> install.packages("remotes")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/remotes_2.2.0.tgz'
Content type 'application/x-gzip' length 386257 bytes (377 KB)
==================================================
downloaded 377 KB
The downloaded binary packages are in
/var/folders/3m/dcxq5q_m8xj_zp001s74__6r0000gn/T//RtmpQPNpUU/downloaded_packages
> remotes::install_github("tidymodels/TMwR")
Downloading GitHub repo tidymodels/TMwR@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: recipes (0.1.12 -> c9b9987e7...) [GitHub]
5: Rcpp (1.0.4.6 -> 1.0.5 ) [CRAN]
6: pillar (1.4.4 -> 1.4.6 ) [CRAN]
7: ellipsis (0.3.0 -> 0.3.1 ) [CRAN]
8: vctrs (0.3.0 -> 0.3.4 ) [CRAN]
9: tibble (3.0.1 -> 3.0.3 ) [CRAN]
10: rlang (0.4.6 -> 0.4.7 ) [CRAN]
11: glue (1.4.0 -> 1.4.2 ) [CRAN]
12: ps (1.3.3 -> 1.3.4 ) [CRAN]
13: processx (3.4.2 -> 3.4.4 ) [CRAN]
14: callr (3.4.3 -> 3.4.4 ) [CRAN]
15: pkgbuild (1.0.8 -> 1.1.0 ) [CRAN]
16: pkgload (1.0.2 -> 1.1.0 ) [CRAN]
17: withr (2.2.0 -> 2.3.0 ) [CRAN]
18: isoband (0.2.1 -> 0.2.2 ) [CRAN]
19: stringi (1.4.6 -> 1.5.3 ) [CRAN]
20: data.table (1.12.8 -> 1.13.0 ) [CRAN]
21: backports (1.1.6 -> 1.1.10 ) [CRAN]
22: xfun (0.13 -> 0.17 ) [CRAN]
23: tinytex (0.22 -> 0.26 ) [CRAN]
24: jsonlite (1.6.1 -> 1.7.1 ) [CRAN]
25: htmltools (0.4.0 -> 0.5.0 ) [CRAN]
26: knitr (1.28 -> 1.30 ) [CRAN]
27: rmarkdown (2.1 -> 2.3 ) [CRAN]
28: fs (1.4.1 -> 1.5.0 ) [CRAN]
29: cpp11 (0.1.0 -> 0.2.1 ) [CRAN]
30: dplyr (1.0.0 -> 1.0.2 ) [CRAN]
31: tidyr (1.0.3 -> 1.1.2 ) [CRAN]
32: broom (0.5.6 -> 0.7.0 ) [CRAN]
33: sys (3.3 -> 3.4 ) [CRAN]
34: openssl (1.4.1 -> 1.4.3 ) [CRAN]
35: later (1.0.0 -> 1.1.0.1 ) [CRAN]
36: httpuv (1.5.2 -> 1.5.4 ) [CRAN]
37: promises (1.1.0 -> 1.1.1 ) [CRAN]
38: xts (0.12-0 -> 0.12.1 ) [CRAN]
39: DT (0.13 -> 0.15 ) [CRAN]
40: colourpicker (1.0 -> 1.1.0 ) [CRAN]
41: shiny (1.4.0.2 -> 1.5.0 ) [CRAN]
42: V8 (3.0.2 -> 3.2.0 ) [CRAN]
43: matrixStats (0.56.0 -> 0.57.0 ) [CRAN]
44: nloptr (1.2.2.1 -> 1.2.2.2 ) [CRAN]
45: StanHeaders (2.21.0-1 -> 2.21.0-6 ) [CRAN]
46: rstantools (2.0.0 -> 2.1.1 ) [CRAN]
47: rstan (2.19.3 -> 2.21.2 ) [CRAN]
48: loo (2.2.0 -> 2.3.1 ) [CRAN]
49: bayesplot (1.7.1 -> 1.7.2 ) [CRAN]
50: globals (0.12.5 -> 0.13.0 ) [CRAN]
51: parsnip (0.1.1 -> 0.1.3 ) [CRAN]
52: SQUAREM (2020.2 -> 2020.4 ) [CRAN]
53: lava (1.6.7 -> 1.6.8 ) [CRAN]
54: future (1.17.0 -> 1.19.1 ) [CRAN]
55: slider (0.1.2 -> 0.1.5 ) [CRAN]
56: modeldata (0.0.1 -> 0.0.2 ) [CRAN]
57: lubridate (1.7.8 -> 1.7.9 ) [CRAN]
58: gower (0.2.1 -> 0.2.2 ) [CRAN]
59: rsample (0.0.6 -> 0.0.8 ) [CRAN]
60: yardstick (0.0.6 -> 0.0.7 ) [CRAN]
61: httr (1.4.1 -> 1.4.2 ) [CRAN]
62: gplots (3.0.4 -> 3.1.0 ) [CRAN]
63: dendextend (1.13.4 -> 1.14.0 ) [CRAN]
64: rvest (0.3.5 -> 0.3.6 ) [CRAN]
65: modelr (0.1.7 -> 0.1.8 ) [CRAN]
66: haven (2.2.0 -> 2.3.1 ) [CRAN]
67: dbplyr (1.4.3 -> 1.4.4 ) [CRAN]
68: kableExtra (1.1.0 -> 1.2.1 ) [CRAN]
69: bookdown (0.18 -> 0.20 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
Downloading GitHub repo tidymodels/tune@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rsample (0.0.6 -> ae99c8624...) [GitHub]
5: cpp11 (0.1.0 -> 0.2.1 ) [CRAN]
6: pillar (1.4.4 -> 1.4.6 ) [CRAN]
7: ellipsis (0.3.0 -> 0.3.1 ) [CRAN]
8: vctrs (0.3.0 -> 0.3.4 ) [CRAN]
9: globals (0.12.5 -> 0.13.0 ) [CRAN]
10: tidyr (1.0.3 -> 1.1.2 ) [CRAN]
11: glue (1.4.0 -> 1.4.2 ) [CRAN]
12: tibble (3.0.1 -> 3.0.3 ) [CRAN]
13: rlang (0.4.6 -> 0.4.7 ) [CRAN]
14: dplyr (1.0.0 -> 1.0.2 ) [CRAN]
15: Rcpp (1.0.4.6 -> 1.0.5 ) [CRAN]
16: future (1.17.0 -> 1.19.1 ) [CRAN]
17: ps (1.3.3 -> 1.3.4 ) [CRAN]
18: processx (3.4.2 -> 3.4.4 ) [CRAN]
19: backports (1.1.6 -> 1.1.10 ) [CRAN]
20: callr (3.4.3 -> 3.4.4 ) [CRAN]
21: pkgbuild (1.0.8 -> 1.1.0 ) [CRAN]
22: withr (2.2.0 -> 2.3.0 ) [CRAN]
23: pkgload (1.0.2 -> 1.1.0 ) [CRAN]
24: SQUAREM (2020.2 -> 2020.4 ) [CRAN]
25: lava (1.6.7 -> 1.6.8 ) [CRAN]
26: parsnip (0.1.1 -> 0.1.3 ) [CRAN]
27: slider (0.1.2 -> 0.1.5 ) [CRAN]
28: modeldata (0.0.1 -> 0.0.2 ) [CRAN]
29: isoband (0.2.1 -> 0.2.2 ) [CRAN]
30: lubridate (1.7.8 -> 1.7.9 ) [CRAN]
31: gower (0.2.1 -> 0.2.2 ) [CRAN]
32: yardstick (0.0.6 -> 0.0.7 ) [CRAN]
33: recipes (0.1.12 -> 0.1.13 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
Downloading GitHub repo tidymodels/workflows@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rlang (0.4.6 -> 0.4.7 ) [CRAN]
5: pillar (1.4.4 -> 1.4.6 ) [CRAN]
6: cpp11 (0.1.0 -> 0.2.1 ) [CRAN]
7: vctrs (0.3.0 -> 0.3.4 ) [CRAN]
8: tibble (3.0.1 -> 3.0.3 ) [CRAN]
9: glue (1.4.0 -> 1.4.2 ) [CRAN]
10: ellipsis (0.3.0 -> 0.3.1 ) [CRAN]
11: dplyr (1.0.0 -> 1.0.2 ) [CRAN]
12: globals (0.12.5 -> 0.13.0) [CRAN]
13: tidyr (1.0.3 -> 1.1.2 ) [CRAN]
14: parsnip (0.1.1 -> 0.1.3 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
Installing 1 packages: hardhat
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/hardhat_0.1.4.tgz'
Content type 'application/x-gzip' length 716341 bytes (699 KB)
==================================================
downloaded 699 KB
The downloaded binary packages are in
/var/folders/3m/dcxq5q_m8xj_zp001s74__6r0000gn/T//RtmpQPNpUU/downloaded_packages
✓ checking for file ‘/private/var/folders/3m/dcxq5q_m8xj_zp001s74__6r0000gn/T/RtmpQPNpUU/remotesfca15751d737/tidymodels-workflows-213d4cd/DESCRIPTION’ ...
─ preparing ‘workflows’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘workflows_0.2.0.9000.tar.gz’
* installing *source* package ‘workflows’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘parsnip’ 0.1.1 is being loaded, but >= 0.1.3 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘workflows’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/workflows’
Error: Failed to install 'TMwR' from GitHub:
Failed to install 'tune' from GitHub:
Failed to install 'workflows' from GitHub:
(converted from warning) installation of package ‘/var/folders/3m/dcxq5q_m8xj_zp001s74__6r0000gn/T//RtmpQPNpUU/filefca13b440ff4/workflows_0.2.0.9000.tar.gz’ had non-zero exit status
> bookdown::render_book("index.Rmd", "bookdown::gitbook")
Error in bookdown::render_book("index.Rmd", "bookdown::gitbook") :
No input R Markdown files found from the current directory /Users/theoneal/Desktop/R_desktop/Tidy_models or in the rmd_files field of _bookdown.yml
> remotes::install_github("tidymodels/TMwR")
Downloading GitHub repo tidymodels/TMwR@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: recipes (0.1.12 -> c9b9987e7...) [GitHub]
5: Rcpp (1.0.4.6 -> 1.0.5 ) [CRAN]
6: pillar (1.4.4 -> 1.4.6 ) [CRAN]
7: ellipsis (0.3.0 -> 0.3.1 ) [CRAN]
8: vctrs (0.3.0 -> 0.3.4 ) [CRAN]
9: tibble (3.0.1 -> 3.0.3 ) [CRAN]
10: rlang (0.4.6 -> 0.4.7 ) [CRAN]
11: glue (1.4.0 -> 1.4.2 ) [CRAN]
12: ps (1.3.3 -> 1.3.4 ) [CRAN]
13: processx (3.4.2 -> 3.4.4 ) [CRAN]
14: callr (3.4.3 -> 3.4.4 ) [CRAN]
15: pkgbuild (1.0.8 -> 1.1.0 ) [CRAN]
16: pkgload (1.0.2 -> 1.1.0 ) [CRAN]
17: withr (2.2.0 -> 2.3.0 ) [CRAN]
18: isoband (0.2.1 -> 0.2.2 ) [CRAN]
19: stringi (1.4.6 -> 1.5.3 ) [CRAN]
20: data.table (1.12.8 -> 1.13.0 ) [CRAN]
21: backports (1.1.6 -> 1.1.10 ) [CRAN]
22: xfun (0.13 -> 0.17 ) [CRAN]
23: tinytex (0.22 -> 0.26 ) [CRAN]
24: jsonlite (1.6.1 -> 1.7.1 ) [CRAN]
25: htmltools (0.4.0 -> 0.5.0 ) [CRAN]
26: knitr (1.28 -> 1.30 ) [CRAN]
27: rmarkdown (2.1 -> 2.3 ) [CRAN]
28: fs (1.4.1 -> 1.5.0 ) [CRAN]
29: cpp11 (0.1.0 -> 0.2.1 ) [CRAN]
30: dplyr (1.0.0 -> 1.0.2 ) [CRAN]
31: tidyr (1.0.3 -> 1.1.2 ) [CRAN]
32: broom (0.5.6 -> 0.7.0 ) [CRAN]
33: sys (3.3 -> 3.4 ) [CRAN]
34: openssl (1.4.1 -> 1.4.3 ) [CRAN]
35: later (1.0.0 -> 1.1.0.1 ) [CRAN]
36: httpuv (1.5.2 -> 1.5.4 ) [CRAN]
37: promises (1.1.0 -> 1.1.1 ) [CRAN]
38: xts (0.12-0 -> 0.12.1 ) [CRAN]
39: DT (0.13 -> 0.15 ) [CRAN]
40: colourpicker (1.0 -> 1.1.0 ) [CRAN]
41: shiny (1.4.0.2 -> 1.5.0 ) [CRAN]
42: V8 (3.0.2 -> 3.2.0 ) [CRAN]
43: matrixStats (0.56.0 -> 0.57.0 ) [CRAN]
44: nloptr (1.2.2.1 -> 1.2.2.2 ) [CRAN]
45: StanHeaders (2.21.0-1 -> 2.21.0-6 ) [CRAN]
46: rstantools (2.0.0 -> 2.1.1 ) [CRAN]
47: rstan (2.19.3 -> 2.21.2 ) [CRAN]
48: loo (2.2.0 -> 2.3.1 ) [CRAN]
49: bayesplot (1.7.1 -> 1.7.2 ) [CRAN]
50: globals (0.12.5 -> 0.13.0 ) [CRAN]
51: parsnip (0.1.1 -> 0.1.3 ) [CRAN]
52: SQUAREM (2020.2 -> 2020.4 ) [CRAN]
53: lava (1.6.7 -> 1.6.8 ) [CRAN]
54: future (1.17.0 -> 1.19.1 ) [CRAN]
55: slider (0.1.2 -> 0.1.5 ) [CRAN]
56: modeldata (0.0.1 -> 0.0.2 ) [CRAN]
57: lubridate (1.7.8 -> 1.7.9 ) [CRAN]
58: gower (0.2.1 -> 0.2.2 ) [CRAN]
59: rsample (0.0.6 -> 0.0.8 ) [CRAN]
60: yardstick (0.0.6 -> 0.0.7 ) [CRAN]
61: httr (1.4.1 -> 1.4.2 ) [CRAN]
62: gplots (3.0.4 -> 3.1.0 ) [CRAN]
63: dendextend (1.13.4 -> 1.14.0 ) [CRAN]
64: rvest (0.3.5 -> 0.3.6 ) [CRAN]
65: modelr (0.1.7 -> 0.1.8 ) [CRAN]
66: haven (2.2.0 -> 2.3.1 ) [CRAN]
67: dbplyr (1.4.3 -> 1.4.4 ) [CRAN]
68: kableExtra (1.1.0 -> 1.2.1 ) [CRAN]
69: bookdown (0.18 -> 0.20 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
Downloading GitHub repo tidymodels/tune@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rsample (0.0.6 -> ae99c8624...) [GitHub]
5: cpp11 (0.1.0 -> 0.2.1 ) [CRAN]
6: pillar (1.4.4 -> 1.4.6 ) [CRAN]
7: ellipsis (0.3.0 -> 0.3.1 ) [CRAN]
8: vctrs (0.3.0 -> 0.3.4 ) [CRAN]
9: globals (0.12.5 -> 0.13.0 ) [CRAN]
10: tidyr (1.0.3 -> 1.1.2 ) [CRAN]
11: glue (1.4.0 -> 1.4.2 ) [CRAN]
12: tibble (3.0.1 -> 3.0.3 ) [CRAN]
13: rlang (0.4.6 -> 0.4.7 ) [CRAN]
14: dplyr (1.0.0 -> 1.0.2 ) [CRAN]
15: Rcpp (1.0.4.6 -> 1.0.5 ) [CRAN]
16: future (1.17.0 -> 1.19.1 ) [CRAN]
17: ps (1.3.3 -> 1.3.4 ) [CRAN]
18: processx (3.4.2 -> 3.4.4 ) [CRAN]
19: backports (1.1.6 -> 1.1.10 ) [CRAN]
20: callr (3.4.3 -> 3.4.4 ) [CRAN]
21: pkgbuild (1.0.8 -> 1.1.0 ) [CRAN]
22: withr (2.2.0 -> 2.3.0 ) [CRAN]
23: pkgload (1.0.2 -> 1.1.0 ) [CRAN]
24: SQUAREM (2020.2 -> 2020.4 ) [CRAN]
25: lava (1.6.7 -> 1.6.8 ) [CRAN]
26: parsnip (0.1.1 -> 0.1.3 ) [CRAN]
27: slider (0.1.2 -> 0.1.5 ) [CRAN]
28: modeldata (0.0.1 -> 0.0.2 ) [CRAN]
29: isoband (0.2.1 -> 0.2.2 ) [CRAN]
30: lubridate (1.7.8 -> 1.7.9 ) [CRAN]
31: gower (0.2.1 -> 0.2.2 ) [CRAN]
32: yardstick (0.0.6 -> 0.0.7 ) [CRAN]
33: recipes (0.1.12 -> 0.1.13 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
Downloading GitHub repo tidymodels/workflows@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rlang (0.4.6 -> 0.4.7 ) [CRAN]
5: pillar (1.4.4 -> 1.4.6 ) [CRAN]
6: cpp11 (0.1.0 -> 0.2.1 ) [CRAN]
7: vctrs (0.3.0 -> 0.3.4 ) [CRAN]
8: tibble (3.0.1 -> 3.0.3 ) [CRAN]
9: glue (1.4.0 -> 1.4.2 ) [CRAN]
10: ellipsis (0.3.0 -> 0.3.1 ) [CRAN]
11: dplyr (1.0.0 -> 1.0.2 ) [CRAN]
12: globals (0.12.5 -> 0.13.0) [CRAN]
13: tidyr (1.0.3 -> 1.1.2 ) [CRAN]
14: parsnip (0.1.1 -> 0.1.3 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
✓ checking for file ‘/private/var/folders/3m/dcxq5q_m8xj_zp001s74__6r0000gn/T/RtmpQPNpUU/remotesfca138f53ca7/tidymodels-workflows-213d4cd/DESCRIPTION’ ...
─ preparing ‘workflows’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘workflows_0.2.0.9000.tar.gz’
* installing *source* package ‘workflows’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘parsnip’ 0.1.1 is being loaded, but >= 0.1.3 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘workflows’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/workflows’
Error: Failed to install 'TMwR' from GitHub:
Failed to install 'tune' from GitHub:
Failed to install 'workflows' from GitHub:
(converted from warning) installation of package ‘/var/folders/3m/dcxq5q_m8xj_zp001s74__6r0000gn/T//RtmpQPNpUU/filefca16c611527/workflows_0.2.0.9000.tar.gz’ had non-zero exit status
Can you try it from a fresh R session? It looks like parsnip was already loaded and needed to update.
The error messages indicate compilation failures, which often occur on macOS for reasons usually having to do with lack of a properly updated XCode app and its command line utilities.
The configuration shown in the OP indicates another likely source of errors: a lagging version of R.
Updating to Catalina, R 4, XCode current version, installing the command line utilities may, but is not assured, to resolve the problem. Whenever possible install binaries.
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