Problems with 'compilation' of package

[tetomonti]

@lia978 When trying to 'compile' the package, the following errors occur (this was after a fresh pull of the repository from github, and no modifications):

> CBMGIT
[1] "/Users/smonti/Research/CBMmetagit"
> setwd(paste(CBMGIT,'/CBMRtools/CBMRtools/inst/package_make',sep=''))
> source("CBMRtools.build.R") 
Loading required package: devtools
Loading required package: staticdocs
Error : object 'colourise' is not exported by ‘namespace:testthat'
...
Error in (function (dep_name, dep_ver = NA, dep_compare = NA)  : 
  Dependency package XLConnect not available.

I thought it was possible to have a package automatically install the packages on which it depends. Can it be done? Also, please notice the first error message about the object 'colourize'.

[tetomonti]

The 'colourise' error message was resolved by re-installing staticdocs:

> require(staticdocs)
Loading required package: staticdocs
Error : object 'colourise' is not exported by 'namespace:testthat'
> install_github("hadley/staticdocs")
...
> require(staticdocs)
Loading required package: staticdocs

[lia978]

Hi Stefano,

Could you try installing again from master?

I fixed the instruction for "building" to include installing dependencies at: https://github.com/montilab/CBMRtools/blob/master/CBMRtools/inst/package_make/CBMRtools.build.R this worked fine on my computer if I delete XLConnect and ran the package building. Let me know if this works, if so I'm make another tag

[tetomonti]

Thank you Amy, I will check asap.

On Oct 6, 2015, at 2:43 PM, lia978 notifications@github.com wrote:

Hi Stefano,

Could you try installing again from master?

I fixed the instruction for "building" to include installing dependencies at: https://github.com/montilab/CBMRtools/blob/master/CBMRtools/inst/package_make/CBMRtools.build.R https://github.com/montilab/CBMRtools/blob/master/CBMRtools/inst/package_make/CBMRtools.build.R this worked fine on my computer if I delete XLConnect and ran the package building. Let me know if this works, if so I'm make another tag

— Reply to this email directly or view it on GitHub https://github.com/montilab/CBMRtools/issues/1#issuecomment-145960311.

[tetomonti]

Hi Amy, looks like the fix took care of XLconnect (an R package) but not of the Bioconductor pacakges:

source("CBMRtools.build.R") Loading required package: staticdocs Installing.. Installing CBMRtools Skipping 3 packages not available: Biobase, oligo, oligoClasses Installing 4 packages: XLConnect, XLConnectJars, chron, data.table '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \ --no-save --no-restore CMD INSTALL \ '/Users/smonti/Research/CBMmetagit/CBMRtools/CBMRtools' \ --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' \ --install-tests

ERROR: dependencies 'oligo', 'oligoClasses' are not available for package 'CBMRtools'

• removing '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/CBMRtools'

On Oct 6, 2015, at 2:43 PM, lia978 notifications@github.com wrote:

Hi Stefano,

Could you try installing again from master?

I fixed the instruction for "building" to include installing dependencies at: https://github.com/montilab/CBMRtools/blob/master/CBMRtools/inst/package_make/CBMRtools.build.R https://github.com/montilab/CBMRtools/blob/master/CBMRtools/inst/package_make/CBMRtools.build.R this worked fine on my computer if I delete XLConnect and ran the package building. Let me know if this works, if so I'm make another tag

— Reply to this email directly or view it on GitHub https://github.com/montilab/CBMRtools/issues/1#issuecomment-145960311.

[tetomonti]

Thank you Amy! Shall we create a new tag of the package?

—ste

On Mar 14, 2017, at 3:14 PM, lia978 notifications@github.com wrote:

Closed #1 https://github.com/montilab/CBMRtools/issues/1.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/montilab/CBMRtools/issues/1#event-999668040, or mute the thread https://github.com/notifications/unsubscribe-auth/AJADHyshsC6hPbD-CrrUVtqle3T7Rggcks5rlucigaJpZM4GJ7Iv.

[lia978]

just created new tag: v1.0.4 edit: new tag: v1.1.1 (didn't see there was a v1.1.0 already).