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'Biostrings' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'AnnotationDbi:::makeFlatBimapUsingSelect'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.blastSequencesToDNAMultipleAlignment: no visible global function
definition for 'xpathSApply'
.blastSequencesToDNAMultipleAlignment: no visible global function
definition for 'IRanges'
.blastSequencesToDataFrame: no visible global function definition for
'xpathSApply'
.blastSequencesToDataFrame: no visible global function definition for
'xmlToDataFrame'
.blastSequencesToDataFrame: no visible binding for global variable
'xpathSApply'
getGOChildren: no visible binding for global variable 'GOMFCHILDREN'
getGOChildren: no visible binding for global variable 'GOBPCHILDREN'
getGOChildren: no visible binding for global variable 'GOCCCHILDREN'
getGOOntology: no visible binding for global variable 'GOTERM'
getGOParents: no visible binding for global variable 'GOMFPARENTS'
getGOParents: no visible binding for global variable 'GOBPPARENTS'
getGOParents: no visible binding for global variable 'GOCCPARENTS'
getGOTerm: no visible binding for global variable 'GOTERM'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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, timeout=40, as="data.frame")
estimated response time 289 seconds
Error: 'blastSequences' timeout after 42 seconds
Execution halted
** running examples for arch 'x64' ... 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, timeout=40, as="data.frame")
estimated response time 221 seconds
Error: 'blastSequences' timeout after 43 seconds
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'annotate_unit_tests.R' [7s]
[7s] OK
** running tests for arch 'x64' ...
Running 'annotate_unit_tests.R' [8s]
[8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/annotate.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'annotate' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'annotate' as annotate_1.46.1.zip
* DONE (annotate)