yihui/xfun

xfun wont

tropidendro opened this issue · 5 comments

tropidendro commented

Hi, trying to download the KNITR package but it appears to not be unpacking the 'xfun' package (has non-zero exit status).
I've attached session info and the verbatim text below. Thank you.

sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] ggplot2_3.3.2 plyr_1.8.6 dplyr_1.0.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 pillar_1.4.4 compiler_4.0.1 tools_4.0.1
[5] extrafont_0.17 digest_0.6.25 lattice_0.20-41 nlme_3.1-148
[9] lifecycle_0.2.0 tibble_3.0.1 gtable_0.3.0 mgcv_1.8-31
[13] pkgconfig_2.0.3 rlang_0.4.6 Matrix_1.2-18 rstudioapi_0.11
[17] Rttf2pt1_1.3.8 withr_2.2.0 generics_0.0.2 vctrs_0.3.1
[21] grid_4.0.1 tidyselect_1.1.0 glue_1.4.1 R6_2.4.1
[25] farver_2.0.3 purrr_0.3.4 extrafontdb_1.0 magrittr_1.5
[29] splines_4.0.1 scales_1.1.1 ellipsis_0.3.1 htmltools_0.5.0
[33] colorspace_1.4-1 labeling_0.3 munsell_0.5.0 crayon_1.3.4

install.packages("knitr")
also installing the dependency ‘xfun’

There are binary versions available but the source versions are
later:
binary source needs_compilation
xfun 0.14 0.15 TRUE
knitr 1.28 1.29 FALSE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source packages ‘xfun’, ‘knitr’

trying URL 'https://cran.rstudio.com/src/contrib/xfun_0.15.tar.gz'
Content type 'application/x-gzip' length 74045 bytes (72 KB)

downloaded 72 KB

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.29.tar.gz'
Content type 'application/x-gzip' length 885623 bytes (864 KB)

downloaded 864 KB

  • installing source package ‘xfun’ ...
    ** package ‘xfun’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
    ERROR: compilation failed for package ‘xfun’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/xfun’
  • restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/xfun’
    Warning in install.packages :
    installation of package ‘xfun’ had non-zero exit status
  • installing source package ‘knitr’ ...
    ** package ‘knitr’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** demo
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
    namespace ‘xfun’ 0.14 is being loaded, but >= 0.15 is required
    Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
    Execution halted
    ERROR: lazy loading failed for package ‘knitr’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/knitr’
    Warning in install.packages :
    installation of package ‘knitr’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/rq/sykzqqds59ncjt51mk870gd12z7tby/T/RtmpQAaA3A/downloaded_packages’

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yihui commented

Please either run xcode-select --install in your terminal, or wait for a few days for CRAN to have the binary version: https://cran.r-project.org/package=xfun Thanks!

tropidendro commented
yihui commented

You are welcome! Please let me know if you could install the new version of xfun successfully this time. Thanks!

1beb commented

PSA: I received a similar error recently. However, it was because of another install of rJava or RStan that created inappropriate makevars. After removing / moving / fixing the .R/Makevars file I was able to install xfun appropriately. (Mac OS - Catalina)

  • 👍1
yihui commented

All binary versions are available on CRAN now.