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tomwenseleers / export

R package for streamlined export of graphs and data tables.
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installation #30

Closed boris191055 closed 4 years ago

boris191055 commented 4 years ago

Hi I am trying to install export from github to Rstudio based on R 4.0 and this is what I got (below). Any help will be greatly appreciated because export is an extremely useful package.

devtools::install_github("tomwenseleers/export") WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from https://cran.r-project.org/bin/windows/Rtools/. Downloading GitHub repo tomwenseleers/export@master These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: httpuv (1.5.3.1 -> 1.5.4 ) [CRAN] 5: later (1.0.0 -> 1.1.0.1) [CRAN] 6: vctrs (0.3.0 -> 0.3.1 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from https://cran.r-project.org/bin/windows/Rtools/. √ checking for file 'C:\Users\Owner\AppData\Local\Temp\RtmpWA1TdW\remotes381826937dd\tomwenseleers-export-269abaf/DESCRIPTION' (442ms)

Installing package into ‘C:/Users/Owner/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

The command graph2ppt works though

cvanderaa commented 4 years ago

Thanks for using our package! This is an issue we are also experiencing and we will be working on as soon as possible.

cvanderaa commented 4 years ago

So, apparently the warnings occur only on Windows, see here for background.

Basically, we've put some links to other packages using for example \link[broom]{tidy}. During installation, the help file called tidy.Rd will be searched for in the broom package. Since it does not exist, the builder throws a warning. I replaced those problematic links with \link{tidy} which should look up the tidy topic in any installed packages, see commit baa0b40.

@tomwenseleers @boris191055 Could check if you still have those warnings?

boris191055 commented 4 years ago

Thanks! What is the new version that needed to be downloaded and checked? BTW, the export package is still absent from the main CRAN depository.

cvanderaa commented 4 years ago

The newest version on GitHub should work now. So you could install it using:

devtools::install_github("tomwenseleers/export")

Indeed it is still absent from CRAN, we will submit a request this week.

boris191055 commented 4 years ago

I removed previously installed export and tried to install the new one. Failed and got the following message:

package ‘backports’ successfully unpacked and MD5 sums checked Error: Failed to install 'export' from GitHub: (converted from warning) cannot remove prior installation of package ‘backports’

remove.packages('backports') Removing package from ‘C:/Users/Owner/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) Error in remove.packages : there is no package called ‘backports’

boris191055 commented 4 years ago

Some update. I just removed "backports' manually from ‘C:/Users/Owner/Documents/R/win-library/4.0 then run devtools::install_github("tomwenseleers/export")

It seems this worked: Here is what I got

devtools::install_github("tomwenseleers/export") WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from https://cran.r-project.org/bin/windows/Rtools/. Downloading GitHub repo tomwenseleers/export@master Installing 1 packages: backports Installing package into ‘C:/Users/Owner/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation backports 1.1.7 1.1.8 TRUE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.1.7.zip' Content type 'application/zip' length 81641 bytes (79 KB) downloaded 79 KB

package ‘backports’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\Owner\AppData\Local\Temp\Rtmpo74yHw\downloaded_packages WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from https://cran.r-project.org/bin/windows/Rtools/. √ checking for file 'C:\Users\Owner\AppData\Local\Temp\Rtmpo74yHw\remotes24884698718b\tomwenseleers-export-baa0b40/DESCRIPTION' ...

Installing package into ‘C:/Users/Owner/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

Rd warning: C:/Users/Owner/AppData/Local/Temp/RtmpSYwlnT/R.INSTALL15b83a9d2b10/export/man/table2office.Rd:116: file link 'tidy' in package 'broom' does not exist and so has been treated as a topic table2spreadsheet html
table2tex html
building package indices testing if installed package can be loaded from temporary location arch - i386 arch - x64 testing if installed package can be loaded from final location ** arch - i386 arch - x64 ** testing if installed package keeps a record of temporary installation path

cvanderaa commented 4 years ago

Oops sorry, I missed one of the links. It should be fixed now. Thanks for testing!

boris191055 commented 4 years ago

And now this:

devtools::install_github("tomwenseleers/export") Error: .onLoad failed in loadNamespace() for 'pkgload', details: call: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) error: there is no package called ‘backports’

boris191055 commented 4 years ago

Installed backports separately, then installed export again but this time did not update backports I mean, I entered empty line after: These packages have more recent versions available. It is recommended to update all of them. Which would you like to update? 1: All
2: CRAN packages only
3: None
4: backports (1.1.7 -> 1.1.8) [CRAN] Enter one or more numbers, or an empty line to skip updates:

Seems worked

cvanderaa commented 4 years ago

Strange this backports issue. I'm working with version 1.1.8 and have no problem... But the link issue is fixed for you now?

LinusEngel commented 4 years ago

Hey there, I got the same trouble: first the installation process was stopped because of 'dplyr', then I omitted updates like boris191055 did, now installation stops at 'glue' package:

Error: Failed to install 'export' from GitHub: (converted from warning) cannot remove prior installation of package ‘glue’

And yes, it is a Windows, R 3.6.3. Hope you can fix it, I'd love to try that package!

cvanderaa commented 4 years ago

Hi @LinusEngel,

It seems it is an error that has been converted from a warning. Did you set options(warn = 2)?

It is really hard for me to reproduce your error. It might be that your glue package is installed in a write protected directory (e.g. somewhere in ProgramFiles), maybe try to locate glue that should be in one of the .libPaths() folders and delete it manually.

LinusEngel commented 4 years ago

Hey there, I have set no options for the warnings. Should I?

I deleted 'glue' manually, which was just normally installed in the same documents/win-library folder like all other packages. Still getting an error referring to it:

devtools::install_github("tomwenseleers/export") Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : error: there is no package called ‘glue’

cvanderaa commented 4 years ago

If options()$warn return 0 than no problem, but anyway there shouldn't be a warning.

So now, it needs you to install back the glue package. There seems to be some confusion during the dependencies installation. I'm wondering if BiocManager could better handle this.

Before trying reinstalling glue, could you first try:

BiocManager::install("tomwenseleers/export")
LinusEngel commented 4 years ago

Sweet, that worked. And glue was installed again with the other dependencies; not sure though I know why it has been working now, but hopefully it helps you as well.

Thanks a lot!