H2o Rd warning: "Missing File Link"

2
votes

When downloading H2o.ai from R on my linux, I receive several warnings that a file is missing, For example: Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.abs.Rd:32: missing file link 'abs'

I'm using the standard install code for H2o: install.packages("h2o", type="source", repos="http://h2o-release.s3.amazonaws.com/h2o/rel-xu/1/R")

Here is the output with the warnings: ` h2o.abs html
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.abs.Rd:32: missing file link ‘abs’ h2o.acos html
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.acos.Rd:24: missing file link ‘acos’

    h2o.ascharacter                         html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.ascharacter.Rd:16: missing file link ‘as.character’
    h2o.asfactor                            html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.asfactor.Rd:16: missing file link ‘as.factor’
    h2o.asnumeric                           html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.asnumeric.Rd:16: missing file link ‘as.numeric’

    h2o.ceiling                             html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.ceiling.Rd:18: missing file link ‘ceiling’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.cos.Rd:16: missing file link ‘cos’
    h2o.cosh                                html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.cosh.Rd:16: missing file link ‘cosh’
    h2o.coxph                               html  
    h2o.createFrame                         html  
    h2o.cross_validation_fold_assignment    html  
    h2o.cross_validation_holdout_predictions
                                            html  
    h2o.cross_validation_models             html  
    h2o.cross_validation_predictions        html  
    h2o.cummax                              html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.cummax.Rd:18: missing file link ‘cummax’
    h2o.cummin                              html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.cummin.Rd:18: missing file link ‘cummin’
    h2o.cumprod                             html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.cumprod.Rd:18: missing file link ‘cumprod’
    h2o.exp                                 html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.exp.Rd:16: missing file link ‘exp’

    h2o.floor                               html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.floor.Rd:18: missing file link ‘floor’

    h2o.ischaracter                         html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.ischaracter.Rd:16: missing file link ‘is.character’
    h2o.isfactor                            html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.isfactor.Rd:16: missing file link ‘is.factor’
    h2o.isnumeric                           html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.isnumeric.Rd:16: missing file link ‘is.numeric’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.log.Rd:16: missing file link ‘log’
    h2o.log10                               html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.log10.Rd:16: missing file link ‘log10’
    h2o.log1p                               html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.log1p.Rd:16: missing file link ‘log1p’
    h2o.log2                                html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.log2.Rd:16: missing file link ‘log2’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.max.Rd:18: missing file link ‘max’
    h2o.mean                                html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.mean.Rd:46: missing file link ‘rowMeans’
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.mean.Rd:46: missing file link ‘colMeans’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.min.Rd:18: missing file link ‘min’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.ncol.Rd:16: missing file link ‘ncol’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.rbind.Rd:32: missing file link ‘rbind’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.round.Rd:21: missing file link ‘round’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.signif.Rd:21: missing file link ‘signif’
    h2o.sin                                 html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.sin.Rd:16: missing file link ‘sin’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.sqrt.Rd:16: missing file link ‘sqrt’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.tan.Rd:16: missing file link ‘tan’
    h2o.tanh                                html  
Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.tanh.Rd:16: missing file link ‘tanh’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.trunc.Rd:17: missing file link ‘trunc’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.var.Rd:36: missing file link ‘var’

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.which_max.Rd:29: missing file link ‘which.max’

 building package indices
 testing if installed package can be loaded
 DONE (h2o)

I believe this issue is causing a downstream error when using automl, Error: DistributedException from localhost/127.0.0.1:54321: 'Categorical value out of bounds

2
rh2oautoml
can you provide some more information about your environment and all the steps you took before trying to install h2o-3. So far when downloading from source or cran on linux the download hasn't thrown the errors you've seen. – Lauren

2 Answers

0
votes

Those are errors in the package, but not very serious ones. For example, the first one you list

Rd warning: /tmp/RtmpdpaSKI/R.INSTALL1d3a6ccc7d9b/h2o/man/h2o.ascharacter.Rd:16: missing file link ‘as.character’

comes because that help file contains the link \link[base]{as.character} which does not exist. It should be \link[base]{character} or \link[base:character]{as.character}, since links to other packages are to the help page name, not to the topic alias. If you ask for help using ?h2o.ascharacter, you might find the link in the help page to as.character doesn't work. (Usually such links do work, because the R dynamic help system figures out what the author meant, but some installations use a static help system with pre-built .html files where the links won't work.)

The rules for cross-package links in the help system are pretty bizarre, and it looks like the h2o authors didn't learn them (or didn't care about static help).

I don't know if your guess about the downstream error is right or not.

0
votes

Can you say more about the system that you're using and the version of R? I am not able to reproduce this on Ubuntu 16.04.5 using R 3.4.4. I tried installing exactly how you did and also just by installing the latest from CRAN (both are version 3.22.0.1).

> install.packages("h2o")
Installing package into '/home/ledell/R/x86_64-pc-linux-gnu-library/3.4'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/h2o_3.22.1.1.tar.gz'
Content type 'application/x-gzip' length 432390 bytes (422 KB)
==================================================
downloaded 422 KB

* installing *source* package 'h2o' ...
** package 'h2o' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Performing one-time download of h2o.jar from
     http://s3.amazonaws.com/h2o-release/h2o/rel-xu/1/Rjar/h2o.jar
(This could take a few minutes, please be patient...)
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (h2o)

The downloaded source packages are in
    '/tmp/RtmpGwtVRB/downloaded_packages'


> install.packages("h2o", type="source", repos="http://h2o-release.s3.amazonaws.com/h2o/rel-xu/1/R")
Installing package into '/home/ledell/R/x86_64-pc-linux-gnu-library/3.4'
(as 'lib' is unspecified)
trying URL 'http://h2o-release.s3.amazonaws.com/h2o/rel-xu/1/R/src/contrib/h2o_3.22.1.1.tar.gz'
Content type 'application/x-tar' length 120971891 bytes (115.4 MB)
==================================================
downloaded 115.4 MB

* installing *source* package 'h2o' ...
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (h2o)

The downloaded source packages are in
    '/tmp/RtmpGwtVRB/downloaded_packages'

The downstream error is not related. If you can post the code you are running as a separate question with reproducible code, we can try to sort that out.