Opened 12 years ago

Closed 12 years ago

#38966 closed defect (wontfix)

qrupdate build error

Reported by: sam.petulla@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.1.3
Keywords: Cc: him.p.sel@…, lawrence.ong@…, steven.levis@…
Port: qrupdate

Description

Hi

In trying to install octave using: sudo port install octave-devel +atlas+docs

I am running into the problem in the log.

I am on Mountain Lion and Xcode 4.6.2.

Attachments (3)

main.log​ (14.0 KB) - added by sam.petulla@… 12 years ago.
qrupdate
main.2.log​ (33.7 KB) - added by sam.petulla@… 12 years ago.
After cleaning
main.3.log​ (65.1 KB) - added by himpsel@… 12 years ago.
Another qrupdate log

Download all attachments as: .zip

Change History (16)

Changed 12 years ago by sam.petulla@…

Attachment: main.log​ added

qrupdate

comment:1 Changed 12 years ago by mf2k (Frank Schima)

Port: qrupdate added
Summary: octave install @2.1.3 +qrupdate install error - build failure" → qrupdate build error

In the future, please fill in the Port field of the failed port.

Error is: 

:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2/src'
:info:build gfortran-mp-4.7 -m64 -fimplicit-none -O3 -funroll-loops   -dynamiclib -o ../libqrupdate.dylib -install_name /opt/local/lib/libqrupdate.1.dylib caxcpy.o cch1dn.o cch1up.o cchdex.o cchinx.o cchshx.o cgqvec.o cqhqr.o cqr1up.o cqrdec.o cqrder.o cqrinc.o cqrinr.o cqrot.o cqrqh.o cqrshc.o cqrtv1.o dch1dn.o dch1up.o dchdex.o dchinx.o dchshx.o dgqvec.o dqhqr.o dqr1up.o dqrdec.o dqrder.o dqrinc.o dqrinr.o dqrot.o dqrqh.o dqrshc.o dqrtv1.o sch1dn.o sch1up.o schdex.o schinx.o schshx.o sgqvec.o sqhqr.o sqr1up.o sqrdec.o sqrder.o sqrinc.o sqrinr.o sqrot.o sqrqh.o sqrshc.o sqrtv1.o zaxcpy.o zch1dn.o zch1up.o zchdex.o zchinx.o zchshx.o zgqvec.o zqhqr.o zqr1up.o zqrdec.o zqrder.o zqrinc.o zqrinr.o zqrot.o zqrqh.o zqrshc.o zqrtv1.o clu1up.o dlu1up.o slu1up.o zlu1up.o clup1up.o dlup1up.o slup1up.o zlup1up.o \
:info:build 		-L/opt/local/lib -ltatlas -L/opt/local/lib -llapack
:info:build Undefined symbols for architecture x86_64:
:info:build   "_caxpy_", referenced from:
:info:build       _cgqvec_ in cgqvec.o
:info:build       _cqr1up_ in cqr1up.o
:info:build       _cqrinc_ in cqrinc.o
:info:build       _clup1up_ in clup1up.o
:info:build   "_ccopy_", referenced from:
:info:build       _cchdex_ in cchdex.o
:info:build       _cchinx_ in cchinx.o
:info:build       _cchshx_ in cchshx.o
:info:build       _cqrdec_ in cqrdec.o
:info:build       _cqrder_ in cqrder.o
:info:build       _cqrinc_ in cqrinc.o
:info:build       _cqrinr_ in cqrinr.o
:info:build       ...
:info:build   "_cdotc_", referenced from:
:info:build       _cqr1up_ in cqr1up.o
:info:build       _cqrinc_ in cqrinc.o
:info:build   "_cdotu_", referenced from:
:info:build       _cgqvec_ in cgqvec.o
:info:build   "_cgemv_", referenced from:
:info:build       _clup1up_ in clup1up.o
:info:build   "_cgeru_", referenced from:
:info:build       _clup1up_ in clup1up.o
:info:build   "_clartg_", referenced from:
:info:build       _cch1dn_ in cch1dn.o
:info:build       _cch1up_ in cch1up.o
:info:build       _cqhqr_ in cqhqr.o
:info:build       _cqrtv1_ in cqrtv1.o
:info:build   "_crot_", referenced from:
:info:build       _cqr1up_ in cqr1up.o
:info:build       _cqrot_ in cqrot.o
:info:build   "_csscal_", referenced from:
:info:build       _cgqvec_ in cgqvec.o
:info:build       _cqr1up_ in cqr1up.o
:info:build       _cqrinc_ in cqrinc.o
:info:build   "_cswap_", referenced from:
:info:build       _clup1up_ in clup1up.o
:info:build   "_ctrsv_", referenced from:
:info:build       _cch1dn_ in cch1dn.o
:info:build       _cchinx_ in cchinx.o
:info:build       _clup1up_ in clup1up.o
:info:build   "_daxpy_", referenced from:
:info:build       _dgqvec_ in dgqvec.o
:info:build       _dqr1up_ in dqr1up.o
:info:build       _dqrinc_ in dqrinc.o
:info:build       _dlup1up_ in dlup1up.o
:info:build   "_dcopy_", referenced from:
:info:build       _dchdex_ in dchdex.o
:info:build       _dchinx_ in dchinx.o
:info:build       _dchshx_ in dchshx.o
:info:build       _dqrdec_ in dqrdec.o
:info:build       _dqrder_ in dqrder.o
:info:build       _dqrinc_ in dqrinc.o
:info:build       _dqrinr_ in dqrinr.o
:info:build       ...
:info:build   "_ddot_", referenced from:
:info:build       _dgqvec_ in dgqvec.o
:info:build       _dqr1up_ in dqr1up.o
:info:build       _dqrinc_ in dqrinc.o
:info:build   "_dgemv_", referenced from:
:info:build       _dlup1up_ in dlup1up.o
:info:build   "_dger_", referenced from:
:info:build       _dlup1up_ in dlup1up.o
:info:build   "_dlamch_", referenced from:
:info:build       _dqr1up_ in dqr1up.o
:info:build       _zqr1up_ in zqr1up.o
:info:build   "_dlartg_", referenced from:
:info:build       _dch1dn_ in dch1dn.o
:info:build       _dch1up_ in dch1up.o
:info:build       _dqhqr_ in dqhqr.o
:info:build       _dqrtv1_ in dqrtv1.o
:info:build   "_dnrm2_", referenced from:
:info:build       _dch1dn_ in dch1dn.o
:info:build       _dchinx_ in dchinx.o
:info:build       _dgqvec_ in dgqvec.o
:info:build       _dqr1up_ in dqr1up.o
:info:build       _dqrinc_ in dqrinc.o
:info:build   "_drot_", referenced from:
:info:build       _dqr1up_ in dqr1up.o
:info:build       _dqrot_ in dqrot.o
:info:build   "_dscal_", referenced from:
:info:build       _dgqvec_ in dgqvec.o
:info:build       _dqr1up_ in dqr1up.o
:info:build       _dqrinc_ in dqrinc.o
:info:build   "_dswap_", referenced from:
:info:build       _dlup1up_ in dlup1up.o
:info:build   "_dtrsv_", referenced from:
:info:build       _dch1dn_ in dch1dn.o
:info:build       _dchinx_ in dchinx.o
:info:build       _dlup1up_ in dlup1up.o
:info:build   "_dznrm2_", referenced from:
:info:build       _zch1dn_ in zch1dn.o
:info:build       _zchinx_ in zchinx.o
:info:build       _zgqvec_ in zgqvec.o
:info:build       _zqr1up_ in zqr1up.o
:info:build       _zqrinc_ in zqrinc.o
:info:build   "_lsame_", referenced from:
:info:build       _cqrot_ in cqrot.o
:info:build       _dqrot_ in dqrot.o
:info:build       _sqrot_ in sqrot.o
:info:build       _zqrot_ in zqrot.o
:info:build   "_saxpy_", referenced from:
:info:build       _sgqvec_ in sgqvec.o
:info:build       _sqr1up_ in sqr1up.o
:info:build       _sqrinc_ in sqrinc.o
:info:build       _slup1up_ in slup1up.o
:info:build   "_scnrm2_", referenced from:
:info:build       _cch1dn_ in cch1dn.o
:info:build       _cchinx_ in cchinx.o
:info:build       _cgqvec_ in cgqvec.o
:info:build       _cqr1up_ in cqr1up.o
:info:build       _cqrinc_ in cqrinc.o
:info:build   "_scopy_", referenced from:
:info:build       _schdex_ in schdex.o
:info:build       _schinx_ in schinx.o
:info:build       _schshx_ in schshx.o
:info:build       _sqrdec_ in sqrdec.o
:info:build       _sqrder_ in sqrder.o
:info:build       _sqrinc_ in sqrinc.o
:info:build       _sqrinr_ in sqrinr.o
:info:build       ...
:info:build   "_sdot_", referenced from:
:info:build       _sgqvec_ in sgqvec.o
:info:build       _sqr1up_ in sqr1up.o
:info:build       _sqrinc_ in sqrinc.o
:info:build   "_sgemv_", referenced from:
:info:build       _slup1up_ in slup1up.o
:info:build   "_sger_", referenced from:
:info:build       _slup1up_ in slup1up.o
:info:build   "_slamch_", referenced from:
:info:build       _cqr1up_ in cqr1up.o
:info:build       _sqr1up_ in sqr1up.o
:info:build   "_slartg_", referenced from:
:info:build       _sch1dn_ in sch1dn.o
:info:build       _sch1up_ in sch1up.o
:info:build       _sqhqr_ in sqhqr.o
:info:build       _sqrtv1_ in sqrtv1.o
:info:build   "_snrm2_", referenced from:
:info:build       _sch1dn_ in sch1dn.o
:info:build       _schinx_ in schinx.o
:info:build       _sgqvec_ in sgqvec.o
:info:build       _sqr1up_ in sqr1up.o
:info:build       _sqrinc_ in sqrinc.o
:info:build   "_srot_", referenced from:
:info:build       _sqr1up_ in sqr1up.o
:info:build       _sqrot_ in sqrot.o
:info:build   "_sscal_", referenced from:
:info:build       _sgqvec_ in sgqvec.o
:info:build       _sqr1up_ in sqr1up.o
:info:build       _sqrinc_ in sqrinc.o
:info:build   "_sswap_", referenced from:
:info:build       _slup1up_ in slup1up.o
:info:build   "_strsv_", referenced from:
:info:build       _sch1dn_ in sch1dn.o
:info:build       _schinx_ in schinx.o
:info:build       _slup1up_ in slup1up.o
:info:build   "_xerbla_", referenced from:
:info:build       _cch1dn_ in cch1dn.o
:info:build       _cchdex_ in cchdex.o
:info:build       _cchinx_ in cchinx.o
:info:build       _cchshx_ in cchshx.o
:info:build       _cgqvec_ in cgqvec.o
:info:build       _cqhqr_ in cqhqr.o
:info:build       _cqr1up_ in cqr1up.o
:info:build       ...
:info:build   "_zaxpy_", referenced from:
:info:build       _zgqvec_ in zgqvec.o
:info:build       _zqr1up_ in zqr1up.o
:info:build       _zqrinc_ in zqrinc.o
:info:build       _zlup1up_ in zlup1up.o
:info:build   "_zcopy_", referenced from:
:info:build       _zchdex_ in zchdex.o
:info:build       _zchinx_ in zchinx.o
:info:build       _zchshx_ in zchshx.o
:info:build       _zqrdec_ in zqrdec.o
:info:build       _zqrder_ in zqrder.o
:info:build       _zqrinc_ in zqrinc.o
:info:build       _zqrinr_ in zqrinr.o
:info:build       ...
:info:build   "_zdotc_", referenced from:
:info:build       _zqr1up_ in zqr1up.o
:info:build       _zqrinc_ in zqrinc.o
:info:build   "_zdotu_", referenced from:
:info:build       _zgqvec_ in zgqvec.o
:info:build   "_zdscal_", referenced from:
:info:build       _zgqvec_ in zgqvec.o
:info:build       _zqr1up_ in zqr1up.o
:info:build       _zqrinc_ in zqrinc.o
:info:build   "_zgemv_", referenced from:
:info:build       _zlup1up_ in zlup1up.o
:info:build   "_zgeru_", referenced from:
:info:build       _zlup1up_ in zlup1up.o
:info:build   "_zlartg_", referenced from:
:info:build       _zch1dn_ in zch1dn.o
:info:build       _zch1up_ in zch1up.o
:info:build       _zqhqr_ in zqhqr.o
:info:build       _zqrtv1_ in zqrtv1.o
:info:build   "_zrot_", referenced from:
:info:build       _zqr1up_ in zqr1up.o
:info:build       _zqrot_ in zqrot.o
:info:build   "_zswap_", referenced from:
:info:build       _zlup1up_ in zlup1up.o
:info:build   "_ztrsv_", referenced from:
:info:build       _zch1dn_ in zch1dn.o
:info:build       _zchinx_ in zchinx.o
:info:build       _zlup1up_ in zlup1up.o
:info:build ld: symbol(s) not found for architecture x86_64
:info:build collect2: error: ld returned 1 exit status

This is not a clean build log. clean the qrupdate port and try again and attach the complete main.log if it fails again.

Changed 12 years ago by sam.petulla@…

Attachment: main.2.log​ added

After cleaning

comment:2 Changed 12 years ago by sam.petulla@…

Thnks I've attached post-cleaning.

Changed 12 years ago by himpsel@…

Attachment: main.3.log​ added

Another qrupdate log

comment:3 Changed 12 years ago by himpsel@…

I am having the same problem: trying to instal octave on OS X 10.8.3 with xcode 4.6.2 and qrupdate fails to build. I have attached my logfile as main.3.log

comment:4 Changed 12 years ago by him.p.sel@…

Cc: him.p.sel@… added

Cc Me!

comment:5 Changed 12 years ago by lawrence.ong@…

Cc: lawrence.ong@… added

Cc Me!

comment:6 Changed 12 years ago by steven.levis@…

Cc: steven.levis@… added

Cc Me!

comment:7 Changed 12 years ago by lawrence.ong@…

A temporary solution is to install "qrupdate -atlas" and/or "octave-devel -atlas".

Last edited 12 years ago by lawrence.ong@… (previous) (diff)

comment:8 Changed 12 years ago by Veence (Vincent)

I just tried and it works just fine for me: 

gfortran-mp-4.7 -m64 -fimplicit-none -O3 -funroll-loops   -dynamiclib -o ../libqrupdate.dylib -install_name /opt/local/lib/libqrupdate.1.dylib caxcpy.o cch1dn.o cch1up.o cchdex.o cchinx.o cchshx.o cgqvec.o cqhqr.o cqr1up.o cqrdec.o cqrder.o cqrinc.o cqrinr.o cqrot.o cqrqh.o cqrshc.o cqrtv1.o dch1dn.o dch1up.o dchdex.o dchinx.o dchshx.o dgqvec.o dqhqr.o dqr1up.o dqrdec.o dqrder.o dqrinc.o dqrinr.o dqrot.o dqrqh.o dqrshc.o dqrtv1.o sch1dn.o sch1up.o schdex.o schinx.o schshx.o sgqvec.o sqhqr.o sqr1up.o sqrdec.o sqrder.o sqrinc.o sqrinr.o sqrot.o sqrqh.o sqrshc.o sqrtv1.o zaxcpy.o zch1dn.o zch1up.o zchdex.o zchinx.o zchshx.o zgqvec.o zqhqr.o zqr1up.o zqrdec.o zqrder.o zqrinc.o zqrinr.o zqrot.o zqrqh.o zqrshc.o zqrtv1.o clu1up.o dlu1up.o slu1up.o zlu1up.o clup1up.o dlup1up.o slup1up.o zlup1up.o \
                -L/opt/local/lib -ltatlas -L/opt/local/lib -llapack
make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2/src'
make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2'
--->  Staging qrupdate into destroot
. changed
        gid expected 0 found 80 modified
./usr missing (created)
. missing (directory not created: File exists)
./Applications missing (created)
./Developer missing (created)
./Library missing (created)
. changed
        gid expected 80 found 0 modified
./bin missing (created)
./etc missing (created)
./include missing (created)
./lib missing (created)
./lib/pkgconfig missing (created)
./libexec missing (created)
./sbin missing (created)
./share missing (created)
./share/info missing (created)
./share/man missing (created)
./share/man/cat1 missing (created)
./share/man/cat2 missing (created)
./share/man/cat3 missing (created)
./share/man/cat4 missing (created)
./share/man/cat5 missing (created)
./share/man/cat6 missing (created)
./share/man/cat7 missing (created)
./share/man/cat8 missing (created)
./share/man/cat9 missing (created)
./share/man/catl missing (created)
./share/man/catn missing (created)
./share/man/man1 missing (created)
./share/man/man2 missing (created)
./share/man/man3 missing (created)
./share/man/man4 missing (created)
./share/man/man5 missing (created)
./share/man/man6 missing (created)
./share/man/man7 missing (created)
./share/man/man8 missing (created)
./share/man/man9 missing (created)
./share/man/manl missing (created)
./share/man/mann missing (created)
./share/nls missing (created)
./share/nls/C missing (created)
./share/nls/af_ZA.ISO8859-1 missing (created)
./share/nls/af_ZA.ISO8859-15 missing (created)
./share/nls/bg_BG.CP1251 missing (created)
./share/nls/cs_CZ.ISO8859-2 missing (created)
./share/nls/da_DK.ISO8859-1 missing (created)
./share/nls/da_DK.ISO8859-15 missing (created)
./share/nls/de_AT.ISO8859-1 missing (created)
./share/nls/de_AT.ISO8859-15 missing (created)
./share/nls/de_CH.ISO8859-1 missing (created)
./share/nls/de_CH.ISO8859-15 missing (created)
./share/nls/de_DE.ISO8859-1 missing (created)
./share/nls/de_DE.ISO8859-15 missing (created)
./share/nls/el_GR.ISO8859-7 missing (created)
./share/nls/en_AU.ISO8859-1 missing (created)
./share/nls/en_AU.ISO8859-15 missing (created)
./share/nls/en_AU.US-ASCII missing (created)
./share/nls/en_CA.ISO8859-1 missing (created)
./share/nls/en_CA.ISO8859-15 missing (created)
./share/nls/en_CA.US-ASCII missing (created)
./share/nls/en_GB.ISO8859-1 missing (created)
./share/nls/en_GB.ISO8859-15 missing (created)
./share/nls/en_GB.US-ASCII missing (created)
./share/nls/en_NZ.ISO8859-1 missing (created)
./share/nls/en_NZ.ISO8859-15 missing (created)
./share/nls/en_NZ.US-ASCII missing (created)
./share/nls/en_US.ISO8859-1 missing (created)
./share/nls/en_US.ISO8859-15 missing (created)
./share/nls/es_ES.ISO8859-1 missing (created)
./share/nls/es_ES.ISO8859-15 missing (created)
./share/nls/et_EE.ISO8859-15 missing (created)
./share/nls/fi_FI.ISO8859-1 missing (created)
./share/nls/fi_FI.ISO8859-15 missing (created)
./share/nls/fr_BE.ISO8859-1 missing (created)
./share/nls/fr_BE.ISO8859-15 missing (created)
./share/nls/fr_CA.ISO8859-1 missing (created)
./share/nls/fr_CA.ISO8859-15 missing (created)
./share/nls/fr_CH.ISO8859-1 missing (created)
./share/nls/fr_CH.ISO8859-15 missing (created)
./share/nls/fr_FR.ISO8859-1 missing (created)
./share/nls/fr_FR.ISO8859-15 missing (created)
./share/nls/hi_IN.ISCII-DEV missing (created)
./share/nls/hr_HR.ISO8859-2 missing (created)
./share/nls/hu_HU.ISO8859-2 missing (created)
./share/nls/is_IS.ISO8859-1 missing (created)
./share/nls/is_IS.ISO8859-15 missing (created)
./share/nls/it_CH.ISO8859-1 missing (created)
./share/nls/it_CH.ISO8859-15 missing (created)
./share/nls/it_IT.ISO8859-1 missing (created)
./share/nls/it_IT.ISO8859-15 missing (created)
./share/nls/ja_JP.SJIS missing (created)
./share/nls/ja_JP.eucJP missing (created)
./share/nls/ko_KR.eucKR missing (created)
./share/nls/la_LN.ISO8859-1 missing (created)
./share/nls/la_LN.ISO8859-15 missing (created)
./share/nls/la_LN.ISO8859-2 missing (created)
./share/nls/la_LN.ISO8859-4 missing (created)
./share/nls/la_LN.US-ASCII missing (created)
./share/nls/lt_LT.ISO8859-4 missing (created)
./share/nls/nl_BE.ISO8859-1 missing (created)
./share/nls/nl_BE.ISO8859-15 missing (created)
./share/nls/nl_NL.ISO8859-1 missing (created)
./share/nls/nl_NL.ISO8859-15 missing (created)
./share/nls/no_NO.ISO8859-1 missing (created)
./share/nls/no_NO.ISO8859-15 missing (created)
./share/nls/pl_PL.ISO8859-2 missing (created)
./share/nls/pt_BR.ISO8859-1 missing (created)
./share/nls/pt_PT.ISO8859-1 missing (created)
./share/nls/pt_PT.ISO8859-15 missing (created)
./share/nls/ro_RO.ISO8859-2 missing (created)
./share/nls/ru_RU.CP866 missing (created)
./share/nls/ru_RU.ISO8859-5 missing (created)
./share/nls/ru_RU.KOI8-R missing (created)
./share/nls/sk_SK.ISO8859-2 missing (created)
./share/nls/sl_SI.ISO8859-2 missing (created)
./share/nls/sv_SE.ISO8859-1 missing (created)
./share/nls/sv_SE.ISO8859-15 missing (created)
./share/nls/tr_TR.ISO8859-9 missing (created)
./share/nls/uk_UA.ISO8859-5 missing (created)
./share/nls/uk_UA.KOI8-U missing (created)
./share/nls/zh_CN.eucCN missing (created)
./share/nls/zh_TW.Big5 missing (created)
./share/skel missing (created)
./src missing (created)
./var missing (created)
./www missing (created)
make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2'
make -C src/ install
make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2/src'
install -m644 ../libqrupdate.dylib /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/destroot/opt/local/lib/libqrupdate.1.1.dylib
ln -s libqrupdate.1.1.dylib /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/destroot/opt/local/lib/libqrupdate.1.dylib
ln -s libqrupdate.1.1.dylib /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/destroot/opt/local/lib/libqrupdate.dylib
install -m644 ../libqrupdate.a /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/destroot/opt/local/lib/libqrupdate.a
make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2/src'
make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2'
--->  Installing qrupdate @1.1.2_2+atlas+gcc47
…

It seems somehow your Atlas library are buggy. What is the output of: 

ls -l /opt/local/lib/lib*atlas*

and 

ls -l /opt/local/lib/liblapack.a

?

comment:9 Changed 12 years ago by lawrence.ong@…

I am running Xcode 4.6.2 on Mac OS X 10.8.3.

Atlas compiles fine. But qrupdate fails with the following error: 

libtool -o ../libqrupdate.a caxcpy.o cch1dn.o cch1up.o cchdex.o cchinx.o cchshx.o cgqvec.o cqhqr.o cqr1up.o cqrdec.o cqrder.o cqrinc.o cqrinr.o cqrot.o cqrqh.o cqrshc.o cqrtv1.o dch1dn.o dch1up.o dchdex.o dchinx.o dchshx.o dgqvec.o dqhqr.o dqr1up.o dqrdec.o dqrder.o dqrinc.o dqrinr.o dqrot.o dqrqh.o dqrshc.o dqrtv1.o sch1dn.o sch1up.o schdex.o schinx.o schshx.o sgqvec.o sqhqr.o sqr1up.o sqrdec.o sqrder.o sqrinc.o sqrinr.o sqrot.o sqrqh.o sqrshc.o sqrtv1.o zaxcpy.o zch1dn.o zch1up.o zchdex.o zchinx.o zchshx.o zgqvec.o zqhqr.o zqr1up.o zqrdec.o zqrder.o zqrinc.o zqrinr.o zqrot.o zqrqh.o zqrshc.o zqrtv1.o clu1up.o dlu1up.o slu1up.o zlu1up.o clup1up.o dlup1up.o slup1up.o zlup1up.o
make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2/src'
Undefined symbols for architecture x86_64:

...

ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [../libqrupdate.dylib] Error 1
make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2/src'
make: *** [solib] Error 2
make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2'
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2" && /usr/bin/make -j4 -w lib solib PREFIX=/opt/local BLAS="-framework Accelerate" LAPACK="-framework Accelerate" BLAS="-L/opt/local/lib -ltatlas" LAPACK="-L/opt/local/lib -llapack"

Atlas outputs are as follows: 

$ ls -l /opt/local/lib/lib*atlas*
-rw-r--r--  1 root  wheel  6215920 14 May 13:30 /opt/local/lib/libatlas.a
-rwxr-xr-x  1 root  wheel  4121352 14 May 13:30 /opt/local/lib/libsatlas.dylib
-rwxr-xr-x  1 root  wheel  4227648 14 May 13:30 /opt/local/lib/libtatlas.dylib

and 

$ ls -l /opt/local/lib/liblapack.a
-rw-r--r--  1 root  wheel  587024 14 May 13:30 /opt/local/lib/liblapack.a

comment:10 in reply to:  9 Changed 12 years ago by Veence (Vincent)

Replying to lawrence.ong@…:

I am running Xcode 4.6.2 on Mac OS X 10.8.3.

Atlas compiles fine. But qrupdate fails with the following error: 

> Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_qrupdate/qrupdate/work/qrupdate-1.1.2" && /usr/bin/make -j4 -w lib solib PREFIX=/opt/local BLAS="-framework Accelerate" LAPACK="-framework Accelerate" BLAS="-L/opt/local/lib -ltatlas" LAPACK="-L/opt/local/lib -llapack" 
> }}}
> 
> Atlas outputs are as follows:
> […]

Your Atlas libraries look correct. However it appears the command you execute defines BLAS and LAPACK twice, first to use Accelerate framework and then to use Atlas instead. This is probably causing the linking mess you experience.

Last edited 12 years ago by Veence (Vincent) (previous) (diff)

comment:11 in reply to:  9 Changed 12 years ago by Veence (Vincent)

Atlas outputs are as follows: 

$ ls -l /opt/local/lib/lib*atlas*
-rw-r--r--  1 root  wheel  6215920 14 May 13:30 /opt/local/lib/libatlas.a
-rwxr-xr-x  1 root  wheel  4121352 14 May 13:30 /opt/local/lib/libsatlas.dylib
-rwxr-xr-x  1 root  wheel  4227648 14 May 13:30 /opt/local/lib/libtatlas.dylib

Contrarily to what I wrote in my previous message, and after checking on my own machines, your lib?atlas seem more than slender. They should weigh around 10 MiB for each architecture your built Atlas for. So, in your case, there is obviously something wrong with Atlas, and the symbols looked for by the linker are probably not there.

What output gives you 

nm /opt/local/lib/libtalas.dylib | grep _caxpy_

?

PS : The libatlas.a file seems correct, so I guess something went wrong with the dylib generation at the end of the Atlas process. Do you still have got the logs?

Last edited 12 years ago by Veence (Vincent) (previous) (diff)

comment:12 Changed 12 years ago by lawrence.ong@…

Thanks, Vince. You are right that the problem is with BLAS/LPACK and the lib?atlas libraries.

The issue is caused by gcc47 being removed from atlas's dependencies recently (in March I think). Without gcc47 (which provides gfortran-mp-4.7), Atlas compiles without the Fortran API (this gives a smaller lib?atlas.dylib files). This causes qrupdate +atlas, or octave-devel +atlas to fail.

The fix is to put gcc47 back as Atlas's dependency, or compile gcc47 first. This gives the following output: 

$ ls -l /opt/local/lib/lib*atlas*
-rw-r--r--  1 root  wheel   6607552 16 May 13:50 /opt/local/lib/libatlas.a
-rwxr-xr-x  1 root  wheel  10696672 16 May 13:50 /opt/local/lib/libsatlas.dylib
-rwxr-xr-x  1 root  wheel  10802920 16 May 13:50 /opt/local/lib/libtatlas.dylib

If you had gcc installed before installing atlas, then qrupdate +atlas or octave +atlas, you will not have this issue.

Last edited 12 years ago by lawrence.ong@… (previous) (diff)

comment:13 Changed 12 years ago by Veence (Vincent)

Resolution: → wontfix
Status: new → closed

You’re right. Since this not related to qrupdate, I close this ticket, and I have reopened another with the correct diagnosis (#39119) that I’ll fix later today.

Thanks for your sharpness and patience.

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