readxl installation problem

[fbenedett]

Hello I am trying to install "readxl", but I encounter a problem.

Here what I did:

install.packages("readxl")
Installing package into ‘/home/fbenedet/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/readxl_1.4.3.tar.gz'
Content type 'application/x-gzip' length 2093488 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘readxl’ ...
** package ‘readxl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c cpp11.cpp -o cpp11.o
In file included from /usr/lib/R/site-library/cpp11/include/cpp11/as.hpp:11,
                 from /usr/lib/R/site-library/cpp11/include/cpp11.hpp:5,
                 from /usr/lib/R/site-library/cpp11/include/cpp11/declarations.hpp:8,
                 from cpp11.cpp:5:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp: In member function ‘void cpp11::<unnamed struct>::print()’:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:18: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                 ~^                             ~~~~
      |                  |                             |
      |                  unsigned int                  SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                         ~^                           ~~~~~~~~~
      |                          |                              |
      |                          unsigned int                   SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                 ~^                              ~~~~~~~~~
      |                                  |                                 |
      |                                  unsigned int                      SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:42: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                         ~^                                 ~~~~~~~~~
      |                                          |                                    |
      |                                          unsigned int                         SEXP {aka SEXPREC*}
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c XlsWorkBook.cpp -o XlsWorkBook.o
In file included from utils.h:3,
                 from ColSpec.h:3,
                 from XlsWorkBook.h:3,
                 from XlsWorkBook.cpp:1:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp: In member function ‘void cpp11::<unnamed struct>::print()’:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:18: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                 ~^                             ~~~~
      |                  |                             |
      |                  unsigned int                  SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                         ~^                           ~~~~~~~~~
      |                          |                              |
      |                          unsigned int                   SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                 ~^                              ~~~~~~~~~
      |                                  |                                 |
      |                                  unsigned int                      SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:42: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                         ~^                                 ~~~~~~~~~
      |                                          |                                    |
      |                                          unsigned int                         SEXP {aka SEXPREC*}
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c XlsxWorkBook.cpp -o XlsxWorkBook.o
In file included from utils.h:3,
                 from ColSpec.h:3,
                 from XlsxWorkBook.h:3,
                 from XlsxWorkBook.cpp:1:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp: In member function ‘void cpp11::<unnamed struct>::print()’:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:18: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                 ~^                             ~~~~
      |                  |                             |
      |                  unsigned int                  SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                         ~^                           ~~~~~~~~~
      |                          |                              |
      |                          unsigned int                   SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                 ~^                              ~~~~~~~~~
      |                                  |                                 |
      |                                  unsigned int                      SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:42: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                         ~^                                 ~~~~~~~~~
      |                                          |                                    |
      |                                          unsigned int                         SEXP {aka SEXPREC*}
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c zip.cpp -o zip.o
In file included from /usr/lib/R/site-library/cpp11/include/cpp11/as.hpp:11,
                 from /usr/lib/R/site-library/cpp11/include/cpp11/function.hpp:10,
                 from zip.cpp:5:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp: In member function ‘void cpp11::<unnamed struct>::print()’:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:18: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                 ~^                             ~~~~
      |                  |                             |
      |                  unsigned int                  SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                         ~^                           ~~~~~~~~~
      |                          |                              |
      |                          unsigned int                   SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                 ~^                              ~~~~~~~~~
      |                                  |                                 |
      |                                  unsigned int                      SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:42: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                         ~^                                 ~~~~~~~~~
      |                                          |                                    |
      |                                          unsigned int                         SEXP {aka SEXPREC*}
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/progress/include'    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c Read.cpp -o Read.o
In file included from utils.h:3,
                 from ColSpec.h:3,
                 from XlsCell.h:3,
                 from CellLimits.h:3,
                 from SheetView.h:4,
                 from Read.cpp:1:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp: In member function ‘void cpp11::<unnamed struct>::print()’:
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:18: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 2 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                 ~^                             ~~~~
      |                  |                             |
      |                  unsigned int                  SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                         ~^                           ~~~~~~~~~
      |                          |                              |
      |                          unsigned int                   SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                 ~^                              ~~~~~~~~~
      |                                  |                                 |
      |                                  unsigned int                      SEXP {aka SEXPREC*}
/usr/lib/R/site-library/cpp11/include/cpp11/protect.hpp:337:42: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  337 |       REprintf("%x CAR: %x CDR: %x TAG: %x\n", head, CAR(head), CDR(head), TAG(head));
      |                                         ~^                                 ~~~~~~~~~
      |                                          |                                    |
      |                                          unsigned int                         SEXP {aka SEXPREC*}
In file included from Spinner.h:3,
                 from XlsCellSet.h:4,
                 from SheetView.h:8,
                 from Read.cpp:1:
/usr/lib/R/site-library/progress/include/RProgress.h: In member function ‘void RProgress::RProgress::render()’:
/usr/lib/R/site-library/progress/include/RProgress.h:229:17: error: format not a string literal and no format arguments [-Werror=format-security]
  229 |         REprintf(str.c_str());
      |         ~~~~~~~~^~~~~~~~~~~~~
/usr/lib/R/site-library/progress/include/RProgress.h:231:16: error: format not a string literal and no format arguments [-Werror=format-security]
  231 |         Rprintf(str.c_str());
      |         ~~~~~~~^~~~~~~~~~~~~
/usr/lib/R/site-library/progress/include/RProgress.h: In member function ‘void RProgress::RProgress::clear_line(bool, int)’:
/usr/lib/R/site-library/progress/include/RProgress.h:272:15: error: format not a string literal and no format arguments [-Werror=format-security]
  272 |       REprintf(spaces);
      |       ~~~~~~~~^~~~~~~~
/usr/lib/R/site-library/progress/include/RProgress.h:274:14: error: format not a string literal and no format arguments [-Werror=format-security]
  274 |       Rprintf(spaces);
      |       ~~~~~~~^~~~~~~~
cc1plus: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:204: Read.o] Error 1
ERROR: compilation failed for package ‘readxl’
* removing ‘/home/fbenedet/R/x86_64-pc-linux-gnu-library/4.4/readxl’
Warning in install.packages :
  installation of package ‘readxl’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmp05WfBk/downloaded_packages’

System details

> version
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          4.0                         
year           2024                        
month          04                          
day            24                          
svn rev        86474                       
language       R                           
version.string R version 4.4.0 (2024-04-24)
nickname       Puppy Cup  

Rstudio version 2024.04.0 Build 735

RStudio Edition : Desktop
OS Version      :  Ubuntu 22.04

• I have read the guide for submitting good bug reports.
• I have installed the latest version of RStudio, and confirmed that the issue still persists.
• If I am reporting an RStudio crash, I have included a diagnostics report.
• I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.

[ronblum]

@fbenedett Thank you for raising this! What happens if you try to install the package in R, outside of RStudio?

[Med-AL]

Can you try to install progress and Rcpp package

install.package("Rcpp")
install.package("Rcpp11")
install.package("progress")

And reinstall readxl

[fbenedett]

Hello, I tried another solution and I was able to fix the problem.
I had to mofify the file Makevars (there are severals, mine was one under the directory: /home/fbenedet/R/x86_64-pc-linux-gnu-library/4.4/)
I had to add this options. After, I was able to install readxl
CXXFLAGS += -Wno-format-security

[ronblum]

Does the problem occur in R outside of RStudio?

[fbenedett]

I cannot confirm it, because I fixed from within Rstudio with the solution I provided.

[pwkraft]

Can you try to install progress and Rcpp package

install.package("Rcpp") install.package("Rcpp11") install.package("progress")

And reinstall readxl

I encountered the same issue described above (same OS & R Version). The problem also occurred in R outside of RStudio, but (re-)installing Rcpp and progress as suggested by @Med-AL fixed it.