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Comments (13)

vnijs avatar vnijs commented on June 19, 2024

I found a fix by changing the last lines of code in the makeRepo function in makeRepo.R from

if(download) download.packages(pkgs, destdir=pkgPath, repos=repos, type=type)
if(writePACKAGES) tools::write_PACKAGES(dir=pkgPath, type=type)

to

if(download) download.packages(pkgs, destdir=pkgPath, repos=repos, type=type)
if(type == "mac.binary.mavericks") type <- "mac.binary"
if(writePACKAGES) tools::write_PACKAGES(dir=pkgPath, type=type)

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andrie avatar andrie commented on June 19, 2024

This is possibly related to contrib.url() defaulting to system R.version. See #12.

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vnijs avatar vnijs commented on June 19, 2024

Could it be simpler than that? It seems that write_PACKAGES does not have mac.binary.mavericks as a type option and so it cannot write the PACKAGES file. Everything else works fine. It is just the PACKAGES files that are not produced.

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andrie avatar andrie commented on June 19, 2024

Possibly. But I can't test it using R-3.0 because the mavericks binaries exist only for R-3.1 and up. So there is an even deeper underlying problem.

Regardless, can you please test the following:

  1. Does the PACKAGES file exist in the correct mavericks folder in your local repo after you run your changed code?
  2. When you try available.packages() from your local repo, do you get the results you expect, i.e. do all the downloaded packages get displayed?

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vnijs avatar vnijs commented on June 19, 2024

I am running R-3.1.1 and get the expected results. See attached.

I will distribute my own app (Radiant) to students through a read-only dropbox folder with fall and It took me a while to figure out how to install from the local repo. Attached what I came up with. If there is an easier/better way to do this I would love to hear about it. Perhaps an example in the vignette would be useful to others?

Again, great package. I expect it will save me a lot of headaches with 200 students using Radiant in a few weeks.

Vincent

From: Andrie <[email protected]mailto:[email protected]>
Reply-To: andrie/miniCRAN <[email protected]mailto:[email protected]>
Date: Thursday, September 25, 2014 at 6:37 AM
To: andrie/miniCRAN <[email protected]mailto:[email protected]>
Cc: Vincent Nijs <[email protected]mailto:[email protected]>
Subject: Re: [miniCRAN] makeRepo error for mac.binary.mavericks (#11)

Possibly. But I can't test it using R-3.0 because the mavericks binaries exist only for R-3.1 and up. So there is an even deeper underlying problem.

Regardless, can you please test the following:

  1. Does the PACKAGES file exist in the correct mavericks folder in your local repo after you run your changed code?
  2. When you try available.packages() from your local repo, do you get the results you expect, i.e. do all the downloaded packages get displayed?


Reply to this email directly or view it on GitHubhttps://github.com//issues/11#issuecomment-56819154.

available.packages("file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/")
Package Version Priority Depends
AlgDesign "AlgDesign" "1.1-7.2" NA NA
assertthat "assertthat" "0.1" NA NA
BH "BH" "1.54.0-4" NA NA
bitops "bitops" "1.0-6" NA NA
car "car" "2.0-21" NA "R (>= 2.14.0), stats, graphics"
caTools "caTools" "1.17.1" NA "R (>= 2.2.0)"
colorspace "colorspace" "1.2-4" NA "R (>= 2.13.0), methods"
dichromat "dichromat" "2.0-0" NA "R (>= 2.10), stats"
digest "digest" "0.6.4" NA "R (>= 2.4.1)"
dplyr "dplyr" "0.2" NA "R (>= 3.0.2)"
evaluate "evaluate" "0.5.5" NA "R (>= 2.14.0)"
formatR "formatR" "1.0" NA NA
ggplot2 "ggplot2" "1.0.0" NA "R (>= 2.14), stats, methods"
gridExtra "gridExtra" "0.9.1" NA "R(>= 2.5.0), grid"
gtable "gtable" "0.1.2" NA "R (>= 2.14), grid"
hflights "hflights" "0.1" NA "R (>= 2.10)"
highr "highr" "0.3" NA NA
htmltools "htmltools" "0.2.6" NA "R (>= 2.14.1)"
httpuv "httpuv" "1.3.0" NA "R (>= 2.15.1), methods"
knitr "knitr" "1.6" NA "R (>= 2.14.1)"
labeling "labeling" "0.3" NA NA
Lahman "Lahman" "3.0-1" NA "R (>= 2.10)"
lattice "lattice" "0.20-29" "recommended" "R (>= 2.15.1)"
lubridate "lubridate" "1.3.3" NA "methods, R (>= 3.0.0)"
magrittr "magrittr" "1.0.1" NA NA
markdown "markdown" "0.7.4" NA "R (>= 2.11.1)"
MASS "MASS" "7.3-34" "recommended" "R (>= 3.0.0), grDevices, graphics, stats, utils"
memoise "memoise" "0.2.1" NA NA
mime "mime" "0.1.2" NA NA
munsell "munsell" "0.4.2" NA NA
nnet "nnet" "7.3-8" "recommended" "R (>= 2.14.0), stats, utils"
permute "permute" "0.8-3" NA "R (>= 2.14.0)"
plyr "plyr" "1.8.1" NA "R (>= 2.11.0)"
proto "proto" "0.3-10" NA NA
psych "psych" "1.4.8.11" NA "R (>= 2.10)"
R.methodsS3 "R.methodsS3" "1.6.1" NA "R (>= 2.2.0)"
R.oo "R.oo" "1.18.0" NA "R (>= 2.4.0), R.methodsS3 (>= 1.6.1)"
R.utils "R.utils" "1.33.0" NA "R (>= 2.5.0), R.oo (>= 1.18.0)"
RColorBrewer "RColorBrewer" "1.0-5" NA "R (>= 2.0.0)"
Rcpp "Rcpp" "0.11.2" NA "R (>= 3.0.0)"
reshape2 "reshape2" "1.4" NA NA
RJSONIO "RJSONIO" "1.3-0" NA NA
scales "scales" "0.2.4" NA "R (>= 2.13)"
shiny "shiny" "0.10.1" NA "R (>= 2.14.1), methods"
shinyAce "shinyAce" "0.1.0" NA "R (>= 2.15.0)"
slam "slam" "0.1-32" NA "R (>= 2.8.0)"
stringr "stringr" "0.6.2" NA "R (>= 2.14)"
tidyr "tidyr" "0.1" NA "R (>= 3.1.0)"
vegan "vegan" "2.0-10" NA "permute (>= 0.8-0), lattice, R (>= 2.15.0)"
wordcloud "wordcloud" "2.5" NA "methods, RColorBrewer"
xtable "xtable" "1.7-4" NA "R (>= 2.10.0)"
Imports
AlgDesign NA
assertthat NA
BH NA
bitops NA
car "MASS, nnet"
caTools "bitops"
colorspace NA
dichromat NA
digest NA
dplyr "assertthat, utils, methods, Rcpp, magrittr, Lahman, hflights"
evaluate "stringr (>= 0.6.2)"
formatR NA
ggplot2 "plyr (>= 1.7.1), digest, grid, gtable (>= 0.1.1), reshape2, scales (>= 0.2.3), proto, MASS"
gridExtra NA
gtable NA
hflights NA
highr NA
htmltools "utils, digest"
httpuv "Rcpp (>= 0.11.0)"
knitr "evaluate (>= 0.5.3), digest, formatR (>= 0.10), highr (>= 0.3), markdown (>= 0.6.5), stringr (>= 0.6), tools"
labeling NA
Lahman NA
lattice "grid, grDevices, graphics, stats, utils"
lubridate "plyr, stringr, memoise"
magrittr NA
markdown "mime (>= 0.1.1)"
MASS NA
memoise "digest"
mime "tools"
munsell "colorspace"
nnet NA
permute NA
plyr "Rcpp (>= 0.11.0)"
proto NA
psych NA
R.methodsS3 "utils"
R.oo "methods, utils"
R.utils "utils, methods, R.methodsS3 (>= 1.6.1)"
RColorBrewer NA
Rcpp "methods"
reshape2 "plyr (>= 1.8.1), stringr, Rcpp"
RJSONIO "methods"
scales "RColorBrewer, dichromat, munsell (>= 0.2), plyr (>= 1.2), labeling, methods"
shiny "tools, utils, httpuv (>= 1.2.0), caTools, RJSONIO, xtable, digest, htmltools (>= 0.2.4)"
shinyAce "shiny (>= 0.7.0)"
slam "stats"
stringr NA
tidyr "reshape2, dplyr (>= 0.2)"
vegan NA
wordcloud "slam, Rcpp (>= 0.9.4)"
xtable NA
LinkingTo
AlgDesign NA
assertthat NA
BH NA
bitops NA
car NA
caTools NA
colorspace NA
dichromat NA
digest NA
dplyr "Rcpp (>= 0.11.1), BH (>= 1.51.0-2)"
evaluate NA
formatR NA
ggplot2 NA
gridExtra NA
gtable NA
hflights NA
highr NA
htmltools NA
httpuv "Rcpp"
knitr NA
labeling NA
Lahman NA
lattice NA
lubridate NA
magrittr NA
markdown NA
MASS NA
memoise NA
mime NA
munsell NA
nnet NA
permute NA
plyr "Rcpp"
proto NA
psych NA
R.methodsS3 NA
R.oo NA
R.utils NA
RColorBrewer NA
Rcpp NA
reshape2 "Rcpp"
RJSONIO NA
scales NA
shiny NA
shinyAce NA
slam NA
stringr NA
tidyr NA
vegan NA
wordcloud "Rcpp"
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lattice "KernSmooth, MASS"
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munsell "ggplot2 (>= 0.9.2)"
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proto "graph, Rgraphviz"
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R.methodsS3 NA
R.oo "tools"
R.utils "digest (>= 0.6.4)"
RColorBrewer NA
Rcpp "RUnit, inline, rbenchmark, highlight"
reshape2 "testthat (>= 0.8.0), lattice"
RJSONIO NA
scales "testthat (>= 0.8)"
shiny "datasets, Cairo (>= 1.5-5), testthat, knitr (>= 1.6), markdown"
shinyAce "testthat"
slam NA
stringr "testthat (>= 0.3)"
tidyr "knitr, testthat"
vegan "MASS, mgcv, cluster, scatterplot3d, rgl, tcltk"
wordcloud "tm (>= 0.6)"
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assertthat NA "GPL-3" NA
BH NA "BSL-1.0" NA
bitops NA "GPL (>= 2)" NA
car NA "GPL (>= 2)" NA
caTools NA "GPL-3" NA
colorspace NA "BSD_3_clause + file LICENSE" NA
dichromat NA "GPL-2" NA
digest NA "GPL-2" NA
dplyr NA "MIT + file LICENSE" NA
evaluate NA "GPL" NA
formatR NA "GPL" NA
ggplot2 "sp" "GPL-2" NA
gridExtra NA "GPL (>= 2)" NA
gtable NA "GPL-2" NA
hflights NA "CC0" NA
highr NA "GPL" NA
htmltools "knitr" "GPL (>= 2)" NA
httpuv NA "GPL-3 | file LICENSE" NA
knitr NA "GPL" NA
labeling NA "MIT + file LICENSE | Unlimited" NA
Lahman NA "GPL" NA
lattice "chron" "GPL (>= 2)" NA
lubridate "chron, timeDate, zoo, xts, its, tis, timeSeries, fts, tseries" "GPL" NA
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markdown NA "GPL-2" NA
MASS NA "GPL-2 | GPL-3" NA
memoise NA "MIT + file LICENSE" NA
mime NA "GPL" NA
munsell NA "MIT + file LICENSE" NA
nnet NA "GPL-2 | GPL-3" NA
permute NA "GPL-2" NA
plyr NA "MIT + file LICENSE" NA
proto NA "GPL-2" NA
psych NA "GPL (>= 2)" NA
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shinyAce NA "MIT + file LICENSE" NA
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stringr NA "GPL-2" NA
tidyr NA "MIT + file LICENSE" NA
vegan NA "GPL-2" NA
wordcloud NA "LGPL-2.1" NA
xtable NA "GPL (>= 2)" NA
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Repository
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assertthat "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
BH "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
bitops "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
car "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
caTools "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
colorspace "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
dichromat "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
digest "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
dplyr "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
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knitr "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
labeling "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
Lahman "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
lattice "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
lubridate "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
magrittr "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
markdown "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
MASS "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
memoise "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
mime "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
munsell "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
nnet "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
permute "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
plyr "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
proto "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
psych "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
R.methodsS3 "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
R.oo "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
R.utils "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
RColorBrewer "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
Rcpp "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
reshape2 "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
RJSONIO "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
scales "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
shiny "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
shinyAce "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
slam "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
stringr "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
tidyr "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
vegan "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
wordcloud "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"
xtable "file:///Users/vnijs/Dropbox/radiant/radiant-miniCRAN/bin/macosx/mavericks/contrib/3.1/"

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andrie avatar andrie commented on June 19, 2024

I have a slideshare presentation at http://www.slideshare.net/RevolutionAnalytics/through-the-firewall-with-minicran that explains how to refer to your local repo.

The trick is to use options(repos="file:///...")

I hope this helps.

Thank you for trying the package and reporting what you find. I'll include additional help and documentation in the next few days.

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vnijs avatar vnijs commented on June 19, 2024

Thanks @andrie. That does help.

Is it possible to add the one line of code to makeRepo.R?

if(type == "mac.binary.mavericks") type <- "mac.binary"

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andrie avatar andrie commented on June 19, 2024

@mostly-harmless Can you please contact me via email? You can find my contact details in the maintainer field of the package DESCRIPTION.

I am keen to resolve this issue, but I need to find a reliable way to test. You can help with that.

I wrote some additional unit tests and I need to see the test results on a mac.

Thanks in advance.

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andrie avatar andrie commented on June 19, 2024

@mostly-harmless I have now fixed this issue in a more general way in the development branch. Please let me know if this works for you.

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vnijs avatar vnijs commented on June 19, 2024

Thanks for the update @andrie. Everything seems to work fine except for mavericks. The directory structure is created but the PACKAGES files are not. See message below:

pkgList <- pkgDep(pkgs, repos=repos, type="mac.binary.mavericks", suggests = FALSE)
makeRepo(pkgList, path=pth, type="mac.binary.mavericks")

Error in match.arg(type) :
'arg' should be one of “source”, “mac.binary”, “win.binary”

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] miniCRAN_0.1-1

loaded via a namespace (and not attached):
[1] httr_0.6.0 igraph_0.7.1 stringr_0.6.2 tools_3.1.2 XML_3.98-1.1

From: Andrie <[email protected]mailto:[email protected]>
Reply-To: andrie/miniCRAN <[email protected]mailto:[email protected]>
Date: Sunday, December 14, 2014 at 7:20 AM
To: andrie/miniCRAN <[email protected]mailto:[email protected]>
Cc: Vincent Nijs <[email protected]mailto:[email protected]>
Subject: Re: [miniCRAN] makeRepo error for mac.binary.mavericks (#11)

@mostly-harmlesshttps://github.com/mostly-harmless I have now fixed this issue in a more general way in the development branch. Please let me know if this works for you.


Reply to this email directly or view it on GitHubhttps://github.com//issues/11#issuecomment-66916355.

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andrie avatar andrie commented on June 19, 2024

@mostly-harmless That still looks like the error in the master branch. Did you install from the dev branch?

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vnijs avatar vnijs commented on June 19, 2024

I guess I must have done something wrong the first time (I used ref = “dev” initially). I uninstalled and restarted R. Then ran the code below and the PACKAGES files are created. The final thing printed is now.

[[1]]
[1] 60

Thanks!!

Question: Is there a way in miniCRAN to add-in packages built using devtools::install_github()? For example, most of the packages I use are from CRAN but some (e.g., ggvis or rvest) may not be or the version on CRAN is older.

require(devtools)
Loading required package: devtools
install_github("andrie/miniCRAN@dev")
Downloading github repo andrie/miniCRAN@dev
Installing miniCRAN
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/n4/rlnqcs4101b9m602tytx0kbc0000gn/T/RtmpiVBxEO/devtools2e454813f99c/andrie-miniCRAN-55fdf4d'
--library='/Users/vnijs/Library/R/3.1/library' --install-tests

  • installing source package ‘miniCRAN’ ...
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** tests
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
  • DONE (miniCRAN)

    pth <- "~/Desktop/GitHub/radiant_dev/miniCRAN"
    setwd(pth)
    options(repos = c(CRAN = "http://cran.rstudio.com"))
    require(miniCRAN)
    Loading required package: miniCRAN
    source('pkgs.R')
    repos <- "http://cran.rstudio.com"
    pkgList <- pkgDep(pkgs, repos=repos, type="mac.binary.mavericks", suggests = FALSE)
    makeRepo(pkgList, path=pth, type="mac.binary.mavericks")

From: Andrie <[email protected]mailto:[email protected]>
Reply-To: andrie/miniCRAN <[email protected]mailto:[email protected]>
Date: Monday, December 15, 2014 at 1:49 AM
To: andrie/miniCRAN <[email protected]mailto:[email protected]>
Cc: Vincent Nijs <[email protected]mailto:[email protected]>
Subject: Re: [miniCRAN] makeRepo error for mac.binary.mavericks (#11)

@mostly-harmlesshttps://github.com/mostly-harmless That still looks like the error in the master branch. Did you install from the dev branch?


Reply to this email directly or view it on GitHubhttps://github.com//issues/11#issuecomment-66970525.

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andrie avatar andrie commented on June 19, 2024

@mostly-harmless You asked:

Question: Is there a way in miniCRAN to add-in packages built using devtools::install_github() ?

I opened a new issue #50 to track this. I'd like to have this functionality in due course.

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