Issues with installing R package cli from source

[rxxiang89]

I was trying to install ggplot 3.4.0, which needs lifecycle > 1.0.1. Seems to be an issue with cli? Thanks!

> library(lifecycle)
Error in library(lifecycle) : there is no package called ‘lifecycle’
> install.packages("lifecycle","C:/R/library")
also installing the dependency ‘cli’


  There are binary versions available but the source versions are later:
          binary source needs_compilation
cli        3.2.0  3.6.1              TRUE
lifecycle  1.0.1  1.0.4             FALSE

installing the source packages ‘cli’, ‘lifecycle’

trying URL 'https://cran.rstudio.com/src/contrib/cli_3.6.1.tar.gz'
Content type 'application/x-gzip' length 567293 bytes (553 KB)
downloaded 553 KB

trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.4.tar.gz'
Content type 'application/x-gzip' length 107656 bytes (105 KB)
downloaded 105 KB

* installing *source* package 'cli' ...
** package 'cli' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ansi.c -o ansi.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cleancall.c -o cleancall.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c diff.c -o diff.o
diff.c: In function 'clic_diff_chr':
diff.c:114:3: warning: 'sn' may be used uninitialized in this function [-Wmaybe-uninitialized]
   for (i = 0; i < sn; i++, op_ptr++, off_ptr++, len_ptr++) {
   ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c errors.c -o errors.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c glue.c -o glue.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inst.c -o inst.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c keypress-unix.c -o keypress-unix.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c keypress-win.c -o keypress-win.o
In file included from C:/PROGRA~1/R/R-40~1.0/include/R.h:91,
                 from keypress.h:5,
                 from keypress-win.c:8:
C:/PROGRA~1/R/R-40~1.0/include/R_ext/RS.h:55: warning: "ERROR" redefined
 #define ERROR   ),error(R_problem_buf);}
 
In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/windows.h:71,
                 from errors.h:24,
                 from keypress-win.c:7:
C:/rtools40/mingw32/i686-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition
 #define ERROR 0
 
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c keypress.c -o keypress.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c md5.c -o md5.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c progress-altrep.c -o progress-altrep.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c progress.c -o progress.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sha1.c -o sha1.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sha256.c -o sha256.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c thread.c -o thread.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tty.c -o tty.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utf8.c -o utf8.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vt.c -o vt.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vtparse.c -o vtparse.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vtparse_table.c -o vtparse_table.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c win-utf8.c -o win-utf8.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c winfiles.c -o winfiles.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o cli.dll tmp.def ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -LC:/PROGRA~1/R/R-40~1.0/bin/i386 -lR
installing to C:/R/library/00LOCK-cli/00new/cli/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ansi.c -o ansi.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cleancall.c -o cleancall.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c diff.c -o diff.o
diff.c: In function 'clic_diff_chr':
diff.c:85:7: warning: 'sn' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int sn;
       ^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c errors.c -o errors.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c glue.c -o glue.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inst.c -o inst.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c keypress-unix.c -o keypress-unix.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c keypress-win.c -o keypress-win.o
In file included from C:/PROGRA~1/R/R-40~1.0/include/R.h:91,
                 from keypress.h:5,
                 from keypress-win.c:8:
C:/PROGRA~1/R/R-40~1.0/include/R_ext/RS.h:55: warning: "ERROR" redefined
 #define ERROR   ),error(R_problem_buf);}
 
In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/windows.h:71,
                 from errors.h:24,
                 from keypress-win.c:7:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/wingdi.h:75: note: this is the location of the previous definition
 #define ERROR 0
 
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c keypress.c -o keypress.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c md5.c -o md5.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c progress-altrep.c -o progress-altrep.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c progress.c -o progress.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sha1.c -o sha1.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sha256.c -o sha256.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c thread.c -o thread.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tty.c -o tty.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utf8.c -o utf8.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vt.c -o vt.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vtparse.c -o vtparse.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vtparse_table.c -o vtparse_table.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c win-utf8.c -o win-utf8.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG        -I../inst/include   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c winfiles.c -o winfiles.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o cli.dll tmp.def ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -LC:/PROGRA~1/R/R-40~1.0/bin/x64 -lR
installing to C:/R/library/00LOCK-cli/00new/cli/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cli'
    finding HTML links ... done
    ansi-styles                             html  
    ansi_align                              html  
    ansi_collapse                           html  
    ansi_columns                            html  
    ansi_grep                               html  
    ansi_has_any                            html  
    ansi_hide_cursor                        html  
    ansi_html                               html  
    ansi_html_style                         html  
    ansi_nchar                              html  
    ansi_nzchar                             html  
    ansi_palettes                           html  
    ansi_regex                              html  
    ansi_simplify                           html  
    ansi_strip                              html  
    ansi_strsplit                           html  
    ansi_strtrim                            html  
    ansi_strwrap                            html  
    ansi_substr                             html  
    ansi_substring                          html  
    ansi_toupper                            html  
    ansi_trimws                             html  
    boxx                                    html  
    builtin_theme                           html  
    cat_line                                html  
    cli-config                              html  
    cli-package                             html  
    cli                                     html  
    cli_abort                               html  
    cli_alert                               html  
    cli_blockquote                          html  
    cli_bullets                             html  
    cli_bullets_raw                         html  
    cli_code                                html  
    cli_debug_doc                           html  
    cli_div                                 html  
    cli_dl                                  html  
    cli_end                                 html  
    cli_fmt                                 html  
    cli_format                              html  
    cli_format_method                       html  
    cli_h1                                  html  
    cli_li                                  html  
    cli_list_themes                         html  
    cli_ol                                  html  
    cli_output_connection                   html  
    cli_par                                 html  
    cli_process_start                       html  
    cli_progress_along                      html  
    cli_progress_bar                        html  
    cli_progress_builtin_handlers           html  
    cli_progress_demo                       html  
    cli_progress_message                    html  
    cli_progress_output                     html  
    cli_progress_step                       html  
    cli_progress_styles                     html  
    cli_rule                                html  
    cli_sitrep                              html  
    cli_status                              html  
    cli_status_clear                        html  
    cli_status_update                       html  
    cli_text                                html  
    cli_ul                                  html  
    cli_vec                                 html  
    cli_verbatim                            html  
    code_highlight                          html  
    code_theme_list                         html  
    combine_ansi_styles                     html  
    console_width                           html  
    containers                              html  
    demo_spinners                           html  
    diff_chr                                html  
    diff_str                                html  
    faq                                     html  
    format_error                            html  
    format_inline                           html  
    get_spinner                             html  
    has_keypress_support                    html  
    hash_animal                             html  
    hash_emoji                              html  
    hash_md5                                html  
    hash_sha1                               html  
    hash_sha256                             html  
    inline-markup                           html  
    is_ansi_tty                             html  
    is_dynamic_tty                          html  
    is_utf8_output                          html  
    keypress                                html  
    links                                   html  
    list_spinners                           html  
    make_ansi_style                         html  
    make_spinner                            html  
    match_selector                          html  
    match_selector_node                     html  
    num_ansi_colors                         html  
    parse_selector                          html  
    pluralization-helpers                   html  
    pluralization                           html  
    pluralize                               html  
    pretty_print_code                       html  
    progress-c                              html  
    progress-utils                          html  
    progress-variables                      html  
    rule                                    html  
    ruler                                   html  
    simple_theme                            html  
    spark_bar                               html  
    spark_line                              html  
    start_app                               html  
    style_hyperlink                         html  
    symbol                                  html  
    test_that_cli                           html  
Error: error reading from connection
* removing 'C:/R/library/cli'
* restoring previous 'C:/R/library/cli'
Warning in install.packages :
  installation of package ‘cli’ had non-zero exit status
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lifecycle'
    finding HTML links ... done
    badge                                   html  
    deprecate_soft                          html  
    deprecated                              html  
    expect_deprecated                       html  
Error: error reading from connection
* removing 'C:/R/library/lifecycle'
Warning in install.packages :
  installation of package ‘lifecycle’ had non-zero exit status

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0  

[gaborcsardi]

This does not seem like an issue with the cli package, it also happens to the other package you are installing:

* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lifecycle'
    finding HTML links ... done
    badge                                   html  
    deprecate_soft                          html  
    deprecated                              html  
    expect_deprecated                       html  
Error: error reading from connection
* removing 'C:/R/library/lifecycle'
Warning in install.packages :
  installation of package ‘lifecycle’ had non-zero exit status