I have this issue when with guix time-machine shell when using --emulate-fhs option and having gcc-toolset and clang-toolset in my manifest.scm.

I this this could be solved with this patch:

diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm

index 9f851a478e..7a276569e9 100644

--- a/gnu/packages/llvm.scm

+++ b/gnu/packages/llvm.scm

@@ -512,8 +512,10 @@ (define-public (make-clang-toolchain clang libomp)

                      ;; Create 'cc' and 'c++' so that one can use it as a

                      ;; drop-in replacement for the default tool chain and

                      ;; have configure scripts find the compiler.

-                     (symlink "clang" (string-append out "/bin/cc"))

-                     (symlink "clang++" (string-append out "/bin/c++"))

+                     (unless (file-exists? "/bin/cc")

+                         (symlink "clang" (string-append out "/bin/cc")))

+                     (unless (file-exists? "/bin/c++")

+                         (symlink "clang++" (string-append out "/bin/c++")))

 

                      (union-build (assoc-ref %outputs "debug")

                                   (list (assoc-ref %build-inputs

diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm

index a219b2ac89..72e56367a8 100644

--- a/guix/scripts/environment.scm

+++ b/guix/scripts/environment.scm

@@ -465,7 +465,8 @@ (define* (link-contents dir #:key (exclude '()))

   ;; bin directories will link to /bin.

   (let ((gcc-path (string-append profile "/bin/gcc")))

     (if (file-exists? gcc-path)

-        (symlink gcc-path "/bin/cc")))

+        (unless (file-exists? "/bin/cc")

+            (symlink gcc-path "/bin/cc"))))

 

   ;; Guix's ldconfig doesn't search in FHS default locations, so provide a

   ;; minimal ld.so.conf.


This patch will create the symlinks only if destination files is not already present.

Thanks