problem installing RcppParallel on Windows 7, R 4.0.2

[hansvancalster]

When I try to install from source it fails:

> install.packages("RcppParallel", type = "source")
Installing package into ‘C:/R/Library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/RcppParallel_5.0.2.tar.gz'
Content type 'application/x-gzip' length 1341240 bytes (1.3 MB)
downloaded 1.3 MB

Warning message:
In options(papersize = "a4", tab.width = 2, width = 80, help_type = "html",  :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
* installing *source* package 'RcppParallel' ...
** package 'RcppParallel' successfully unpacked and MD5 sums checked
** using staged installation
Warning message:
In options(papersize = "a4", tab.width = 2, width = 80, help_type = "html",  :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** preparing to configure package 'RcppParallel' ...
*** configured file: 'src/Makevars.in' => 'src/Makevars'
** finished configure for package 'RcppParallel'
** libs

*** arch - i386
Created ../build/lib_release directory
../../build/Makefile.tbb:32: CONFIG: cfg=release arch=ia32 compiler=gcc target=windows runtime=mingw
g++.exe: error: unrecognized command line option '-flifetime-dse=1'
make[2]: *** [../../build/common_rules.inc:119: concurrent_hash_map.o] Error 1
make[1]: *** [Makefile:104: tbb_release] Error 2
cp: cannot stat 'tbb/build/lib_release/tbb*.dll': No such file or directory
make: *** [Makevars:89: tbb] Error 1
ERROR: compilation failed for package 'RcppParallel'
* removing 'C:/R/Library/RcppParallel'
* restoring previous 'C:/R/Library/RcppParallel'

The downloaded source packages are in
        ‘C:\Users\hans_vancalster\AppData\Local\Temp\Rtmp4o9TSI\downloaded_packages’
Warning message:
In install.packages("RcppParallel", type = "source") :
  installation of package ‘RcppParallel’ had non-zero exit status

Installing the binary seems to work:

tall.packages("RcppParallel")
Installing package into ‘C:/R/Library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.0:
  cannot open URL 'https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.0/PACKAGES'
trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.0/RcppParallel_5.0.2.zip'
Content type 'application/zip' length 5167790 bytes (4.9 MB)
downloaded 4.9 MB

package ‘RcppParallel’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\hans_vancalster\AppData\Local\Temp\Rtmp4o9TSI\downloaded_packages

but when I do

library(RcppParallel)
> devtools::session_info()
- Session info ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Windows 7 x64 SP 1          
 system   x86_64, mingw32             
 ui       Rgui                        
 language (EN)                        
 collate  Dutch_Belgium.1252          
 ctype    Dutch_Belgium.1252          
 tz       Europe/Paris                
 date     2020-07-16                  

- Packages --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 ! package      * version date       lib source        
   assertthat     0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
   backports      1.1.7   2020-05-13 [1] CRAN (R 4.0.0)
   callr          3.4.3   2020-03-28 [1] CRAN (R 4.0.0)
   cli            2.0.2   2020-02-28 [1] CRAN (R 4.0.0)
   crayon         1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
   desc           1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
   devtools       2.3.0   2020-04-10 [1] CRAN (R 4.0.2)
   digest         0.6.25  2020-02-23 [1] CRAN (R 4.0.0)
   ellipsis       0.3.1   2020-05-15 [1] CRAN (R 4.0.2)
   fansi          0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
   fortunes       1.5-4   2016-12-29 [1] CRAN (R 4.0.0)
   fs             1.4.2   2020-06-30 [1] CRAN (R 4.0.2)
   git2r          0.27.1  2020-05-03 [1] CRAN (R 4.0.2)
   glue           1.4.1   2020-05-13 [1] CRAN (R 4.0.2)
   magrittr       1.5     2014-11-22 [1] CRAN (R 4.0.0)
   memoise        1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
   pkgbuild       1.1.0   2020-07-13 [1] CRAN (R 4.0.0)
   pkgload        1.1.0   2020-05-29 [1] CRAN (R 4.0.2)
   prettyunits    1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
   processx       3.4.3   2020-07-05 [1] CRAN (R 4.0.2)
   ps             1.3.3   2020-05-08 [1] CRAN (R 4.0.2)
   R6             2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
 D RcppParallel * 5.0.2   2020-06-24 [1] CRAN (R 4.0.2)
   remotes        2.1.1   2020-02-15 [1] CRAN (R 4.0.0)
   rlang          0.4.6   2020-05-02 [1] CRAN (R 4.0.2)
   rprojroot      1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
   sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
   testthat       2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
   usethis        1.6.1   2020-04-29 [1] CRAN (R 4.0.0)
   withr          2.2.0   2020-04-20 [1] CRAN (R 4.0.0)

[1] C:/R/Library
[2] C:/Program Files/R/R-4.0.2/library

 D -- DLL MD5 mismatch, broken installation.
> 

It indicates D -- DLL MD5 mismatch, broken installation. for the RcppPackage so something seems to be wrong?

I have rtools40:

Sys.which("make")
                              make 
"C:\\rtools40\\usr\\bin\\make.exe" 

Any ideas what goes wrong here with installation from source?
And (maybe unrelated?) why after installing the windows binary, devtools::session_info flags the RcppPackage as D -- DLL MD5 mismatch, broken installation.
I upgraded to R 4.02 (from R 4.0.0), could that be a reason?

Originally posted by @hansvancalster in #118 (comment)

[VoronDM]

Same problem with upgrade RcppParallel from source at R 4.0.5:

> install.packages("RcppParallel")
Installing package into ‘C:/Users/vit1234/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
             binary source needs_compilation
RcppParallel  5.0.3  5.1.1              TRUE

installing the source package ‘RcppParallel’

пробую URL 'https://cran.rstudio.com/src/contrib/RcppParallel_5.1.1.tar.gz'
Content type 'application/x-gzip' length 2042413 bytes (1.9 MB)
downloaded 1.9 MB

* installing *source* package 'RcppParallel' ...
** пакет 'RcppParallel' удачно распакован, MD5 sums проверены
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'src/Makevars.in' => 'src/Makevars'
** finished configure for package 'RcppParallel'
** libs
Using bundled TBB library ...
Created ../build/lib_release directory
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=windows runtime=mingw
sh: C:Program: command not found
make[2]: *** [../../build/common_rules.inc:162: version_string.ver] Error 127
make[2]: *** Deleting file 'version_string.ver'
make[1]: *** [Makefile:100: tbb_release] Error 2
cp: cannot stat 'tbb/build/lib_release/tbb*.dll': No such file or directory
make: *** [Makevars:126: tbb] Error 1
ERROR: compilation failed for package 'RcppParallel'
* removing 'C:/Users/vit1234/Documents/R/win-library/4.0/RcppParallel'
* restoring previous 'C:/Users/vit1234/Documents/R/win-library/4.0/RcppParallel'
Warning in install.packages :
  installation of package ‘RcppParallel’ had non-zero exit status

> library(RcppParallel)
> devtools::session_info()
- Session info -----------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.5 (2021-03-31)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  Russian_Russia.1251         
 ctype    Russian_Russia.1251         
 tz       Europe/Moscow               
 date     2021-04-14                  

- Packages ---------------------------------------------------------------------------------------------------
 ! package      * version date       lib source        
   cachem         1.0.4   2021-02-13 [1] CRAN (R 4.0.3)
   callr          3.6.0   2021-03-28 [1] CRAN (R 4.0.4)
   cli            2.4.0   2021-04-05 [1] CRAN (R 4.0.4)
   crayon         1.4.1   2021-02-08 [1] CRAN (R 4.0.3)
   desc           1.3.0   2021-03-05 [1] CRAN (R 4.0.4)
   devtools       2.4.0   2021-04-07 [1] CRAN (R 4.0.5)
   ellipsis       0.3.1   2020-05-15 [1] CRAN (R 4.0.3)
   fastmap        1.1.0   2021-01-25 [1] CRAN (R 4.0.3)
   fs             1.5.0   2020-07-31 [1] CRAN (R 4.0.4)
   glue           1.4.2   2020-08-27 [1] CRAN (R 4.0.3)
   lifecycle      1.0.0   2021-02-15 [1] CRAN (R 4.0.4)
   magrittr       2.0.1   2020-11-17 [1] CRAN (R 4.0.3)
   memoise        2.0.0   2021-01-26 [1] CRAN (R 4.0.5)
   pkgbuild       1.2.0   2020-12-15 [1] CRAN (R 4.0.4)
   pkgload        1.2.1   2021-04-06 [1] CRAN (R 4.0.4)
   prettyunits    1.1.1   2020-01-24 [1] CRAN (R 4.0.3)
   processx       3.5.1   2021-04-04 [1] CRAN (R 4.0.4)
   ps             1.6.0   2021-02-28 [1] CRAN (R 4.0.4)
   purrr          0.3.4   2020-04-17 [1] CRAN (R 4.0.4)
   R6             2.5.0   2020-10-28 [1] CRAN (R 4.0.3)
 D RcppParallel * 5.0.3   2021-02-24 [1] CRAN (R 4.0.5)
   remotes        2.3.0   2021-04-01 [1] CRAN (R 4.0.5)
   rlang          0.4.10  2020-12-30 [1] CRAN (R 4.0.3)
   rprojroot      2.0.2   2020-11-15 [1] CRAN (R 4.0.4)
   rstudioapi     0.13    2020-11-12 [1] CRAN (R 4.0.4)
   sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 4.0.5)
   testthat       3.0.2   2021-02-14 [1] CRAN (R 4.0.4)
   usethis        2.0.1   2021-02-10 [1] CRAN (R 4.0.5)
   withr          2.4.1   2021-01-26 [1] CRAN (R 4.0.4)

[1] C:/Users/vit1234/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.5/library

 D -- DLL MD5 mismatch, broken installation.

[kevinushey]

Seems like the error is coming from here:

RcppParallel/src/tbb/build/common_rules.inc

Lines 160 to 163 in b79b508

	# TODO: make version strings directly representative for all the libraries
	version_string.ver:
	$(MAKE_VERSIONS)
	endif

And that definition would be coming from here:

RcppParallel/src/tbb/build/windows.inc

Lines 119 to 124 in b79b508

	MAKE_VERSIONS = $(CMD) cscript //NoLogo //E:JScript \
	"$(subst \,/,$(tbb_root)/build/version_info_windows.js)" \
	"$(subst \,/,$(CONLY))" \
	"$(arch)" \
	"$(subst \,/,$(VERSION_FLAGS))" \
	> version_string.ver

My guess, based on the error message:

sh: C:Program: command not found

is that the issue is caused either by the use of backslashes, or by spaces in the path being used here (whatever it is).

Unfortunately, debugging these sorts of issues is quite challenging. Do you see any extra information if you set the VERBOSE environment variable; e.g.

Sys.setenv(VERBOSE = "1")
install.packages("RcppParallel", type = "source")

[kevinushey]

One potential guess is that the CMD environment variable is set to some unexpected path?

[VoronDM]

Sys.setenv(VERBOSE = "1")
install.packages("RcppParallel", type = "source")

C:\Program Files\CMD cscript //NoLogo //E:JScript "../../build/version_info_windows.js" "C:/rtools40/mingw64/bin/gcc " "intel64" "C:/rtools40/mingw64/bin/g++  -O2 -DUSE_WINTHREAD -D_WIN32_WINNT=0x0502 -DMINGW_HAS_SECURE_API=1 -D__MSVCRT_VERSION__=0x0700 -msse -mthreads -m64 -mrtm   -flifetime-dse=1 -D__TBB_BUILD=1 -Wall  -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DTBB_NO_LEGACY=1 -std=c++0x -I../../src -I../../src/rml/include -I../../include -I." > version_string.ver
sh: C:Program: command not found
make[2]: *** [../../build/common_rules.inc:162: version_string.ver] Error 127
make[2]: *** Deleting file 'version_string.ver'
make[2]: Leaving directory '/c/Users/vit1234/AppData/Local/Temp/RtmpMxvjhy/R.INSTALL30b47fd84509/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [Makefile:100: tbb_release] Error 2
make[1]: Leaving directory '/c/Users/vit1234/AppData/Local/Temp/RtmpMxvjhy/R.INSTALL30b47fd84509/RcppParallel/src/tbb/src'
cp: cannot stat 'tbb/build/lib_release/tbb*.dll': No such file or directory
make: *** [Makevars:126: tbb] Error 1
ERROR: compilation failed for package 'RcppParallel'

I found in the system environment curious variable CMD with nonexisting path C:\Program Files\CMD
Maybe this is the reason of the error?

[kevinushey]

That sounds like it. Can you try Sys.unsetenv("CMD") and attempt to install again?

[VoronDM]

Yesterday I installed an 5.1.1. version of the RcppParallel package from the precompiled code. Version 5.1.2 was reliased today. I tried Sys.unsetenv ("CMD") and it compiled from source without any troubles. I don't know if this recommendation worked or if something has changed in the package itself. But in fact, the problem has now been resolved.

[hansvancalster]

I can also confirm that installing the binary and from source work as expected (although I am now on a Windows 10 machine and was using a Windows 7 machine at the time I opened this issue).

As a side note: updating RcppParallel broke rstan (current CRAN version): when compiling a model it could not find dynamic load libraries. I could fix this by installing the experimental version of rstan from stan-dev/rstan#899 (comment).

[kevinushey]

These issues should all be resolved now.