installation of package had non-zero exit status
I've just updated R to version 3.6.2 "dark and stormy night" released December 12th last year. I've tried installing the following packages but have received the same error, "installation of package X had non-zero exit status".
The packages include: broom, tidyr, tidyselect, vctrs, and rlang.
I've examined documentation for broom and I didn't see anything saying that it explicitly is only supported by some previous version. For context, this afternoon I had version 5.2.1, received similar errors and decided to upgrade.
Is there a chance the problem is on my end, mac OSX Catalina? What can I do to resolve the issue?
Here's more info from the error as requested:
> library("tidyverse", lib.loc="/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘broom’
Edit 2: An exhaustive printout of all errors and messages as requested in comments:
> install.packages("tidyverse")
also installing the dependencies ‘colorspace’, ‘sys’, ‘ps’, ‘highr’, ‘markdown’, ‘farver’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘askpass’, ‘rematch’, ‘prettyunits’, ‘processx’, ‘knitr’, ‘yaml’, ‘htmltools’, ‘evaluate’, ‘base64enc’, ‘tinytex’, ‘xfun’, ‘DBI’, ‘tidyselect’, ‘gtable’, ‘lazyeval’, ‘scales’, ‘viridisLite’, ‘withr’, ‘vctrs’, ‘curl’, ‘mime’, ‘openssl’, ‘clipr’, ‘cellranger’, ‘progress’, ‘callr’, ‘fs’, ‘rmarkdown’, ‘whisker’, ‘selectr’, ‘broom’, ‘dbplyr’, ‘forcats’, ‘ggplot2’, ‘haven’, ‘hms’, ‘httr’, ‘jsonlite’, ‘lubridate’, ‘modelr’, ‘readr’, ‘readxl’, ‘reprex’, ‘rlang’, ‘rstudioapi’, ‘rvest’, ‘tidyr’, ‘xml2’
There are binary versions available but the source versions are later:
binary source needs_compilation
prettyunits 1.1.0 1.1.1 FALSE
tidyselect 0.2.5 1.0.0 TRUE
vctrs 0.2.1 0.2.2 TRUE
callr 3.4.0 3.4.1 FALSE
broom 0.5.3 0.5.4 FALSE
rlang 0.4.2 0.4.3 TRUE
tidyr 1.0.0 1.0.2 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/colorspace_1.4-1.tgz'
Content type 'application/x-gzip' length 2522321 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/sys_3.3.tgz'
Content type 'application/x-gzip' length 47231 bytes (46 KB)
==================================================
downloaded 46 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/ps_1.3.0.tgz'
Content type 'application/x-gzip' length 209460 bytes (204 KB)
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downloaded 204 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/highr_0.8.tgz'
Content type 'application/x-gzip' length 41180 bytes (40 KB)
==================================================
downloaded 40 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/markdown_1.1.tgz'
Content type 'application/x-gzip' length 199930 bytes (195 KB)
==================================================
downloaded 195 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/farver_2.0.3.tgz'
Content type 'application/x-gzip' length 1828397 bytes (1.7 MB)
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downloaded 1.7 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/labeling_0.3.tgz'
Content type 'application/x-gzip' length 61520 bytes (60 KB)
==================================================
downloaded 60 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/munsell_0.5.0.tgz'
Content type 'application/x-gzip' length 243642 bytes (237 KB)
==================================================
downloaded 237 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/RColorBrewer_1.1-2.tgz'
Content type 'application/x-gzip' length 53161 bytes (51 KB)
==================================================
downloaded 51 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21926 bytes (21 KB)
==================================================
downloaded 21 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rematch_1.0.1.tgz'
Content type 'application/x-gzip' length 12480 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/processx_3.4.1.tgz'
Content type 'application/x-gzip' length 236878 bytes (231 KB)
==================================================
downloaded 231 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/knitr_1.27.tgz'
Content type 'application/x-gzip' length 1380627 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/yaml_2.2.0.tgz'
Content type 'application/x-gzip' length 201073 bytes (196 KB)
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downloaded 196 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/htmltools_0.4.0.tgz'
Content type 'application/x-gzip' length 342242 bytes (334 KB)
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downloaded 334 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/evaluate_0.14.tgz'
Content type 'application/x-gzip' length 74657 bytes (72 KB)
==================================================
downloaded 72 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/base64enc_0.1-3.tgz'
Content type 'application/x-gzip' length 32230 bytes (31 KB)
==================================================
downloaded 31 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/tinytex_0.19.tgz'
Content type 'application/x-gzip' length 98971 bytes (96 KB)
==================================================
downloaded 96 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/xfun_0.12.tgz'
Content type 'application/x-gzip' length 178520 bytes (174 KB)
==================================================
downloaded 174 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/DBI_1.1.0.tgz'
Content type 'application/x-gzip' length 586234 bytes (572 KB)
==================================================
downloaded 572 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/gtable_0.3.0.tgz'
Content type 'application/x-gzip' length 432473 bytes (422 KB)
==================================================
downloaded 422 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/lazyeval_0.2.2.tgz'
Content type 'application/x-gzip' length 158838 bytes (155 KB)
==================================================
downloaded 155 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/scales_1.1.0.tgz'
Content type 'application/x-gzip' length 544693 bytes (531 KB)
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downloaded 531 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/viridisLite_0.3.0.tgz'
Content type 'application/x-gzip' length 57231 bytes (55 KB)
==================================================
downloaded 55 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/withr_2.1.2.tgz'
Content type 'application/x-gzip' length 152438 bytes (148 KB)
==================================================
downloaded 148 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/curl_4.3.tgz'
Content type 'application/x-gzip' length 741337 bytes (723 KB)
==================================================
downloaded 723 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/mime_0.8.tgz'
Content type 'application/x-gzip' length 35364 bytes (34 KB)
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downloaded 34 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/openssl_1.4.1.tgz'
Content type 'application/x-gzip' length 2690137 bytes (2.6 MB)
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downloaded 2.6 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/clipr_0.7.0.tgz'
Content type 'application/x-gzip' length 48251 bytes (47 KB)
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downloaded 47 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/cellranger_1.1.0.tgz'
Content type 'application/x-gzip' length 103127 bytes (100 KB)
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downloaded 100 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/progress_1.2.2.tgz'
Content type 'application/x-gzip' length 82991 bytes (81 KB)
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downloaded 81 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/fs_1.3.1.tgz'
Content type 'application/x-gzip' length 852880 bytes (832 KB)
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downloaded 832 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rmarkdown_2.1.tgz'
Content type 'application/x-gzip' length 3556971 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/whisker_0.4.tgz'
Content type 'application/x-gzip' length 65424 bytes (63 KB)
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downloaded 63 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/selectr_0.4-2.tgz'
Content type 'application/x-gzip' length 490483 bytes (478 KB)
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downloaded 478 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/dbplyr_1.4.2.tgz'
Content type 'application/x-gzip' length 578881 bytes (565 KB)
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downloaded 565 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/forcats_0.4.0.tgz'
Content type 'application/x-gzip' length 343715 bytes (335 KB)
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downloaded 335 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/ggplot2_3.2.1.tgz'
Content type 'application/x-gzip' length 3973186 bytes (3.8 MB)
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downloaded 3.8 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/haven_2.2.0.tgz'
Content type 'application/x-gzip' length 1077133 bytes (1.0 MB)
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downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/hms_0.5.3.tgz'
Content type 'application/x-gzip' length 103612 bytes (101 KB)
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downloaded 101 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/httr_1.4.1.tgz'
Content type 'application/x-gzip' length 492648 bytes (481 KB)
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downloaded 481 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/jsonlite_1.6.tgz'
Content type 'application/x-gzip' length 1117755 bytes (1.1 MB)
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downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/lubridate_1.7.4.tgz'
Content type 'application/x-gzip' length 1512972 bytes (1.4 MB)
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downloaded 1.4 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/modelr_0.1.5.tgz'
Content type 'application/x-gzip' length 199606 bytes (194 KB)
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downloaded 194 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/readr_1.3.1.tgz'
Content type 'application/x-gzip' length 792657 bytes (774 KB)
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downloaded 774 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/readxl_1.3.1.tgz'
Content type 'application/x-gzip' length 1646895 bytes (1.6 MB)
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downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/reprex_0.3.0.tgz'
Content type 'application/x-gzip' length 424791 bytes (414 KB)
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downloaded 414 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rstudioapi_0.10.tgz'
Content type 'application/x-gzip' length 214537 bytes (209 KB)
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downloaded 209 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rvest_0.3.5.tgz'
Content type 'application/x-gzip' length 662160 bytes (646 KB)
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downloaded 646 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/xml2_1.2.2.tgz'
Content type 'application/x-gzip' length 1102370 bytes (1.1 MB)
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downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/tidyverse_1.3.0.tgz'
Content type 'application/x-gzip' length 433010 bytes (422 KB)
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downloaded 422 KB
The downloaded binary packages are in
/var/folders/rb/qs7xx8rs633bk4njyk_6t7bh0000gn/T//RtmphOGt7Z/downloaded_packages
installing the source packages ‘prettyunits’, ‘tidyselect’, ‘vctrs’, ‘callr’, ‘broom’, ‘rlang’, ‘tidyr’
trying URL 'https://cran.rstudio.com/src/contrib/prettyunits_1.1.1.tar.gz'
Content type 'application/x-gzip' length 10366 bytes (10 KB)
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downloaded 10 KB
trying URL 'https://cran.rstudio.com/src/contrib/tidyselect_1.0.0.tar.gz'
Content type 'application/x-gzip' length 151161 bytes (147 KB)
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downloaded 147 KB
trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.2.2.tar.gz'
Content type 'application/x-gzip' length 721926 bytes (705 KB)
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downloaded 705 KB
trying URL 'https://cran.rstudio.com/src/contrib/callr_3.4.1.tar.gz'
Content type 'application/x-gzip' length 67676 bytes (66 KB)
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downloaded 66 KB
trying URL 'https://cran.rstudio.com/src/contrib/broom_0.5.4.tar.gz'
Content type 'application/x-gzip' length 1228129 bytes (1.2 MB)
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downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/rlang_0.4.3.tar.gz'
Content type 'application/x-gzip' length 813395 bytes (794 KB)
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downloaded 794 KB
trying URL 'https://cran.rstudio.com/src/contrib/tidyr_1.0.2.tar.gz'
Content type 'application/x-gzip' length 812005 bytes (792 KB)
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downloaded 792 KB
* installing *source* package ‘prettyunits’ ...
** package ‘prettyunits’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (prettyunits)
* installing *source* package ‘callr’ ...
** package ‘callr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (callr)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.
ERROR: compilation failed for package ‘rlang’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
ERROR: dependency ‘rlang’ is not available for package ‘vctrs’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/vctrs’
Warning in install.packages :
installation of package ‘vctrs’ had non-zero exit status
ERROR: dependencies ‘rlang’, ‘vctrs’ are not available for package ‘tidyselect’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tidyselect’
Warning in install.packages :
installation of package ‘tidyselect’ had non-zero exit status
ERROR: dependencies ‘rlang’, ‘tidyselect’, ‘vctrs’ are not available for package ‘tidyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tidyr’
Warning in install.packages :
installation of package ‘tidyr’ had non-zero exit status
ERROR: dependency ‘tidyr’ is not available for package ‘broom’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/broom’
Warning in install.packages :
installation of package ‘broom’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/rb/qs7xx8rs633bk4njyk_6t7bh0000gn/T/RtmphOGt7Z/downloaded_packages’
Answer
When you call install.packages("broom") (or insert package), it appears the message you receive is:
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) to which you have answered yes.
Try no and compare results. This should fix the issue.