Hello Alexander: "clang Š | grep unknown" did not return anything. I've made the edit to compiler_wrapper you recommended and this fixed the problem. Bioperl has installed and runs as expected.
Cheers, Kurt Wollenberg, Ph.D. Contractor - MSC, Inc. Phylogenetics Specialist Computational Biology Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62 Bethesda, MD 20892-0485 Office 301-402-8628 http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov <http://exon.niaid.nih.gov/> (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives On 4/10/14 12:06 PM, "Alexander Hansen" <alexanderk.han...@gmail.com> wrote: >On 4/10/14, 8:37 AM, Wollenberg, Kurt (NIH/NIAID) [C] wrote: >> Hello everybody: >> >> I've been trying to use fink to install bioperl on my desktop machine >>(Mac quad-core running OS 10.8.5) using "sudo fink install >>bioperl-pm5124" and get the following error and resulting behavior: >> >> gcc -DHAVE_CONFIG_H -I. -I/sw/include -Werror -no-cpp-precomp -g -O2 >>-g -Wall -MT usb.lo -MD -MP -MF .deps/usb.Tpo -c usb.c -DPIC >> error: unknown warning option >>'-Werror=unused-command-line-argument-hard-error-in-future'; did you >>mean '-Werror=unused-command-line-argument'? >>[-Werror,-Wunknown-warning-option] >> make[2]: *** [usb.lo] Error 1 >> make[1]: *** [all-recursive] Error 1 >> make: *** [all] Error 2 >> ### execution of /tmp/fink.M6Uxt failed, exit code 2 >> ### execution of /tmp/fink.6F99e failed, exit code 2 >> >> Here's my system information: >> Also include the following system information: >> Package manager version: 0.36.4 >> Distribution version: selfupdate-rsync Thu Apr 10 11:21:44 2014, 10.8, >>x86_64 >> Trees: local/main stable/main >> Xcode.app: 5.0 >> Xcode command-line tools: 5.0.1.0.1.1377666378 >> Max. Fink build jobs: 1 >> >> I've run "fink self update" and reconfigured fink to to have max build >>jobs = 1 and I'm still getting this same error. >> >> Help? >> >> Cheers, >> Kurt Wollenberg, Ph.D. >> Contractor - MSC, Inc. >> Phylogenetics Specialist >> Computational Biology Section >> Bioinformatics and Computational Biosciences Branch (BCBB) >> OCICB/OSMO/OD/NIAID/NIH >> >> 31 Center Drive, Room 3B62 >> Bethesda, MD 20892-0485 >> Office 301-402-8628 >> >>http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> >> (Within NIH) >> http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) >> >> Disclaimer: >> The information in this e-mail and any of its attachments is >>confidential >> and may contain sensitive information. It should not be used by anyone >>who >> is not the original intended recipient. If you have received this >>e-mail in >> error please inform the sender and delete it from your mailbox or any >>other >> storage devices. National Institute of Allergy and Infectious Diseases >>shall >> not accept liability for any statements made that are sender's own and >>not >> expressly made on behalf of the NIAID by one of its representatives >> > >The flag which is causing your error comes from Fink's compiler >wrappers. They're supposed to be checking whether clang supports that >flag or not. I had thought that your version of clang wouldn't trigger >that flag to be set, though I didn't have the Xcode 5.0 CL tools handy >for verification. > >What do you get from > >clang -Wno-error=unused-command-line-argument-hard-error-in-future 2>&1 >| grep unknown > >? > >As a workaround while a proper fix is developed, edit >/sw/var/lib/fink/path-prefix-clang/compiler_wrapper as an administrator >and change the bottom uncommented line to > >exec $compiler "$@" > >-- >Alexander Hansen, Ph.D. >Fink User Liaison >My package updates: http://finkakh.wordpress.com/ ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
