hojsgaard
commented
7 years ago Dear Knut,
Thanks for your suggestions; much is related to that time flies... Will look into them!
My packages depend on packages on bioconductor. Do you have any idea how to make packages also install bioconductor dependencies? In that case, please let me know!
Regarding Springers charges: I recieve 2 USD per sold copy of our book, so I am not becoming a rich man from this activity...
Best Søren
Fra: Knut Behrends [notifications@github.com] Sendt: 2. juli 2017 12:33 Til: hojsgaard/gRbase Cc: Subscribed Emne: [hojsgaard/gRbase] Package Demos do not work, book Ch1 code doesn't either, + more (#6)
On my system, the 4 demos for gRbase are all broken
For example, the output of the Demo for the gmData dataset: it produces this error:
demo(package = "gRbase", gmData)
demo(gmData)
---- ~~~~~~Type
R> ## ################################################################### R> ## examples: R> R> ## add new type of variable R> oldtypes <- validVarTypes()
R> validVarTypes <- function() {
- c(oldtypes,"MyVarType")
- }
R> newgmData(1:3,"MyVarType") Error in FUN(X[[i]], ...) : 'arg' should be one of “Discrete”, “Ordinal”, “Continuous” Calls: demo ... eval -> eval -> newgmData -> sapply -> lapply -> FUN
On page 3 (but also pp 9, 10, 21, 24) of your book, the function call myiplot(ug0i, layout=layout.spring) to the myiplot function does no longer produce a result as displayed in the book, but produces a different layout. Output/Warning:
Spring layout was removed, we use Fruchterman-Reingold instead.
(layout.circle still works. There should be a call to set.seed() first)
I think there have been various API changes to the igraph package since 2012 when your book was released. Springer charges a lot for this textbook, and it might be a disappointment for users who actually purchase it for the full price. You could put a generic warning on your homepage. Or create a new github repository with updated versions of the code used in the book.
The "book errata" link on your homepage does not work. However, there is a link on another page (http://people.math.aau.dk/~sorenh/software/gR/index.htmlhttp://people.math.aau.dk/%7Esorenh/software/gR/index.html) that does work. it is linking to http://people.math.aau.dk/~sorenh/software/gR/GMwR-errata.txthttp://people.math.aau.dk/%7Esorenh/software/gR/GMwR-errata.txt
The installation notes for the packages should also note that the RBGL package (a dependency of gRbase) is also not on CRAN but on Bioconductor.
My System:
R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS
Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] grid parallel stats graphics grDevices utils [7] datasets methods base
other attached packages: [1] igraph_1.0.1 gRain_1.3-0 gRbase_1.8-3 [4] RBGL_1.52.0 Rgraphviz_2.20.0 graph_1.54.0 [7] BiocGenerics_0.22.0 BiocInstaller_1.26.0 knitr_1.16 [10] clipr_0.3.3 tibble_1.3.3 colorout_1.1-2
loaded via a namespace (and not attached): [1] Rcpp_0.12.11 lattice_0.20-35 magrittr_1.5 stats4_3.4.1 [5] rlang_0.1.1 Matrix_1.2-10 functional_0.6 tools_3.4.1 [9] yaml_2.1.14 compiler_3.4.1
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knbknb
On my system, the 4 demos for gRbase are all broken
For example, the output of the Demo for the gmData dataset: it produces this error:
On page 3 (but also pp 9, 10, 21, 24) of your book, the function call
myiplot(ug0i, layout=layout.spring)to themyiplotfunction does no longer produce a result as displayed in the book, but produces a different layout. Output/Warning:Spring layout was removed, we use Fruchterman-Reingold instead.(
layout.circlestill works. There should be a call toset.seed()first)I think there have been various API changes to the
igraphpackage since 2012 when your book was released. Springer charges a lot for this textbook, and it might be a disappointment for users who actually purchase it for the full price. You could put a generic warning on your homepage. Or create a new github repository with updated versions of the code used in the book.The "book errata" link on your homepage does not work. However, there is a link on another page (http://people.math.aau.dk/~sorenh/software/gR/index.html) that does work. it is linking to http://people.math.aau.dk/~sorenh/software/gR/GMwR-errata.txt
The installation notes for the packages should also note that the RBGL package (a dependency of gRbase) is also not on CRAN but on Bioconductor.
My System: