DASiR 1.11.2
Ricard Illa
| Snapshot Date: 2016-05-01 16:20:05 -0700 (Sun, 01 May 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DASiR | | Last Changed Rev: 116520 / Revision: 116959 | | Last Changed Date: 2016-04-18 21:20:35 -0700 (Mon, 18 Apr 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### rm -rf DASiR.buildbin-libdir DASiR.Rcheck && mkdir DASiR.buildbin-libdir DASiR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DASiR.buildbin-libdir DASiR_1.11.2.tar.gz >DASiR.Rcheck\00install.out 2>&1 && cp DASiR.Rcheck\00install.out DASiR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DASiR.buildbin-libdir --install="check:DASiR-install.out" --force-multiarch --no-vignettes --timings DASiR_1.11.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/DASiR.Rcheck'
* using R version 3.3.0 RC (2016-04-28 r70561)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DASiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DASiR' version '1.11.2'
* 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 'DASiR' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
See 'D:/biocbld/bbs-3.4-bioc/meat/DASiR.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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
getDasStructure: no visible global function definition for
'download.file'
plotFeatures: no visible binding for global variable 'plot.default'
plotFeatures: no visible global function definition for 'dev.cur'
plotFeatures: no visible global function definition for 'rainbow'
plotFeatures: no visible global function definition for 'rect'
plotFeatures: no visible global function definition for 'text'
Undefined global functions or variables:
dev.cur download.file plot.default rainbow rect text
Consider adding
importFrom("grDevices", "dev.cur", "rainbow")
importFrom("graphics", "plot.default", "rect", "text")
importFrom("utils", "download.file")
to your NAMESPACE file.
* 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 'DASiR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DASiR-package
> ### Title: Distributed Annotation System in R
> ### Aliases: DASiR-package DASiR
> ### Keywords: package
>
> ### ** Examples
>
> setDasServer(server="http://www.ensembl.org/das")
DAS server for this session is: http://www.ensembl.org/das
> print(getDasServer())
[1] "http://www.ensembl.org/das"
>
> # See the sources (supported organisms)
> sources <- getDasSource()
Querying url: http://www.ensembl.org/das/sources
Error: could not find function "xmlStructuredStop"...
> head(sources)
NULL
>
> dsn_sources <- getDasDsn()
Querying url: http://www.ensembl.org/das/dsn
failed to load external entity "http://www.ensembl.org/das/dsn"
Error: 1: failed to load external entity "http://www.ensembl.org/das/dsn"
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'DASiR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DASiR-package
> ### Title: Distributed Annotation System in R
> ### Aliases: DASiR-package DASiR
> ### Keywords: package
>
> ### ** Examples
>
> setDasServer(server="http://www.ensembl.org/das")
DAS server for this session is: http://www.ensembl.org/das
> print(getDasServer())
[1] "http://www.ensembl.org/das"
>
> # See the sources (supported organisms)
> sources <- getDasSource()
Querying url: http://www.ensembl.org/das/sources
Error: could not find function "xmlStructuredStop"...
> head(sources)
NULL
>
> dsn_sources <- getDasDsn()
Querying url: http://www.ensembl.org/das/dsn
failed to load external entity "http://www.ensembl.org/das/dsn"
Error: 1: failed to load external entity "http://www.ensembl.org/das/dsn"
Execution halted
* 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, 1 WARNING, 1 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/DASiR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'DASiR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
version 3.3
install for x64
* installing *source* package 'DASiR' ...
** testing if installed package can be loaded
Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
version 3.3
* MD5 sums
packaged installation of 'DASiR' as DASiR_1.11.2.zip
* DONE (DASiR)