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csgillespie / efficientR

Efficient R programming: a book
https://csgillespie.github.io/efficientR/
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Fails to build on Ubuntu 14.04 64bit #116

Closed adamryczkowski closed 8 years ago

adamryczkowski commented 8 years ago

Here is what happened after I do make cleaner and then make pdf:

⏚ [adam:~/tmp/efficientR] master 2s ± make pdf
Rscript -e 'bookdown::render_book("index.Rmd", output_format = "bookdown::pdf_book")'

processing file: _main.Rmd
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cropping _main_files/figure-latex/5-1-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/5-1-1.pdf'.

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 *** caught segfault ***
address 0x2b1ce00000cb, cause 'memory not mapped'

Here is my sesion info:

Session info --------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, linux-gnu           
 ui       RStudio (0.99.1266)         
 language en_US                       
 collate  en_US.UTF-8                 
 tz       <NA>                        
 date     2016-07-29                  

Packages ------------------------------------------------------------------------------------------------------
 package   * version    date       source                                  
 bookdown    0.1.3      2016-07-28 Github (rstudio/bookdown@cbe9f10)       
 devtools    1.12.0     2016-06-24 CRAN (R 3.3.1)                          
 digest      0.6.9      2016-01-08 CRAN (R 3.2.4)                          
 evaluate    0.9        2016-05-28 Github (adamryczkowski/evaluate@a6501ed)
 htmltools   0.3.5      2016-03-21 CRAN (R 3.3.0)                          
 httpuv      1.3.3      2015-08-04 CRAN (R 3.3.1)                          
 magrittr    1.5        2014-11-22 CRAN (R 3.2.0)                          
 memoise     1.0.0      2016-01-29 CRAN (R 3.3.0)                          
 mime        0.5        2016-07-07 cran (@0.5)                             
 miniUI      0.1.1      2016-01-15 cran (@0.1.1)                           
 R6          2.1.2      2016-01-26 CRAN (R 3.3.0)                          
 Rcpp        0.12.6     2016-07-19 cran (@0.12.6)                          
 rmarkdown   1.0.9001   2016-07-29 Github (rstudio/rmarkdown@f7211d5)      
 rsconnect   0.4.3      2016-05-02 cran (@0.4.3)                           
 shiny       0.13.2     2016-03-28 CRAN (R 3.3.1)                          
 stringi     1.1.1      2016-05-27 CRAN (R 3.3.0)                          
 stringr     1.0.0.9000 2016-07-28 Github (hadley/stringr@4cdeb50)         
 withr       1.0.2      2016-06-20 CRAN (R 3.3.1)                          
 xtable      1.8-2      2016-02-05 CRAN (R 3.3.1)                          
 yaml        2.1.13     2014-06-12 CRAN (R 3.3.0)

I use recent git version: commit 9e7fa9635ac11771783fb840a65c1557a6c8b418

Author: Colin Gillespie <csgillespie@gmail.com>
Date:   Sun Jul 24 13:33:31 2016 +0100

    Merge pull request #114 from Robinlovelace/R-object-classes

Do you have any ideas what can I do?

adamryczkowski commented 8 years ago

Subsequent compilation also fails, but with different error:

⏚ θ60° [adam:~] $ cd tmp/efficientR/
⏚ [adam:~/tmp/efficientR] master ± make pdf
Rscript -e 'bookdown::render_book("index.Rmd", output_format = "bookdown::pdf_book")'

processing file: _main.Rmd
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-------------------------------------------------------------------------
data.table + dplyr code now lives in dtplyr.
Please library(dtplyr)!
-------------------------------------------------------------------------

Attaching package: 'dplyr'

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cropping _main_files/figure-latex/5-2-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/5-2-1.pdf'.

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Parsed with column specification:
cols(
  `Country Name` = col_character(),
  `Country Code` = col_character(),
  Year = col_integer(),
  `Year Code` = col_character(),
  `Income share held by highest 10% [SI.DST.10TH.10]` = col_character(),
  `Income share held by lowest 10% [SI.DST.FRST.10]` = col_character(),
  `GINI index [SI.POV.GINI]` = col_character(),
  `Survey mean consumption or income per capita, bottom 40% (2005 PPP $ per day) [SI.SPR.PC40]` = col_character(),
  `Survey mean consumption or income per capita, total population (2005 PPP $ per day) [SI.SPR.PCAP]` = col_character()
)
Quitting from lines 3355-3358 (_main.Rmd) 
Error in read_tokens_(data, tokenizer, col_specs, col_names, locale_,  : 
  attempt to set index 1000/1000 in SET_STRING_ELT
Calls: <Anonymous> ... read_delimited -> read_tokens -> read_tokens_ -> .Call
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Execution halted
make: *** [pdf] Error 1
⏚ θ64° [adam:~/tmp/efficientR] master 4s 2 ±
csgillespie commented 8 years ago

Hmmm, I'm stumped on this one. Could you go through each chapter and click knit? That should help pinpoint the offending section.

adamryczkowski commented 8 years ago

Well.., I've tried the first chapter and I've got another error. I've entered the repo's directory, typed make cleaner, and then:

[adam:~/tmp/efficientR] master(+5/-0) ± R

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> bookdown::render_book('01-introduction.Rmd')

processing file: _main.Rmd
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Quitting from lines 2001-2004 (_main.Rmd) 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'efficient'

>
csgillespie commented 8 years ago

The efficient package is the associated book R package. If you run 

devtools::install_github("csgillespie/efficientR")

it should install. I suspect you are running an old version of devtools. If you run update.packages that should solve the problem (I hope). I've tweaked the DESCRIPTION file to enforce the newer version.

adamryczkowski commented 8 years ago

Yes, it did help. You should also consider adding rio and feather packages to the list of dependencies as well.

csgillespie commented 8 years ago

Great.

The trouble with rio and feather is that the packages require significant messing about with the travis.yml. Those packages are sneakily installed in appendix.Rmd. Not ideal, but it save time.

adamryczkowski commented 8 years ago

Well, they haven't (in my case at least). The compilation simply failed and I learned about those dependencies from the log, and then I installed them manually.

csgillespie commented 8 years ago

That's odd (it builds on travis without feather and rio). I've made minor changes, so hopefully it won't affect anyone in the future.