csgillespie / efficientr Goto Github PK
View Code? Open in Web Editor NEWEfficient R programming: a book
Home Page: https://csgillespie.github.io/efficientR/
License: Other
Efficient R programming: a book
Home Page: https://csgillespie.github.io/efficientR/
License: Other
... throws an error using R 3.2.3:
...
label: voyages-pre (with options)
List of 3
$ echo : logi FALSE
$ results: chr "hide"
$ warning: logi FALSE
Quitting from lines 2930-2941 (_main.Rmd)
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: ... withVisible -> eval -> eval -> read.delim -> read.table
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former
Execution halted
make: *** [pdf] Error 1
I couldn't find _main.Rmd to check the respective lines
Hi,
I´ve installed the dependencies, cloned the repo and presss Knit.
But this error message arose:
Error 5977
Error in parse(text = x) : <text>:4:25: unexpected symbol
3: person("Romain", "Francois", , "[email protected]", "aut"),
4: person("Kirill", "M"uller
^
Calls: <Anonymous> ... citation -> .read_authors_at_R_field -> eval -> parse
Ejecuci'on interrumpida
Any hints?
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
| | 0%
inline R code fragments
label: unnamed-chunk-1 (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE
ordinary text without R code
| | 1%
label: unnamed-chunk-2 (with options)
List of 2
$ echo : logi FALSE
$ out.width: chr "33%"
ordinary text without R code
label: unnamed-chunk-3 (with options)
List of 2
$ eval : logi FALSE
$ indent: chr " "
|. | 1%
ordinary text without R code
label: unnamed-chunk-4 (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE
ordinary text without R code
label: 1-1 (with options)
List of 3
$ echo : logi FALSE
$ fig.cap : chr "The starting position for touch typing, with the fingers over the 'home keys'. Source: [Wikipedia](https://commons.wikimedia.or"| __truncated__
$ out.width: chr "100%"
ordinary text without R code
|. | 2%
label: unnamed-chunk-5
ordinary text without R code
label: test-ice (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: 1-2 (with options)
List of 3
$ echo : logi FALSE
$ fig.cap : chr "Profiling results of loading and plotting NASA data on icesheet retreat."
$ out.width: chr "100%"
ordinary text without R code
label: 1-3 (with options)
List of 2
$ echo : logi FALSE
$ fig.cap: chr "Visualisation of North Pole icesheet decline, generated using the code profiled using the profvis package."
|.. | 2%
ordinary text without R code
|.. | 3%
label: unnamed-chunk-6 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-7 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-8 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-9 (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE
ordinary text without R code
|.. | 4%
label: unnamed-chunk-10 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: unnamed-chunk-11 (with options)
List of 1
$ eval: logi FALSE
|... | 4%
ordinary text without R code
label: assertive.reflection (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-12 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
|... | 5%
label: unnamed-chunk-13 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: 2-1 (with options)
List of 3
$ echo : logi FALSE
$ fig.cap : chr "Output from a system monitor (`gnome-system-monitor` running on Ubuntu) showing the resources consumed by running the code pres"| __truncated__
$ out.width: chr "100%"
ordinary text without R code
label: unnamed-chunk-14 (with options)
List of 2
$ eval : logi FALSE
$ indent: chr " "
ordinary text without R code
label: timings-tests (with options)
List of 2
$ echo: logi FALSE
$ eval: logi FALSE
|.... | 5%
ordinary text without R code
|.... | 6%
label: packrat (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-15 (with options)
List of 2
$ eval : logi FALSE
$ engine: chr "bash"
ordinary text without R code
label: unnamed-chunk-16 (with options)
List of 2
$ eval : logi FALSE
$ engine: chr "bash"
ordinary text without R code
label: unnamed-chunk-17 (with options)
List of 2
$ eval : logi FALSE
$ indent: chr " "
ordinary text without R code
|.... | 7%
label: unnamed-chunk-18 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-19 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|..... | 7%
label: unnamed-chunk-20 (with options)
List of 2
$ engine: chr "bash"
$ eval : logi FALSE
ordinary text without R code
label: unnamed-chunk-21 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|..... | 8%
label: unnamed-chunk-22 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: update-rprofile (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: rstudio-tip (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-23 (with options)
List of 2
$ eval : logi FALSE
$ engine: chr "bash"
ordinary text without R code
|...... | 9%
label: startup-warn (with options)
List of 2
$ type : chr "rmdwarning"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-24 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: file.path (with options)
List of 2
$ type : chr "rmdwarning"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-25 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|...... | 10%
label: pathological (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-26 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|....... | 10%
label: unnamed-chunk-27 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-28 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|....... | 11%
label: unnamed-chunk-29 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-30
ordinary text without R code
label: continuetip (with options)
List of 2
$ style : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-31 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|........ | 12%
label: unnamed-chunk-32 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-33
ordinary text without R code
label: unnamed-chunk-34 (with options)
List of 1
$ results: chr "hide"
ordinary text without R code
label: unnamed-chunk-35 (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
|........ | 13%
label: unnamed-chunk-36 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-37
ordinary text without R code
label: unnamed-chunk-38 (with options)
List of 1
$ eval: logi FALSE
|......... | 13%
ordinary text without R code
label: unnamed-chunk-39 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|......... | 14%
label: unnamed-chunk-40 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-41
ordinary text without R code
label: unnamed-chunk-42
ordinary text without R code
label: unnamed-chunk-43
ordinary text without R code
|......... | 15%
label: unnamed-chunk-44 (with options)
List of 1
$ message: logi FALSE
The following object is masked _by_ .GlobalEnv:
ht
|.......... | 15%
ordinary text without R code
label: unnamed-chunk-45 (with options)
List of 2
$ engine: chr "bash"
$ eval : logi FALSE
ordinary text without R code
label: unnamed-chunk-46
ordinary text without R code
label: unnamed-chunk-47
ordinary text without R code
|.......... | 16%
label: unnamed-chunk-48 (with options)
List of 2
$ engine: chr "bash"
$ eval : logi FALSE
ordinary text without R code
label: unnamed-chunk-49 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: 2-2 (with options)
List of 3
$ fig.cap : chr "RStudio Panels"
$ echo : logi FALSE
$ out.width: chr "100%"
|........... | 16%
ordinary text without R code
label: unnamed-chunk-50 (with options)
List of 2
$ eval : logi FALSE
$ indent: chr " "
ordinary text without R code
|........... | 17%
label: unnamed-chunk-51 (with options)
List of 1
$ indent: chr " "
ordinary text without R code
label: unnamed-chunk-52 (with options)
List of 2
$ echo : logi FALSE
$ indent: chr " "
ordinary text without R code
label: 2-3 (with options)
List of 4
$ echo : logi FALSE
$ fig.cap : chr "The data viewing tab in RStudio."
$ out.width: chr "100%"
$ indent : chr " "
ordinary text without R code
label: unnamed-chunk-53 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
|........... | 18%
label: autocompletion (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
|............ | 18%
label: unnamed-chunk-54 (with options)
List of 2
$ eval: logi FALSE
$ echo: num 2
ordinary text without R code
label: unnamed-chunk-55 (with options)
List of 2
$ engine: chr "bash"
$ eval : logi FALSE
ordinary text without R code
label: unnamed-chunk-56 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
|............ | 19%
label: unnamed-chunk-57 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-58 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: blas-bench (with options)
List of 6
$ fig.width : num 6
$ fig.height: num 4
$ echo : logi FALSE
$ out.width : chr "70%"
$ fig.align : chr "center"
$ fig.cap : chr "Performance gains obtained changing the underlying BLAS library (tests from `benchmark\\_std()`)."
cropping _main_files/figure-latex/blas-bench-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/blas-bench-1.pdf'.
ordinary text without R code
|............. | 19%
label: unnamed-chunk-59 (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE
ordinary text without R code
|............. | 20%
label: unnamed-chunk-60 (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-61 (with options)
List of 2
$ eval : logi TRUE
$ results: chr "hide"
ordinary text without R code
label: unnamed-chunk-62 (with options)
List of 1
$ echo: num 3
ordinary text without R code
label: bad_loop
ordinary text without R code
|............. | 21%
label: unnamed-chunk-63 (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
|.............. | 21%
label: unnamed-chunk-64 (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-65 (with options)
List of 2
$ echo: logi TRUE
$ tidy: logi FALSE
ordinary text without R code
label: unnamed-chunk-66 (with options)
List of 2
$ echo: logi TRUE
$ tidy: logi FALSE
ordinary text without R code
|.............. | 22%
label: unnamed-chunk-67 (with options)
List of 2
$ eval: logi TRUE
$ echo: logi TRUE
ordinary text without R code
label: unnamed-chunk-68 (with options)
List of 2
$ tidy: logi FALSE
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-69 (with options)
List of 1
$ echo: num 2
ordinary text without R code
|............... | 22%
label: unnamed-chunk-70 (with options)
List of 3
$ eval: logi FALSE
$ echo: logi TRUE
$ tidy: logi FALSE
ordinary text without R code
|............... | 23%
label: unnamed-chunk-71 (with options)
List of 2
$ type : chr "rmdwarning"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-72 (with options)
List of 1
$ eval: logi TRUE
ordinary text without R code
label: unnamed-chunk-73 (with options)
List of 1
$ tidy: logi FALSE
ordinary text without R code
label: unnamed-chunk-74 (with options)
List of 1
$ cache: logi TRUE
ordinary text without R code
|............... | 24%
label: unnamed-chunk-75 (with options)
List of 1
$ echo: logi TRUE
ordinary text without R code
label: 3-1 (with options)
List of 6
$ fig.cap : chr "Example of Monte-Carlo integration. To estimate the area under the curve throw random points at the graph and count the number "| __truncated__
$ echo : logi FALSE
$ fig.width : num 6
$ fig.height: num 4
$ fig.align : chr "center"
$ out.width : chr "70%"
cropping _main_files/figure-latex/3-1-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/3-1-1.pdf'.
|................ | 24%
ordinary text without R code
label: unnamed-chunk-76
ordinary text without R code
label: unnamed-chunk-77
ordinary text without R code
|................ | 25%
label: unnamed-chunk-78
ordinary text without R code
label: unnamed-chunk-79 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-80
ordinary text without R code
label: unnamed-chunk-81 (with options)
List of 1
$ eval: logi FALSE
|................. | 25%
ordinary text without R code
|................. | 26%
label: unnamed-chunk-82 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-83 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-84 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-85
ordinary text without R code
|................. | 27%
label: unnamed-chunk-86 (with options)
List of 2
$ fig.keep: chr "none"
$ echo : num 2
ordinary text without R code
label: unnamed-chunk-87
|.................. | 27%
ordinary text without R code
label: unnamed-chunk-88
ordinary text without R code
label: unnamed-chunk-89 (with options)
List of 2
$ fig.keep: chr "none"
$ echo : num 6
ordinary text without R code
|.................. | 28%
label: boxplot_factor (with options)
List of 2
$ eval : logi TRUE
$ fig.keep: chr "none"
ordinary text without R code
label: unnamed-chunk-90 (with options)
List of 1
$ echo: num 2
ordinary text without R code
label: unnamed-chunk-91
ordinary text without R code
label: unnamed-chunk-92 (with options)
List of 2
$ type : chr "rmdwarning"
$ engine: chr "block"
|................... | 28%
ordinary text without R code
|................... | 29%
label: unnamed-chunk-93
ordinary text without R code
label: unnamed-chunk-94 (with options)
List of 2
$ echo: logi FALSE
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-95 (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-96 (with options)
List of 1
$ echo: num 2
ordinary text without R code
|................... | 30%
label: unnamed-chunk-97
ordinary text without R code
label: unnamed-chunk-98
ordinary text without R code
|.................... | 30%
label: unnamed-chunk-99
ordinary text without R code
label: image_dist_s3
ordinary text without R code
|.................... | 31%
label: 3-2 (with options)
List of 5
$ fig.cap : chr "S3 image method for data of class `dist`."
$ echo : logi FALSE
$ fig.asp : num 0.7
$ fig.width: num 5
$ fig.align: chr "center"
cropping _main_files/figure-latex/3-2-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/3-2-1.pdf'.
ordinary text without R code
label: unnamed-chunk-100 (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: apply-family (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: unnamed-chunk-101 (with options)
List of 1
$ results: chr "hide"
ordinary text without R code
|..................... | 32%
label: unnamed-chunk-102 (with options)
List of 1
$ results: chr "hide"
ordinary text without R code
label: unnamed-chunk-103
ordinary text without R code
label: unnamed-chunk-104
ordinary text without R code
label: unnamed-chunk-105
ordinary text without R code
|..................... | 33%
label: unnamed-chunk-106
ordinary text without R code
label: 3-3 (with options)
List of 7
$ fig.keep : chr "last"
$ echo : language 1:2
$ fig.height: num 4
$ fig.width : num 6
$ fig.cap : chr "Movie voting preferences."
$ fig.align : chr "center"
$ out.width : chr "70%"
cropping _main_files/figure-latex/3-3-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/3-3-1.pdf'.
ordinary text without R code
|...................... | 33%
label: unnamed-chunk-107 (with options)
List of 1
$ results: chr "hide"
ordinary text without R code
label: unnamed-chunk-108
|...................... | 34%
ordinary text without R code
label: benchmark_memoise (with options)
List of 3
$ fig.keep: chr "none"
$ cache : logi TRUE
$ results : chr "hide"
ordinary text without R code
label: unnamed-chunk-109 (with options)
List of 2
$ type : chr "rmdwarning"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-110
ordinary text without R code
label: unnamed-chunk-111
|...................... | 35%
ordinary text without R code
|....................... | 35%
label: unnamed-chunk-112
ordinary text without R code
label: unnamed-chunk-113
ordinary text without R code
label: unnamed-chunk-114 (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-115
|....................... | 36%
ordinary text without R code
label: unnamed-chunk-116
ordinary text without R code
label: unnamed-chunk-117
ordinary text without R code
label: unnamed-chunk-118
|........................ | 36%
ordinary text without R code
label: unnamed-chunk-119
|........................ | 37%
ordinary text without R code
label: unnamed-chunk-120
ordinary text without R code
label: unnamed-chunk-121 (with options)
List of 1
$ results: chr "hide"
ordinary text without R code
label: unnamed-chunk-122 (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-123
|........................ | 38%
ordinary text without R code
label: unnamed-chunk-124
|......................... | 38%
ordinary text without R code
label: unnamed-chunk-125
ordinary text without R code
label: unnamed-chunk-126
ordinary text without R code
label: unnamed-chunk-127 (with options)
List of 2
$ results: chr "hide"
$ eval : logi FALSE
|......................... | 39%
ordinary text without R code
label: 3-4 (with options)
List of 7
$ echo : logi FALSE
$ fig.height: num 4
$ fig.width : num 6
$ fig.cap : chr "Comparsion of mean functions."
$ eval : logi TRUE
$ fig.align : chr "center"
$ out.width : chr "70%"
cropping _main_files/figure-latex/3-4-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/3-4-1.pdf'.
ordinary text without R code
label: unnamed-chunk-128 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-129 (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
|.......................... | 39%
ordinary text without R code
label: unnamed-chunk-130 (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE
|.......................... | 40%
ordinary text without R code
label: 4-1 (with options)
List of 6
$ echo : logi FALSE
$ fig.width : num 6
$ fig.height: num 4
$ fig.cap : chr "Schematic illustrations of key project phases and levels of activity over time, based on @PMBoK2000."
$ out.width : chr "70%"
$ fig.align : chr "center"
cropping _main_files/figure-latex/4-1-1.pdf
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `_main_files/figure-latex/4-1-1.pdf'.
ordinary text without R code
label: 4-2 (with options)
List of 4
$ echo : logi FALSE
$ fig.cap : chr "A Gantt chart created using **DiagrammeR** illustrating the steps needed to complete this book at an early stage of its develop"| __truncated__
$ out.width: chr "80%"
$ fig.align: chr "center"
ordinary text without R code
label: unnamed-chunk-131 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-132 (with options)
List of 2
$ echo: logi FALSE
$ eval: logi FALSE
|.......................... | 41%
ordinary text without R code
label: unnamed-chunk-133
|........................... | 41%
ordinary text without R code
label: unnamed-chunk-134
ordinary text without R code
label: unnamed-chunk-135 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: 4-3 (with options)
List of 2
$ echo : logi FALSE
$ out.width: chr "25%"
|........................... | 42%
ordinary text without R code
label: 4-4 (with options)
List of 2
$ echo : logi FALSE
$ out.width: chr "25%"
ordinary text without R code
label: rmd (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: sampleCode (with options)
List of 1
$ indent: chr " "
ordinary text without R code
|............................ | 42%
label: unnamed-chunk-136
|............................ | 43%
ordinary text without R code
label: unnamed-chunk-137 (with options)
List of 2
$ include: logi FALSE
$ cache : logi FALSE
ordinary text without R code
label: unnamed-chunk-138 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: unnamed-chunk-139 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
label: json (with options)
List of 2
$ type : chr "rmdtip"
$ engine: chr "block"
|............................ | 44%
ordinary text without R code
label: unnamed-chunk-140 (with options)
List of 2
$ results: chr "hide"
$ warning: logi FALSE
ordinary text without R code
|............................. | 44%
label: unnamed-chunk-141 (with options)
List of 1
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-142 (with options)
List of 2
$ type : chr "rmdwarning"
$ engine: chr "block"
ordinary text without R code
label: unnamed-chunk-143 (with options)
List of 1
$ echo: language -1:-2
|............................. | 45%
ordinary text without R code
label: read-table-csv (with options)
List of 2
$ type : chr "rmdnote"
$ engine: chr "block"
ordinary text without R code
label: 5-1 (with options)
List of 6
$ fig.cap : chr "Benchmarks of **base**, **data.table** and **readr** functions for reading csv files. The facets ranging from $2$ to $200$ repr"| __truncated__
$ echo : logi FALSE
$ warning : logi FALSE
$ message : logi FALSE
$ out.width: chr "90%"
$ fig.align: chr "center"
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'.
ordinary text without R code
label: unnamed-chunk-144 (with options)
List of 1
$ eval: logi FALSE
ordinary text without R code
|.............................. | 45%
label: unnamed-chunk-145 (with options)
List of 1
$ cache: logi TRUE
|.............................. | 46%
ordinary text without R code
label: unnamed-chunk-146 (with options)
List of 1
$ cache: logi TRUE
ordinary text without R code
label: unnamed-chunk-147
ordinary text without R code
label: unnamed-chunk-148 (with options)
List of 1
$ warning: logi FALSE
ordinary text without R code
label: unnamed-chunk-149 (with options)
List of 1
$ warning: logi FALSE
*** 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 9e7fa96
Author: Colin Gillespie <[email protected]>
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?
I managed to install the package from the github repos about two weeks ago,
but now, when I try to update or reinstall, I get an error:
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/efficientR/libs
** data
*** moving datasets to lazyload DB
Warning: file ‘05-f2.RData’ has magic number 'X'
Use of save versions prior to 2 is deprecated
Error : bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘efficientR’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/efficientR’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/efficientR’
Error: Command failed (1)
Use Sys.getenv("HOME") not path.expand("~")
@Robinlovelace In the last section of https://github.com/csgillespie/efficientR/blob/master/10-collaboration.Rmd
I expect the problem is on my side if no one else is reporting it, but wonder if you might have any idea why I am receiving the following error when running bookdown::render_book("index.Rmd", bookdown::html_chapters())
after running devtools::install_github("csgillespie/efficientR")
Quitting from lines 17-25 (_main.Rmd)
Error in eval(expr, envir, enclos) : object 'mychart' not found
Interestingly, it turns out that which.max
is always faster than which(...)[[1]]
, and starting with N=1000 the difference is one order of magnitude. You might want to include this info and a chart in the Appendix.
data<-matrix(NA,nrow=100,ncol=2)
ns<-exp(seq(from=log(10),to=log(10^6),length.out = 100))
n.rep<-10 #Number of times to generate a test sample. This smooths the chart.
for (i in seq_along(data))
{
tmp<-matrix(NA,nrow=n.rep,ncol=2)
for(j in 1:n.rep)
{
s<-sample(c(TRUE,FALSE),ns[[i]],TRUE,prob=c(1-0.0001,0.0001))
tmp[j,]<-summary(microbenchmark(
which.max(s),
which(s)[[1]]))[['median']]
}
data[i,1]<-mean(tmp[,1])
data[i,2]<-mean(tmp[,2])
cat(paste0('.'))
}
data<-cbind(ns,data)
data<-as.data.frame(data)
names(data)<-c('N','which.max','which')
colors <- c("which"="blue","which.max"="grey")
ggplot(data,aes(x=N)) +
geom_line(aes(y=which.max, color='which.max')) +
geom_line(aes(y=which,color='which')) +
scale_x_continuous(labels = comma, trans=log10_trans()) +
scale_linetype_manual(values='colors',name='Function') +
scale_y_continuous(labels = comma, trans=log10_trans()) +
ylab("Execution time") + xlab("Vector size")
In Section 5.2 it says "described in (???)(renviron)."
This is wrong.
$ R --quiet --vanilla -e "getOption('defaultPackages')"
> getOption('defaultPackages')
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
$ Rscript --vanilla -e "getOption('defaultPackages')"
[1] "datasets" "utils" "grDevices" "graphics" "stats"
$ export R_DEFAULT_PACKAGES=datasets,utils,grDevices,graphics,stats,methods
$ R --quiet --vanilla -e "getOption('defaultPackages')"
> getOption('defaultPackages')
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
$ Rscript --vanilla -e "getOption('defaultPackages')"
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
Just tried to build the book on my new laptop and got:
Installing rio and feather
Installing packages into '/home/robin/R/x86_64-pc-linux-gnu-library/3.3'
(as 'lib' is unspecified)
Quitting from lines 6005-6038 (_main.Rmd)
Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
Calls: <Anonymous> ... eval -> eval -> install.packages -> grep -> contrib.url
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
Warning message:
Closing open result set
Not sure what the warnings are but will aim to put in a PR to fix this specific issue based on this: http://stackoverflow.com/questions/17705133/package-error-when-running-r-code-on-command-line
Please tell me where I'm going wrong! thanks.
running win7,
R 3.3.1
rstudio 0.99.903
my final lines of ouput:
ordinary text without R code
|.................................................. | 78%
label: unnamed-chunk-247 (with options)
List of 2
$ cache : logi TRUE
$ results: chr "hide"
C:/PROGRA~1/R/R-33~1.1/etc/x64/Makeconf:203: warning: overriding commands for target `.m.o'
C:/PROGRA~1/R/R-33~1.1/etc/x64/Makeconf:196: warning: ignoring old commands for target `.m.o'
C:\PROGRA~2\Gow\bin\make.exe: Interrupt/Exception caught (code = 0xc00000fd, addr = 0x4227d3)
Warning message:
running command 'make -f "C:/PROGRA~1/R/R-33~1.1/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sourceCpp_2.dll" WIN=64 TCLBIN=64 OBJECTS="file2254380d77b5.o"' had status 255
Quitting from lines 4637-4638 (_main.Rmd)
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir, :
Error 1 occurred building shared library.
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> cppFunction -> sourceCpp
Execution halted
The reference can be found in the beginning of chapter 3.7.1 "Function closures".
It is a manifestation of the bookdown's issue 117: Treat blocks as markdown. I read that it would be included in the v0.2 of the bookdown, so no fix will be needed. For pdf, a valid LaTeX still can be put, but for some reasons pandoc doesn't use the cite
package, but use home-grew solution. So the correct walkaround will be tu put:
(\protect\hyperlink{ref-Wickham2014}{Wickham 2014})
in place of the [@Wickham2014]
.
In chapter 2, we have
The output of
example(startup)
is also instructive.
But running example(startup)
doesn't work.
I was reading through the book online at https://csgillespie.github.io/efficientR/ (really great stuff!) and I noticed that the second half of chapter 2 is not rendered in the same font.
It looks like the problem is with escaping the quote symbol in the warning section. Notice the text that shows up:
Specifically, if you use a path that has single backslashes (</code>), such as C:.csv, as provided by Windows
The text does render correctly on github, but the bookdown version isn't escaping it right
Below is an image screenshot:
Instead of stating pre-req once in chapter 1, be explicit for each chapter. Eg. http://r4ds.had.co.nz/data-visualisation.html
In chapter 2, we go from using file.path
site_path = R.home(component = "home")
fname = file.path(site_path, "etc", "Rprofile.site")
file.exists(fname)
to not using file.path
if(!file.exists("~/.Rprofile")) # only create if not already there
file.create("~/.Rprofile") # (don't overwrite it)
file.edit("~/.Rprofile")
We should be consistent. @Robinlovelace Thoughts?
I think you need the line:
LinkingTo: Rcpp
in the DESCRIPTION file to avoid this error:
g++ -I/home/R/R-3.2.4/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mean_c.cpp -o mean_c.o
mean_c.cpp:1:18: fatal error: Rcpp.h: No such file or directory
#include <Rcpp.h>
when building the package
In question 2, lapply
isn't covered until chapter 3.
To avoid constantly updating of index.md
, I've parsed the DESCRIPTION
file to get a list of CRAN dependencies. However it is no longer displayed in a nice way. @Robinlovelace any ideas of how to display it in a friendlier way?
In section 8.4 the last sentence reads
The computer used to compile the published version of this book chapter has r no_of_cores CPUs/Cores.
The "r no_of_cores" is probably supposed to be inline R code
Colin & @Robinlovelace
@Robinlovelace Should this be in data carpentry?
Most R programmers don't ever think about how much space data types take, and for small data sets it's not important. But since this is a book specifically about efficient R usage, maybe it's worth mentioning ie. if you have a 100MB matrix of numbers that are in numeric form but they're actually whole numbers, then casting them to int can save you 50MB
Hi,
I'm trying to build the book. When I run:
devtools::install_github("csgillespie/efficientR")
I get the following error, after being prompted if I want to install additional tools:
Downloading GitHub repo csgillespie/efficientR@master
from URL https://api.github.com/repos/csgillespie/efficientR/zipball/master
Error: running command '"C:/R/R-33~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD config CC' had status 1
Marcus
Suggestion from @jangorecki
Additionally IMO in a title like "efficient R" there should be mentioned context of that section: https://cran.r-project.org/doc/manuals/r-release/R-lang.html#Computing-on-the-language
It is an exceptional feature of R language giving much better flexibility when developed R language consumer app.
Initial thoughts: it fits under Efficient programming. Needs a nice example though
I find it peculiar to prefer =
over <-
as an assignment operator. Sure, Yihui Xie his personal preference is mentioned, but AFAIK no coding standard recommends this.
I copied my collected references about this topic from here to the references section below. Next to this, lintr
(of course, that is Hadley's coding standard as well) will complain by default at this. Why not teach beginners (or pro's) the (AFAICS) golden standard, developing their own personal style later?
Just my two cents, I think the idea of your book is awesome!
The optimal way of changing a factor to numeric is:
as.numeric(levels(x))[x]
There are a few instances in chapter 4 that need changed (@Robinlovelace )
Specifically via apis (e.g. from stplanr?) - to this section: https://github.com/csgillespie/efficientR/blob/master/05-input-output.Rmd#getting-data-from-the-internet-download
Also something on httr
You need to use type="source" when installing packages
y-scale is in MHz but y-axis label says GHz.
I meant fig 8.3 in section 8.6 (CPU)
Thanks for writing this book! Enjoying it so far!
In the example here in chapter two, it says to run these exercises:
#1: Create large dataset
X = matrix(rnorm(1e8), nrow = 1e7)
#2: Find the median of each column using a single core
r1 = lapply(X, median)
#3: Find the median of each column using many cores
r2 = parallel::mclapply(X, median) # runs in serial on Windows
However, I stopped running mine after 20 minutes, because I was still running on r1.
Maybe people have more than 16Gb of ram, and maybe there's something up with my computer, but perhaps it might be a better example doesn't take so long to run, or you mention to the users of the book "hey, this takes a while to run, expect around xx minutes".
Again, thanks for writing this book!
found in "7.2 Cairo type".
While I sympathize and echo the sentiment, prbly best to not directly alienate the 80% of Windows folks who are the main R users out there right in the book (which is why i leave the windows rants to twitter :-)
Totally grok this is a draft and this is a "placeholder/note" but it's also out for the world to see, now.
If you need me to test/validate anything on Macs (i also saw the mac comment), do not hesitate to ask.
Following your pull request, travis no longer builds:
https://travis-ci.org/csgillespie/efficientR/builds/123937951
I think you've used the same knitr label.
The first part of code doesn't run:
library("tidyr") # Need to load readr package
raw = read_csv("data/pew.csv") # read in the 'wide' dataset
Also
rawt[1:3,]
#> # A tibble: 3 x 3
#> religion Income Count
#> <chr> <chr> <int>
#> 1 Agnostic <$10k 27
#> 2 Atheist <$10k 12
#> 3 Buddhist <$10k 27
Is only tibble data frame when you use read_csv
; this impacts the comment in the first rmdnote box.
@Robinlovelace The pdf version of the book won't build (and hence the web version won't get updated). I've narrowed it down to your data carpentry chapter. Would you investigate and fix.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.