GEOquery 2.36.0
Sean Davis
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GEOquery | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ ERROR ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf GEOquery.buildbin-libdir GEOquery.Rcheck && mkdir GEOquery.buildbin-libdir GEOquery.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOquery.buildbin-libdir GEOquery_2.36.0.tar.gz >GEOquery.Rcheck\00install.out 2>&1 && cp GEOquery.Rcheck\00install.out GEOquery-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GEOquery.buildbin-libdir --install="check:GEOquery-install.out" --force-multiarch --no-vignettes --timings GEOquery_2.36.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GEOquery.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.36.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GEOquery' can be installed ... OK
* checking installed package size ... NOTE
installed size is 13.8Mb
sub-directories of 1Mb or more:
extdata 12.8Mb
* 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 'limma' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Biobase'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'GEOquery/R/zzz.R':
.onLoad calls:
packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")
packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")
See section 'Good practice' in '?.onAttach'.
GDS2MA: no visible binding for global variable 'MA'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'GEOquery-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGSEDataTables
> ### Title: Get GSE data tables from GEO into R data structures.
> ### Aliases: getGSEDataTables
> ### Keywords: IO
>
> ### ** Examples
>
> dfl = getGSEDataTables("GSE3494")
error : Unknown IO error
I/O warning : failed to load external entity "http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?targ=self&form=xml&view=full&acc=GSE3494"
Error in UseMethod("xmlRoot") :
no applicable method for 'xmlRoot' applied to an object of class "NULL"
Calls: getGSEDataTables -> xmlRoot
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GEOquery-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGSEDataTables
> ### Title: Get GSE data tables from GEO into R data structures.
> ### Aliases: getGSEDataTables
> ### Keywords: IO
>
> ### ** Examples
>
> dfl = getGSEDataTables("GSE3494")
error : Unknown IO error
I/O warning : failed to load external entity "http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?targ=self&form=xml&view=full&acc=GSE3494"
Error in UseMethod("xmlRoot") :
no applicable method for 'xmlRoot' applied to an object of class "NULL"
Calls: getGSEDataTables -> xmlRoot
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [264s]
[267s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [247s]
[247s] 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, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/GEOquery.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GEOquery' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'GEOquery' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEOquery' as GEOquery_2.36.0.zip
* DONE (GEOquery)