Hi
I am using:
Package manager version: 0.38.2
Distribution version: selfupdate-rsync Wed Nov 26 20:33:40 2014, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.1
And I'm trying to install BioPerl and I keep getting this error
"/usr/bin/arch" -x86_64 perl5.12.4 FCGI.PL FCGI.pm
Running Mkbootstrap for FCGI ()
gcc -c -I. -I/sw3/include -fno-common -DPERL_DARWIN -no-cpp-precomp
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -O3
-DVERSION=\"0.74\" -DXS_VERSION=\"0.74\"
"-I/sw3/lib/perl5-core/5.12.4/darwin-thread-multi-2level/CORE" fcgiapp.c
gcc -c -I. -I/sw3/include -fno-common -DPERL_DARWIN -no-cpp-precomp
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -O3
-DVERSION=\"0.74\" -DXS_VERSION=\"0.74\"
"-I/sw3/lib/perl5-core/5.12.4/darwin-thread-multi-2level/CORE" os_unix.c
chmod 644 "FCGI.bs"
os_unix.c:1169:70: warning: passing 'int *' to parameter of type 'socklen_t *'
(aka 'unsigned int *') converts between pointers to integer types with different
sign [-Wpointer-sign]
socket = accept(listen_sock, (struct sockaddr *)&sa, &len);
^~~~
/usr/include/sys/socket.h:555:69: note: passing argument to parameter here
int accept(int, struct sockaddr * __restrict, socklen_t * __restrict)
^
os_unix.c:1269:51: warning: passing 'int *' to parameter of type 'socklen_t *'
(aka 'unsigned int *') converts between pointers to integer types with different
sign [-Wpointer-sign]
if (getpeername(sock, (struct sockaddr *)&sa, &len) != 0 && errno ==
ENOTCONN) {
^~~~
/usr/include/sys/socket.h:559:74: note: passing argument to parameter here
int getpeername(int, struct sockaddr * __restrict, socklen_t * __restrict)
^
2 warnings generated.
Generating FCGI.pm
cp FCGI.pm blib/arch/FCGI.pm
"/usr/bin/arch" -x86_64 perl5.12.4 -x86_64 perl5.12.4 "-Iblib/arch"
"-Iblib/lib" FCGI.XL FCGI.xs
"/usr/bin/arch" -x86_64 perl5.12.4 -x86_64 perl5.12.4 "-Iblib/arch"
"-Iblib/lib" echo.PL echo.fpl
"/usr/bin/arch" -x86_64 perl5.12.4 -x86_64 perl5.12.4 "-Iblib/arch"
"-Iblib/lib" remote.PL remote.fpl
Can't open perl script "perl5.12.4": No such file or directory
Can't open perl script "perl5.12.4": No such file or directory
Can't open perl script "perl5.12.4": No such file or directory
make: *** [remote.fpl] Error 2
make: *** Waiting for unfinished jobs....
make: *** [echo.fpl] Error 2
make: *** [FCGI.xs] Error 2
### execution of make failed, exit code 2
### execution of /tmp/fink.TJ7CA failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw3/bin/dpkg-lockwait -r fink-buildlock-fcgi-pm5124-0.74-1
(Reading database ... 30934 files and directories currently installed.)
Removing fink-buildlock-fcgi-pm5124-0.74-1 ...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-x86_64
New package:
dists/stable/main/binary-darwin-x86_64/devel/yasm-dev_1.3.0-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/devel/yasm_1.3.0-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/graphics/imlib2-shlibs_1.4.6-2_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/graphics/imlib2_1.4.6-2_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/graphics/libvpx-bin_1.3.0-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/graphics/libvpx_1.3.0-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/languages/perl5124-core_5.12.4-104_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/languages/perl5124_5.12.4-104_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/algorithm-c3-pm5124_0.08-3_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/authen-ntlm-pm5124_1.09-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/class-c3-pm5124_0.25-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/class-c3-xs-pm5124_0.13-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/clone-pm5124_0.36-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/compress-bzip2-pm5124_2.16-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/compress-raw-bzip2-pm5124_2.063-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/compress-raw-zlib-pm5124_2.063-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/cpan-meta-pm5124_2.142690-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/cpan-meta-requirements-pm5124_2.128-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/data-dumper-pm5124_2.151-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/data-optlist-pm5124_0.109-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/data-uuid-pm5124_1.219-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/devel-globaldestruction-xs-pm5124_0.01-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/digest-sha1-pm5124_2.13-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/dime-tools-pm5124_0.03-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/encode-pm5124_2.63-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/eval-closure-pm5124_0.11-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/extutils-makemaker-pm5124_7.00-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/file-temp-pm5124_0.23.04-3_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/file-which-pm5124_1.09-7_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/io-compress-pm5124_2.063-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/io-socket-ip-pm5124_0.29-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/io-tty-pm5124_1.12-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/ipc-run-pm5124_0.92-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/json-xs-pm5124_3.01-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/list-moreutils-pm5124_0.33-2_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/mailtools-pm5124_2.13-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/mime-lite-pm5124_3.030-2_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/module-metadata-pm5124_1.000024-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/net-idn-encode-pm5124_2.201-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/net-ssleay-pm5124_1.66-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/package-stash-xs-pm5124_0.28-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/params-util-pm5124_1.07-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/pathtools-pm5124_3.40-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/perl-ostype-pm5124_1.007-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/pwhich5124_1.09-7_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/scalar-list-utils-pm5124_1.35-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/socket-pm5124_2.013-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/spreadsheet-parseexcel-pm5124_0.59-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/sub-install-pm5124_0.927-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/sub-name-pm5124_0.05-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/task-weaken-pm5124_1.04-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/test-deep-pm5124_0.112-2_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/test-differences-pm5124_0.61-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/test-harness-pm5124_3.33-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/test-nowarnings-pm5124_1.04-2_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/test-simple-pm5124_1.001008-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/text-iconv-pm5124_1.7-3_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/tk-pm5124_804.032-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/unicode-map-pm5124_0.112-16_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/unicode-normalize-pm5124_1.18-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/unicode-string-pm5124_2.09-11_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/version-pm5124_0.99.08-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/xml-filter-buffertext-pm5124_1.01-5_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/xml-sax-pm5124_0.99-3_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/libs/perlmods/xml-sax-writer-pm5124_0.54-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/net/libnghttp2.5-shlibs_0.6.1-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/net/libnghttp2.5_0.6.1-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/net/nghttp_0.6.1-1_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/text/xmlto_0.0.25-6_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/web/w3m-x11_0.5.3-105_darwin-x86_64.deb
New package:
dists/stable/main/binary-darwin-x86_64/web/w3m_0.5.3-105_darwin-x86_64.deb
Failed: phase compiling: fcgi-pm5124-0.74-1 failed
Thanks
Prabh
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