[Bioc-devel] build report with error

Rodriguez Martinez, Andrea andrea.rodriguez-martinez13 at imperial.ac.uk
Tue Mar 7 18:48:45 CET 2017


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
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

	[[alternative HTML version deleted]]



More information about the Bioc-devel mailing list