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genome / bam-readcount

Count bases in BAM/CRAM files
MIT License
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compilation failed #78

Open lmanchon opened 3 years ago

lmanchon commented 3 years ago

failed on libcurl stage with:

make[1]: Entering directory /.../bam-readcount/build/vendor/curl-src/lib' make all-am make[2]: Entering directory/.../bam-readcount/build/vendor/curl-src/lib' CCLD libcurl.la /usr/bin/ld: /.../bam-readcount/build/vendor/mbedtls/lib/libmbedtls.a(ssl_ciphersuites.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /.../bam-readcount/build/vendor/mbedtls/lib/libmbedtls.a: error adding symbols: Bad value collect2: error: ld returned 1 exit status make[2]: *** [libcurl.la] Error 1 make[2]: Leaving directory/.../bam-readcount/build/vendor/curl-src/lib' make[1]: [all] Error 2 make[1]: Leaving directory `/.../bam-readcount/build/vendor/curl-src/lib' make: [all-recursive] Error 1

Stikus commented 3 years ago

I have troubles at curl stage too, but they are linked with multithreaded make. After I removed -j everything started to work again. But we used -j in version 0.8.0 of bam-readcount:

[ 77%] Performing install step for 'curl'
make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
Making install in lib
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libcurl.la '/soft/bam-readcount-1.0.0-src/build/vendor/curl/lib'
libtool: install: /usr/bin/install -c .libs/libcurl.so.4.6.0 /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/libcurl.so.4.6.0
libtool: install: (cd /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib && { ln -s -f libcurl.so.4.6.0 libcurl.so.4 || { rm -f libcurl.so.4 && ln -s libcurl.so.4.6.0 libcurl.so.4; }; })
libtool: install: (cd /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib && { ln -s -f libcurl.so.4.6.0 libcurl.so || { rm -f libcurl.so && ln -s libcurl.so.4.6.0 libcurl.so; }; })
libtool: install: /usr/bin/install -c .libs/libcurl.lai /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/libcurl.la
libtool: install: /usr/bin/install -c .libs/libcurl.a /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/libcurl.a
libtool: install: chmod 644 /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/libcurl.a
libtool: install: ranlib /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/libcurl.a
libtool: finish: PATH="/soft/varscan-2.4.4/bin:/soft/vcftools-0.1.16/bin:/soft/bcftools-1.13/bin:/soft/samtools-1.13/bin:/soft/htslib-1.13/bin:/soft/libdeflate-1.7/bin:/soft/memusage/bin:/soft/cpanm/bin:/soft/cmake-3.20.5-linux-x86_64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin" ldconfig -n /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /soft/bam-readcount-1.0.0-src/build/vendor/curl/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
Making install in src
Making install in ../docs
Making install in .
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man1'
 /usr/bin/install -c -m 644 curl-config.1 /soft/bam-readcount-1.0.0-src/build/vendor/curl-src/docs/curl.1 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man1'
Making install in cmdline-opts
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c curl '/soft/bam-readcount-1.0.0-src/build/vendor/curl/bin'
libtool: install: /usr/bin/install -c .libs/curl /soft/bam-readcount-1.0.0-src/build/vendor/curl/bin/curl
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/bin'
 /usr/bin/install -c curl-config '/soft/bam-readcount-1.0.0-src/build/vendor/curl/bin'
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcurl.pc '/soft/bam-readcount-1.0.0-src/build/vendor/curl/lib/pkgconfig'
Making install in curl
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/include/curl'
 /usr/bin/install -c -m 644 curl.h curlver.h easy.h mprintf.h stdcheaders.h multi.h typecheck-gcc.h system.h urlapi.h '/soft/bam-readcount-1.0.0-src/build/vendor/curl/include/curl'
Making install in .
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man1'
 /usr/bin/install -c -m 644 curl-config.1 /soft/bam-readcount-1.0.0-src/build/vendor/curl-src/docs/curl.1 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man1'
Making install in cmdline-opts
Making install in opts
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLINFO_ACTIVESOCKET.3 CURLINFO_APPCONNECT_TIME.3 CURLINFO_APPCONNECT_TIME_T.3 CURLINFO_CERTINFO.3 CURLINFO_CONDITION_UNMET.3 CURLINFO_CONNECT_TIME.3 CURLINFO_CONNECT_TIME_T.3 CURLINFO_CONTENT_LENGTH_DOWNLOAD.3 CURLINFO_CONTENT_LENGTH_DOWNLOAD_T.3 CURLINFO_CONTENT_LENGTH_UPLOAD.3 CURLINFO_CONTENT_LENGTH_UPLOAD_T.3 CURLINFO_CONTENT_TYPE.3 CURLINFO_COOKIELIST.3 CURLINFO_EFFECTIVE_URL.3 CURLINFO_FILETIME.3 CURLINFO_FILETIME_T.3 CURLINFO_FTP_ENTRY_PATH.3 CURLINFO_HEADER_SIZE.3 CURLINFO_HTTPAUTH_AVAIL.3 CURLINFO_HTTP_CONNECTCODE.3 CURLINFO_HTTP_VERSION.3 CURLINFO_LASTSOCKET.3 CURLINFO_LOCAL_IP.3 CURLINFO_LOCAL_PORT.3 CURLINFO_NAMELOOKUP_TIME.3 CURLINFO_NAMELOOKUP_TIME_T.3 CURLINFO_NUM_CONNECTS.3 CURLINFO_OS_ERRNO.3 CURLINFO_PRETRANSFER_TIME.3 CURLINFO_PRETRANSFER_TIME_T.3 CURLINFO_PRIMARY_IP.3 CURLINFO_PRIMARY_PORT.3 CURLINFO_PRIVATE.3 CURLINFO_PROTOCOL.3 CURLINFO_PROXYAUTH_AVAIL.3 CURLINFO_PROXY_SSL_VERIFYRESULT.3 CURLINFO_REDIRECT_COUNT.3 CURLINFO_REDIRECT_TIME.3 CURLINFO_REDIRECT_TIME_T.3 CURLINFO_REDIRECT_URL.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLINFO_REQUEST_SIZE.3 CURLINFO_RESPONSE_CODE.3 CURLINFO_RETRY_AFTER.3 CURLINFO_RTSP_CLIENT_CSEQ.3 CURLINFO_RTSP_CSEQ_RECV.3 CURLINFO_RTSP_SERVER_CSEQ.3 CURLINFO_RTSP_SESSION_ID.3 CURLINFO_SCHEME.3 CURLINFO_SIZE_DOWNLOAD.3 CURLINFO_SIZE_DOWNLOAD_T.3 CURLINFO_SIZE_UPLOAD.3 CURLINFO_SIZE_UPLOAD_T.3 CURLINFO_SPEED_DOWNLOAD.3 CURLINFO_SPEED_DOWNLOAD_T.3 CURLINFO_SPEED_UPLOAD.3 CURLINFO_SPEED_UPLOAD_T.3 CURLINFO_SSL_ENGINES.3 CURLINFO_SSL_VERIFYRESULT.3 CURLINFO_STARTTRANSFER_TIME.3 CURLINFO_STARTTRANSFER_TIME_T.3 CURLINFO_TLS_SESSION.3 CURLINFO_TLS_SSL_PTR.3 CURLINFO_TOTAL_TIME.3 CURLINFO_TOTAL_TIME_T.3 CURLMOPT_CHUNK_LENGTH_PENALTY_SIZE.3 CURLMOPT_CONTENT_LENGTH_PENALTY_SIZE.3 CURLMOPT_MAXCONNECTS.3 CURLMOPT_MAX_CONCURRENT_STREAMS.3 CURLMOPT_MAX_HOST_CONNECTIONS.3 CURLMOPT_MAX_PIPELINE_LENGTH.3 CURLMOPT_MAX_TOTAL_CONNECTIONS.3 CURLMOPT_PIPELINING.3 CURLMOPT_PIPELINING_SERVER_BL.3 CURLMOPT_PIPELINING_SITE_BL.3 CURLMOPT_PUSHDATA.3 CURLMOPT_PUSHFUNCTION.3 CURLMOPT_SOCKETDATA.3 CURLMOPT_SOCKETFUNCTION.3 CURLMOPT_TIMERDATA.3 CURLMOPT_TIMERFUNCTION.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_ABSTRACT_UNIX_SOCKET.3 CURLOPT_ACCEPTTIMEOUT_MS.3 CURLOPT_ACCEPT_ENCODING.3 CURLOPT_ADDRESS_SCOPE.3 CURLOPT_ALTSVC.3 CURLOPT_ALTSVC_CTRL.3 CURLOPT_APPEND.3 CURLOPT_AUTOREFERER.3 CURLOPT_BUFFERSIZE.3 CURLOPT_CAINFO.3 CURLOPT_CAPATH.3 CURLOPT_CERTINFO.3 CURLOPT_CHUNK_BGN_FUNCTION.3 CURLOPT_CHUNK_DATA.3 CURLOPT_CHUNK_END_FUNCTION.3 CURLOPT_CLOSESOCKETDATA.3 CURLOPT_CLOSESOCKETFUNCTION.3 CURLOPT_CONNECTTIMEOUT.3 CURLOPT_CONNECTTIMEOUT_MS.3 CURLOPT_CONNECT_ONLY.3 CURLOPT_CONNECT_TO.3 CURLOPT_CONV_FROM_NETWORK_FUNCTION.3 CURLOPT_CONV_FROM_UTF8_FUNCTION.3 CURLOPT_CONV_TO_NETWORK_FUNCTION.3 CURLOPT_COOKIE.3 CURLOPT_COOKIEFILE.3 CURLOPT_COOKIEJAR.3 CURLOPT_COOKIELIST.3 CURLOPT_COOKIESESSION.3 CURLOPT_COPYPOSTFIELDS.3 CURLOPT_CRLF.3 CURLOPT_CRLFILE.3 CURLOPT_CURLU.3 CURLOPT_CUSTOMREQUEST.3 CURLOPT_DEBUGDATA.3 CURLOPT_DEBUGFUNCTION.3 CURLOPT_DEFAULT_PROTOCOL.3 CURLOPT_DIRLISTONLY.3 CURLOPT_DISALLOW_USERNAME_IN_URL.3 CURLOPT_DNS_CACHE_TIMEOUT.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_DNS_INTERFACE.3 CURLOPT_DNS_LOCAL_IP4.3 CURLOPT_DNS_LOCAL_IP6.3 CURLOPT_DNS_SERVERS.3 CURLOPT_DNS_SHUFFLE_ADDRESSES.3 CURLOPT_DNS_USE_GLOBAL_CACHE.3 CURLOPT_DOH_URL.3 CURLOPT_EGDSOCKET.3 CURLOPT_ERRORBUFFER.3 CURLOPT_EXPECT_100_TIMEOUT_MS.3 CURLOPT_FAILONERROR.3 CURLOPT_FILETIME.3 CURLOPT_FNMATCH_DATA.3 CURLOPT_FNMATCH_FUNCTION.3 CURLOPT_FOLLOWLOCATION.3 CURLOPT_FORBID_REUSE.3 CURLOPT_FRESH_CONNECT.3 CURLOPT_FTPPORT.3 CURLOPT_FTPSSLAUTH.3 CURLOPT_FTP_ACCOUNT.3 CURLOPT_FTP_ALTERNATIVE_TO_USER.3 CURLOPT_FTP_CREATE_MISSING_DIRS.3 CURLOPT_FTP_FILEMETHOD.3 CURLOPT_FTP_RESPONSE_TIMEOUT.3 CURLOPT_FTP_SKIP_PASV_IP.3 CURLOPT_FTP_SSL_CCC.3 CURLOPT_FTP_USE_EPRT.3 CURLOPT_FTP_USE_EPSV.3 CURLOPT_FTP_USE_PRET.3 CURLOPT_GSSAPI_DELEGATION.3 CURLOPT_HAPPY_EYEBALLS_TIMEOUT_MS.3 CURLOPT_HAPROXYPROTOCOL.3 CURLOPT_HEADER.3 CURLOPT_HEADERDATA.3 CURLOPT_HEADERFUNCTION.3 CURLOPT_HEADEROPT.3 CURLOPT_HTTP09_ALLOWED.3 CURLOPT_HTTP200ALIASES.3 CURLOPT_HTTPAUTH.3 CURLOPT_HTTPGET.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_HTTPHEADER.3 CURLOPT_HTTPPOST.3 CURLOPT_HTTPPROXYTUNNEL.3 CURLOPT_HTTP_CONTENT_DECODING.3 CURLOPT_HTTP_TRANSFER_DECODING.3 CURLOPT_HTTP_VERSION.3 CURLOPT_IGNORE_CONTENT_LENGTH.3 CURLOPT_INFILESIZE.3 CURLOPT_INFILESIZE_LARGE.3 CURLOPT_INTERFACE.3 CURLOPT_INTERLEAVEDATA.3 CURLOPT_INTERLEAVEFUNCTION.3 CURLOPT_IOCTLDATA.3 CURLOPT_IOCTLFUNCTION.3 CURLOPT_IPRESOLVE.3 CURLOPT_ISSUERCERT.3 CURLOPT_KEEP_SENDING_ON_ERROR.3 CURLOPT_KEYPASSWD.3 CURLOPT_KRBLEVEL.3 CURLOPT_LOCALPORT.3 CURLOPT_LOCALPORTRANGE.3 CURLOPT_LOGIN_OPTIONS.3 CURLOPT_LOW_SPEED_LIMIT.3 CURLOPT_LOW_SPEED_TIME.3 CURLOPT_MAIL_AUTH.3 CURLOPT_MAIL_FROM.3 CURLOPT_MAIL_RCPT.3 CURLOPT_MAXAGE_CONN.3 CURLOPT_MAXCONNECTS.3 CURLOPT_MAXFILESIZE.3 CURLOPT_MAXFILESIZE_LARGE.3 CURLOPT_MAXREDIRS.3 CURLOPT_MAX_RECV_SPEED_LARGE.3 CURLOPT_MAX_SEND_SPEED_LARGE.3 CURLOPT_MIMEPOST.3 CURLOPT_NETRC.3 CURLOPT_NETRC_FILE.3 CURLOPT_NEW_DIRECTORY_PERMS.3 CURLOPT_NEW_FILE_PERMS.3 CURLOPT_NOBODY.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_NOPROGRESS.3 CURLOPT_NOPROXY.3 CURLOPT_NOSIGNAL.3 CURLOPT_OPENSOCKETDATA.3 CURLOPT_OPENSOCKETFUNCTION.3 CURLOPT_PASSWORD.3 CURLOPT_PATH_AS_IS.3 CURLOPT_PINNEDPUBLICKEY.3 CURLOPT_PIPEWAIT.3 CURLOPT_PORT.3 CURLOPT_POST.3 CURLOPT_POSTFIELDS.3 CURLOPT_POSTFIELDSIZE.3 CURLOPT_POSTFIELDSIZE_LARGE.3 CURLOPT_POSTQUOTE.3 CURLOPT_POSTREDIR.3 CURLOPT_PREQUOTE.3 CURLOPT_PRE_PROXY.3 CURLOPT_PRIVATE.3 CURLOPT_PROGRESSDATA.3 CURLOPT_PROGRESSFUNCTION.3 CURLOPT_PROTOCOLS.3 CURLOPT_PROXY.3 CURLOPT_PROXYAUTH.3 CURLOPT_PROXYHEADER.3 CURLOPT_PROXYPASSWORD.3 CURLOPT_PROXYPORT.3 CURLOPT_PROXYTYPE.3 CURLOPT_PROXYUSERNAME.3 CURLOPT_PROXYUSERPWD.3 CURLOPT_PROXY_CAINFO.3 CURLOPT_PROXY_CAPATH.3 CURLOPT_PROXY_CRLFILE.3 CURLOPT_PROXY_KEYPASSWD.3 CURLOPT_PROXY_PINNEDPUBLICKEY.3 CURLOPT_PROXY_SERVICE_NAME.3 CURLOPT_PROXY_SSLCERT.3 CURLOPT_PROXY_SSLCERTTYPE.3 CURLOPT_PROXY_SSLKEY.3 CURLOPT_PROXY_SSLKEYTYPE.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_PROXY_SSLVERSION.3 CURLOPT_PROXY_SSL_CIPHER_LIST.3 CURLOPT_PROXY_SSL_OPTIONS.3 CURLOPT_PROXY_SSL_VERIFYHOST.3 CURLOPT_PROXY_SSL_VERIFYPEER.3 CURLOPT_PROXY_TLS13_CIPHERS.3 CURLOPT_PROXY_TLSAUTH_PASSWORD.3 CURLOPT_PROXY_TLSAUTH_TYPE.3 CURLOPT_PROXY_TLSAUTH_USERNAME.3 CURLOPT_PROXY_TRANSFER_MODE.3 CURLOPT_PUT.3 CURLOPT_QUOTE.3 CURLOPT_RANDOM_FILE.3 CURLOPT_RANGE.3 CURLOPT_READDATA.3 CURLOPT_READFUNCTION.3 CURLOPT_REDIR_PROTOCOLS.3 CURLOPT_REFERER.3 CURLOPT_REQUEST_TARGET.3 CURLOPT_RESOLVE.3 CURLOPT_RESOLVER_START_DATA.3 CURLOPT_RESOLVER_START_FUNCTION.3 CURLOPT_RESUME_FROM.3 CURLOPT_RESUME_FROM_LARGE.3 CURLOPT_RTSP_CLIENT_CSEQ.3 CURLOPT_RTSP_REQUEST.3 CURLOPT_RTSP_SERVER_CSEQ.3 CURLOPT_RTSP_SESSION_ID.3 CURLOPT_RTSP_STREAM_URI.3 CURLOPT_RTSP_TRANSPORT.3 CURLOPT_SASL_AUTHZID.3 CURLOPT_SASL_IR.3 CURLOPT_SEEKDATA.3 CURLOPT_SEEKFUNCTION.3 CURLOPT_SERVICE_NAME.3 CURLOPT_SHARE.3 CURLOPT_SOCKOPTDATA.3 CURLOPT_SOCKOPTFUNCTION.3 CURLOPT_SOCKS5_AUTH.3 CURLOPT_SOCKS5_GSSAPI_NEC.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_SOCKS5_GSSAPI_SERVICE.3 CURLOPT_SSH_AUTH_TYPES.3 CURLOPT_SSH_COMPRESSION.3 CURLOPT_SSH_HOST_PUBLIC_KEY_MD5.3 CURLOPT_SSH_KEYDATA.3 CURLOPT_SSH_KEYFUNCTION.3 CURLOPT_SSH_KNOWNHOSTS.3 CURLOPT_SSH_PRIVATE_KEYFILE.3 CURLOPT_SSH_PUBLIC_KEYFILE.3 CURLOPT_SSLCERT.3 CURLOPT_SSLCERTTYPE.3 CURLOPT_SSLENGINE.3 CURLOPT_SSLENGINE_DEFAULT.3 CURLOPT_SSLKEY.3 CURLOPT_SSLKEYTYPE.3 CURLOPT_SSLVERSION.3 CURLOPT_SSL_CIPHER_LIST.3 CURLOPT_SSL_CTX_DATA.3 CURLOPT_SSL_CTX_FUNCTION.3 CURLOPT_SSL_ENABLE_ALPN.3 CURLOPT_SSL_ENABLE_NPN.3 CURLOPT_SSL_FALSESTART.3 CURLOPT_SSL_OPTIONS.3 CURLOPT_SSL_SESSIONID_CACHE.3 CURLOPT_SSL_VERIFYHOST.3 CURLOPT_SSL_VERIFYPEER.3 CURLOPT_SSL_VERIFYSTATUS.3 CURLOPT_STDERR.3 CURLOPT_STREAM_DEPENDS.3 CURLOPT_STREAM_DEPENDS_E.3 CURLOPT_STREAM_WEIGHT.3 CURLOPT_SUPPRESS_CONNECT_HEADERS.3 CURLOPT_TCP_FASTOPEN.3 CURLOPT_TCP_KEEPALIVE.3 CURLOPT_TCP_KEEPIDLE.3 CURLOPT_TCP_KEEPINTVL.3 CURLOPT_TCP_NODELAY.3 CURLOPT_TELNETOPTIONS.3 CURLOPT_TFTP_BLKSIZE.3 CURLOPT_TFTP_NO_OPTIONS.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 CURLOPT_TIMECONDITION.3 CURLOPT_TIMEOUT.3 CURLOPT_TIMEOUT_MS.3 CURLOPT_TIMEVALUE.3 CURLOPT_TIMEVALUE_LARGE.3 CURLOPT_TLS13_CIPHERS.3 CURLOPT_TLSAUTH_PASSWORD.3 CURLOPT_TLSAUTH_TYPE.3 CURLOPT_TLSAUTH_USERNAME.3 CURLOPT_TRAILERDATA.3 CURLOPT_TRAILERFUNCTION.3 CURLOPT_TRANSFERTEXT.3 CURLOPT_TRANSFER_ENCODING.3 CURLOPT_UNIX_SOCKET_PATH.3 CURLOPT_UNRESTRICTED_AUTH.3 CURLOPT_UPKEEP_INTERVAL_MS.3 CURLOPT_UPLOAD.3 CURLOPT_UPLOAD_BUFFERSIZE.3 CURLOPT_URL.3 CURLOPT_USERAGENT.3 CURLOPT_USERNAME.3 CURLOPT_USERPWD.3 CURLOPT_USE_SSL.3 CURLOPT_VERBOSE.3 CURLOPT_WILDCARDMATCH.3 CURLOPT_WRITEDATA.3 CURLOPT_WRITEFUNCTION.3 CURLOPT_XFERINFODATA.3 CURLOPT_XFERINFOFUNCTION.3 CURLOPT_XOAUTH2_BEARER.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/aclocal'
 /usr/bin/install -c -m 644 libcurl.m4 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/aclocal'
 /bin/mkdir -p '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 curl_easy_cleanup.3 curl_easy_duphandle.3 curl_easy_escape.3 curl_easy_getinfo.3 curl_easy_init.3 curl_easy_pause.3 curl_easy_perform.3 curl_easy_recv.3 curl_easy_reset.3 curl_easy_send.3 curl_easy_setopt.3 curl_easy_strerror.3 curl_easy_unescape.3 curl_easy_upkeep.3 curl_escape.3 curl_formadd.3 curl_formfree.3 curl_formget.3 curl_free.3 curl_getdate.3 curl_getenv.3 curl_global_cleanup.3 curl_global_init.3 curl_global_init_mem.3 curl_global_sslset.3 curl_mime_addpart.3 curl_mime_data.3 curl_mime_data_cb.3 curl_mime_encoder.3 curl_mime_filedata.3 curl_mime_filename.3 curl_mime_free.3 curl_mime_headers.3 curl_mime_init.3 curl_mime_name.3 curl_mime_subparts.3 curl_mime_type.3 curl_mprintf.3 curl_multi_add_handle.3 curl_multi_assign.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 curl_multi_cleanup.3 curl_multi_fdset.3 curl_multi_info_read.3 curl_multi_init.3 curl_multi_perform.3 curl_multi_poll.3 curl_multi_remove_handle.3 curl_multi_setopt.3 curl_multi_socket.3 curl_multi_socket_action.3 curl_multi_socket_all.3 curl_multi_strerror.3 curl_multi_timeout.3 curl_multi_wait.3 curl_share_cleanup.3 curl_share_init.3 curl_share_setopt.3 curl_share_strerror.3 curl_slist_append.3 curl_slist_free_all.3 curl_strequal.3 curl_strnequal.3 curl_unescape.3 curl_url.3 curl_url_cleanup.3 curl_url_dup.3 curl_url_get.3 curl_url_set.3 curl_version.3 curl_version_info.3 libcurl-easy.3 libcurl-env.3 libcurl-errors.3 libcurl-multi.3 libcurl-security.3 libcurl-share.3 libcurl-symbols.3 libcurl-thread.3 libcurl-tutorial.3 libcurl-url.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
 /usr/bin/install -c -m 644 libcurl.3 '/soft/bam-readcount-1.0.0-src/build/vendor/curl/share/man/man3'
[ 78%] Completed 'curl'
[ 78%] Built target curl
Makefile:165: recipe for target 'all' failed
make: *** [all] Error 2
lmanchon commented 3 years ago

in which file should I delete the multithreaded make -j1 ?

lmanchon commented 3 years ago

ok, problem is over, i recompiled mbedtls library with CFLAGS='-fPIC' and then recompiled curl to correctly link libmbedtls.a.

bitsyamagu commented 2 years ago

To add CFLAGS='-fPIC' I had to modify BuildSamtools.cmake like this:

--- bam-readcount-fix/cmake/BuildSamtools.cmake Wed Dec 22 18:09:49 2021

* 74,80 ** SOURCE_DIR ${MBEDTLS_SRC} BINARY_DIR ${MBEDTLS_SRC} CONFIGURE_COMMAND echo "Building mbedTLS with make lib" ! BUILD_COMMAND make lib INSTALL_COMMAND make DESTDIR=${MBEDTLS_ROOT} install )

--- 74,80 ---- SOURCE_DIR ${MBEDTLS_SRC} BINARY_DIR ${MBEDTLS_SRC} CONFIGURE_COMMAND echo "Building mbedTLS with make lib" ! BUILD_COMMAND CFLAGS="-fPIC" make lib INSTALL_COMMAND make DESTDIR=${MBEDTLS_ROOT} install )

saraahwallace commented 1 year ago

ok, problem is over, i recompiled mbedtls library with CFLAGS='-fPIC' and then recompiled curl to correctly link libmbedtls.a.

Hi how did you recompiled curl to correctly link libmbedtls.a?