[Bioc-devel] build report with error

[Rodriguez Martinez, Andrea]

Thanks very much

Andrea
________________________________
From: Obenchain, Valerie <Valerie.Obenchain at RoswellPark.org>
Sent: 07 March 2017 17:39:58
To: Rodriguez Martinez, Andrea; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] build report with error

Hi Andrea,

Our emails just crossed:

https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010543.html

Anytime you see the same error across many (in this case hundreds of)
packages it's safe to assume it's a build system error. I'll try to keep
everyone informed of known failures by posting to this list.

Thanks for keeping an eye on the build report.
Valerie



On 03/07/2017 09:28 AM, Rodriguez Martinez, Andrea wrote:
> Hi,
>
>
> I just noticed that my packages MetaboSignal and MWASTools have a build report with error for Windows in the devel branch. I wonder if there is something I can do about this. See the specific error messages below:
>
>
> -For MetaboSignal it says:
>
> ##
> ### Running command:
> ###
> ###   chmod a+r MetaboSignal -R && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MetaboSignal
> ###
> ##############################################################################
> ##############################################################################
>
>
> * checking for file 'MetaboSignal/DESCRIPTION' ... OK
> * preparing 'MetaboSignal':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> Warning: running command '"C:/Users/biocbuild/bbs-3.5-bioc/R/bin/x64/Rcmd.exe" INSTALL -l "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpUdQmpF\Rinst2180771a78c0" --no-multiarch "C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpUdQmpF/Rbuild218072f9557/MetaboSignal"' had status 1
>       -----------------------------------
> * installing *source* package 'MetaboSignal' ...
> ** R
> ** data
> *** moving datasets to lazyload DB
> ** inst
> ** preparing package for lazy loading
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
>   there is no package called 'Biobase'
> ERROR: lazy loading failed for package 'MetaboSignal'
> * removing 'C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpUdQmpF/Rinst2180771a78c0/MetaboSignal'
>       -----------------------------------
> ERROR: package installation failed
>
> -For MWASTools it says:
>
> ##############################################################################
>
> ##############################################################################
> ###
> ### Running command:
> ###
> ###   rm -rf MWASTools.buildbin-libdir && mkdir MWASTools.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/MWASTools_0.99.18.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=MWASTools.buildbin-libdir --merge-multiarch MWASTools_0.99.18.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL MWASTools_0.99.18.zip  && rm MWASTools_0.99.18.tar.gz MWASTools_0.99.18.zip
> ###
> ##############################################################################
> ##############################################################################
>
>
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
>                                  Dload  Upload   Total   Spent    Left  Speed
>
>   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
> 100 1418k  100 1418k    0     0  52.5M      0 --:--:-- --:--:-- --:--:-- 55.4M
>
> install for i386
>
> * installing *source* package 'MWASTools' ...
> ** R
> ** data
> *** moving datasets to lazyload DB
> Warning: namespace 'SummarizedExperiment' is not available and has been replaced
> by .GlobalEnv when processing object 'metabo_SE'
> Warning: namespace 'SummarizedExperiment' is not available and has been replaced
> by .GlobalEnv when processing object 'metabo_SE'
> Warning: namespace 'SummarizedExperiment' is not available and has been replaced
> by .GlobalEnv when processing object 'targetMetabo_SE'
> Warning: namespace 'SummarizedExperiment' is not available and has been replaced
> by .GlobalEnv when processing object 'targetMetabo_SE'
> ** inst
> ** preparing package for lazy loading
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
>   there is no package called 'S4Vectors'
> ERROR: lazy loading failed for package 'MWASTools'
> * removing 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MWASTools.buildbin-libdir/MWASTools'
> Warning: running command 'C:/Users/biocbuild/bbs-3.5-bioc/R/bin/i386/Rcmd.exe INSTALL --library=MWASTools.buildbin-libdir MWASTools_0.99.18.tar.gz --no-multiarch' had status 1
>
> Thanks very much,
>
>
> Andrea
>
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>
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>



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