Dropping --silent from the libtool call:

/bin/bash /home/nikic/php/php-src-fast/libtool --preserve-dup-deps --tag CC --mode=compile cc -Iext/standard/ -I/home/nikic/php/php-src-fast/ext/standard/ -I/home/nikic/php/php-src-fast/include -I/home/nikic/php/php-src-fast/main -I/home/nikic/php/php-src-fast -I/usr/include/valgrind -I/home/nikic/php/php-src-fast/ext/date/lib -I/usr/include/libxml2 -I/usr/include/x86_64-linux-gnu -I/home/nikic/php/php-src-fast/ext/mbstring/libmbfl -I/home/nikic/php/php-src-fast/ext/mbstring/libmbfl/mbfl -I/home/nikic/php/php-src-fast/TSRM -I/home/nikic/php/php-src-fast/Zend    -fno-common -Wformat-truncation -Wlogical-op -Wduplicated-cond -Wno-clobbered -Wall -Wextra -Wno-strict-aliasing -Wno-unused-parameter -Wno-sign-compare -g -O2 -fvisibility=hidden -Wimplicit-fallthrough=1 -DZEND_SIGNALS -fprofile-use  -DZEND_ENABLE_STATIC_TSRMLS_CACHE=1 -c /home/nikic/php/php-src-fast/ext/standard/string.c -o ext/standard/string.lo  -MMD -MF ext/standard/string.dep -MT ext/standard/string.lo
 cc -Iext/standard/ -I/home/nikic/php/php-src-fast/ext/standard/ -I/home/nikic/php/php-src-fast/include -I/home/nikic/php/php-src-fast/main -I/home/nikic/php/php-src-fast -I/usr/include/valgrind -I/home/nikic/php/php-src-fast/ext/date/lib -I/usr/include/libxml2 -I/usr/include/x86_64-linux-gnu -I/home/nikic/php/php-src-fast/ext/mbstring/libmbfl -I/home/nikic/php/php-src-fast/ext/mbstring/libmbfl/mbfl -I/home/nikic/php/php-src-fast/TSRM -I/home/nikic/php/php-src-fast/Zend -fno-common -Wformat-truncation -Wlogical-op -Wduplicated-cond -Wno-clobbered -Wall -Wextra -Wno-strict-aliasing -Wno-unused-parameter -Wno-sign-compare -g -O2 -fvisibility=hidden -Wimplicit-fallthrough=1 -DZEND_SIGNALS -fprofile-use -DZEND_ENABLE_STATIC_TSRMLS_CACHE=1 -c /home/nikic/php/php-src-fast/ext/standard/string.c -MMD -MF ext/standard/string.dep -MT ext/standard/string.lo  -fPIC -DPIC -o ext/standard/.libs/string.o
/home/nikic/php/php-src-fast/ext/standard/string.c: In function ‘zif_utf8_decode’:
/home/nikic/php/php-src-fast/ext/standard/string.c:6196:1: warning: ‘/home/nikic/php/php-src-fast/ext/standard/.libs/string.gcda’ profile count data file not found [-Wmissing-profile]
 6196 | }
      | ^
 cc -Iext/standard/ -I/home/nikic/php/php-src-fast/ext/standard/ -I/home/nikic/php/php-src-fast/include -I/home/nikic/php/php-src-fast/main -I/home/nikic/php/php-src-fast -I/usr/include/valgrind -I/home/nikic/php/php-src-fast/ext/date/lib -I/usr/include/libxml2 -I/usr/include/x86_64-linux-gnu -I/home/nikic/php/php-src-fast/ext/mbstring/libmbfl -I/home/nikic/php/php-src-fast/ext/mbstring/libmbfl/mbfl -I/home/nikic/php/php-src-fast/TSRM -I/home/nikic/php/php-src-fast/Zend -fno-common -Wformat-truncation -Wlogical-op -Wduplicated-cond -Wno-clobbered -Wall -Wextra -Wno-strict-aliasing -Wno-unused-parameter -Wno-sign-compare -g -O2 -fvisibility=hidden -Wimplicit-fallthrough=1 -DZEND_SIGNALS -fprofile-use -DZEND_ENABLE_STATIC_TSRMLS_CACHE=1 -c /home/nikic/php/php-src-fast/ext/standard/string.c -MMD -MF ext/standard/string.dep -MT ext/standard/string.lo -o ext/standard/string.o >/dev/null 2>&1

Looks like it runs cc twice, and the first time it will rewrite the output location to .libs, which is where it will also look for .gcda files.

It seems to me that the warning messages can be ignored. The following is copy-paste from the gcov document. So if a .gcda file is missing, it probably means that the corresponding object file is not built into the PHP execute binary. By the way, may I know what workload you run? The PHP binary I built can work. But I just run some very simple workload before building it.

--------------------------------------------------------------------------------
The .gcda count data file is generated when a program containing object files built with the GCC -fprofile-arcs option is executed. A separate .gcda file is created for each object file compiled with this option. It contains arc transition counts, value profile counts, and some summary information.

There is a workaround. I find that it works with GCC 7.

gcc --version
gcc (Ubuntu 7.5.0-6ubuntu2) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

gcov --version
gcov (Ubuntu 7.5.0-6ubuntu2) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Actually, the warning messages can be ignored. Libtool is used to build the binaries and the libraries. All files in .lib directory are for building the shared libraries. For the modules that are not configured to build as a shared library, libtool still compiles the .c files and puts the .o files in .lib directory. Because those modules are not configured to build as a shared library, there are no .gcda generated in .lib directory. That is why the warning messages are shown up.

So, I suggest that we can close this bug.

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