issue compiling cortex - Githubissues

inti commented 11 years ago

Hi, I am getting a error while compiling cortex. Let me know if you can help. See at the end of the text below thanks in advance, inti

$ python2.7 bcbio_nextgen_install.py --distribution centos --nosudo ~/APP/bcbio_nextgen/install_directory ~/APP/bcbio_nextgen/data_directory Initialized empty Git repository in /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/.git/ remote: Counting objects: 5704, done. remote: Compressing objects: 100% (2337/2337), done. remote: Total 5704 (delta 3383), reused 5513 (delta 3202) Receiving objects: 100% (5704/5704), 5.56 MiB | 466 KiB/s, done. Resolving deltas: 100% (3383/3383), done. Installing tools... [localhost] Executing task 'install_biolinux' INFO: Config start time: 2013-02-06 08:28:50.307292 INFO: This is a Base Flavor - no overrides DBG [init.py]: Minimal Edition 1.5.3 INFO: This is a minimal INFO: Distribution centos INFO: Get local environment INFO: CentOS setup DBG [distribution.py]: Checking target distribution centos DBG [distribution.py]: Unknown target distro DBG [distribution.py]: NixPkgs: Ignored [localhost] run: echo $HOME [localhost] out: /home/pedrosoi [localhost] out:

[localhost] run: uname -m [localhost] out: x86_64 [localhost] out:

INFO: Now, testing connection to host... INFO: Connection to host appears to work! DBG [utils.py]: Expand paths DBG [fabfile.py]: Target is 'None' DBG [config.py]: Using config file /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline/main.yaml INFO: Meta-package information from /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline/main.yaml

Packages: minimal,libraries,python,java,r,bio_nextgen,distributed
Libraries: [localhost] run: echo $PATH [localhost] out: /home/pedrosoi/python/bin:/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/apps/sge/6.2u5/bin/lx24-amd64:/usr/local/bin:/bin:/usr/bin [localhost] out:

[localhost] run: echo '# CloudBioLinux PATH updates' >> ~/.bashrc [localhost] run: echo 'export PATH=$PATH:/home/pedrosoi/APP/bcbio_nextgen/install_directory/bin' >> ~/.bashrc [localhost] run: echo $TMPDIR [localhost] out: [localhost] out: [localhost] run: echo $HOME [localhost] out: /home/pedrosoi [localhost] out:

[localhost] run: wget --no-check-certificate https://raw.github.com/pypa/virtualenv/master/virtualenv.py [localhost] out: --2013-02-06 08:28:52-- https://raw.github.com/pypa/virtualenv/master/virtualenv.py [localhost] out: Resolving raw.github.com... 199.27.77.130 [localhost] out: Connecting to raw.github.com|199.27.77.130|:443... connected. [localhost] out: WARNING: certificate common name “*.a.ssl.fastly.net” doesn’t match requested host name “raw.github.com”. [localhost] out: HTTP request sent, awaiting response... 200 OK [localhost] out: Length: 114330 (112K) [text/plain] [localhost] out: Saving to: “virtualenv.py” [localhost] out: [localhost] out: [localhost] out: 0% [ ] 0 --.-K/s
[localhost] out: 100%[==========================================================================>] 114,330 --.-K/s in 0.01s
[localhost] out: [localhost] out: 2013-02-06 08:28:53 (9.05 MB/s) - “virtualenv.py” saved [114330/114330] [localhost] out: [localhost] out:

[localhost] run: python virtualenv.py /home/pedrosoi/APP/bcbio_nextgen/install_directory [localhost] out: New python executable in /home/pedrosoi/APP/bcbio_nextgen/install_directory/bin/python [localhost] out: Installing setuptools............................done. [localhost] out: Installing pip.....................done. [localhost] out:

[localhost] run: rm -rf /home/pedrosoi/tmp/cloudbiolinux INFO: Target=unknown; Edition=Minimal Edition; Flavor=ngs_pipeline DBG [config.py]: Using config file /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/cloudbio/../config/custom.yaml INFO: Reading /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/cloudbio/../config/custom.yaml DBG [shared.py]: Packages to install: pydoop,seal,leiningen,bx-python,rpy,abyss,cortex_var,ray,transabyss,trinity,velvet,macs,bcbio_variation,crisp,gemini,stacks,tassel,varscan,hydra,cufflinks,freebayes,gatk,gatk_queue,picard,sambamba,samtools,shrec,snpeff,tophat,vep,bfast,novoalign,novosort,plink_seq,ucsc_tools,bedtools,dwgsim,fastqc,fastx_toolkit,varianttools,vcftools,bowtie,bowtie2,bwa,gmap,lastz,mosaik,snap,stampy INFO: Custom install for 'leiningen' start time: 2013-02-06 08:29:10.272973 INFO: Custom install for 'leiningen' start time: 2013-02-06 08:29:10.272973 DBG [fabfile.py]: Import leiningen DBG [fabfile.py]: Import leiningen [localhost] run: echo $TMPDIR [localhost] out: [localhost] out: [localhost] run: echo $HOME [localhost] out: /home/pedrosoi [localhost] out:

[localhost] run: mkdir -p /home/pedrosoi/tmp/cloudbiolinux [localhost] run: wget --no-check-certificate https://raw.github.com/technomancy/leiningen/stable/bin/lein [localhost] out: --2013-02-06 08:29:10-- https://raw.github.com/technomancy/leiningen/stable/bin/lein [localhost] out: Resolving raw.github.com... 199.27.77.130 [localhost] out: Connecting to raw.github.com|199.27.77.130|:443... connected. [localhost] out: WARNING: certificate common name “*.a.ssl.fastly.net” doesn’t match requested host name “raw.github.com”. [localhost] out: HTTP request sent, awaiting response... 200 OK [localhost] out: Length: 10250 (10K) [text/plain] [localhost] out: Saving to: “lein” [localhost] out: [localhost] out: [localhost] out: 0% [ ] 0 --.-K/s
[localhost] out: 100%[==========================================================================>] 10,250 --.-K/s in 0s
[localhost] out: [localhost] out: 2013-02-06 08:29:11 (73.1 MB/s) - “lein” saved [10250/10250] [localhost] out: [localhost] out:

[localhost] run: chmod a+rwx lein [localhost] run: mv [localhost] run: /home/pedros [localhost] out: Downloading [localhost] out: % Total [localhost] out: [localhost] out: [localhost] out: 0 [localhost] out: 3 12.6M [localhost] out: 10 12.6M 10 1294k [localhost] out: 18 12.6M 18 2364k [localhost] out: 27 12.6M 27 3575k [localhost] out: 33 12.6M 33 4390k [localhost] out: 36 12.6M 36 4767k [localhost] out: 40 12.6M 40 5223k [localhost] out: 45 12.6M 45 5936k [localhost] out: 51 12.6M 51 6697k [localhost] out: 53 12.6M 53 6870k [localhost] out: 55 12.6M 55 7140k [localhost] out: 58 12.6M 58 7567k [localhost] out: 63 12.6M 63 8232k [localhost] out: 69 12.6M 69 8953k [localhost] out: 73 12.6M 73 9430k [localhost] out: 75 12.6M 75 9801k [localhost] out: 78 12.6M 78 9.9M [localhost] out: 82 12.6M 82 10.4M [localhost] out: 84 12.6M 84 10.6M [localhost] out: 85 12.6M 85 10.7M [localhost] out: 87 12.6M 87 11.0M [localhost] out: 89 12.6M 89 11.3M [localhost] out: 93 12.6M 93 11.7M [localhost] out: 97 12.6M 97 12.2M [localhost] out: 100 12.6M 100 12.6M [localhost] out: Leiningen [localhost] out: [localhost] out: Several [localhost] out: check [localhost] out: classpath [localhost] out: clean [localhost] out: compile [localhost] out: deploy [localhost] out: deps [localhost] out: do [localhost] out: help [localhost] out: install [localhost] out: jar [localhost] out: javac [localhost] out: new [localhost] out: plugin [localhost] out: pom [localhost] out: repl [localhost] out: retest [localhost] out: run [localhost] out: search [localhost] out: show-profiles [localhost] out: test [localhost] out: trampoline [localhost] out: uberjar [localhost] out: upgrade [localhost] out: version [localhost] out: with-profile [localhost] out: [localhost] out: Run [localhost] out: [localhost] out: See [localhost] out: lein /home/pedrosoi/APP/bcbio_nextgen/install_directory/bin oi/APP/bcbio_nextgen/install_directory/bin/lein Leiningen to /home/pedrosoi/.lein/self-installs/leiningen-2.0.0-standalone.jar now... % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 3 403k 0 0 293k 0 0:00:43 0:00:01 0:00:42 488k 0 0 546k 0 0:00:23 0:00:02 0:00:21 710k 0 0 703k 0 0:00:18 0:00:03 0:00:15 839k 0 0 820k 0 0:00:15 0:00:04 0:00:11 937k 0 0 813k 0 0:00:15 0:00:05 0:00:10 905k 0 0 745k 0 0:00:17 0:00:06 0:00:11 869k 0 0 706k 0 0:00:18 0:00:07 0:00:11 782k 0 0 708k 0 0:00:18 0:00:08 0:00:10 711k 0 0 713k 0 0:00:18 0:00:09 0:00:09 621k 0 0 662k 0 0:00:19 0:00:10 0:00:09 497k 0 0 627k 0 0:00:20 0:00:11 0:00:09 476k 0 0 611k 0 0:00:21 0:00:12 0:00:09 470k 0 0 616k 0 0:00:20 0:00:13 0:00:07 461k 0 0 623k 0 0:00:20 0:00:14 0:00:06 453k 0 0 614k 0 0:00:21 0:00:15 0:00:06 514k 0 0 599k 0 0:00:21 0:00:16 0:00:05 534k 0 0 587k 0 0:00:21 0:00:17 0:00:04 526k 0 0 582k 0 0:00:22 0:00:18 0:00:04 493k 0 0 559k 0 0:00:23 0:00:19 0:00:04 379k 0 0 541k 0 0:00:23 0:00:20 0:00:03 317k 0 0 527k 0 0:00:24 0:00:21 0:00:03 292k 0 0 519k 0 0:00:24 0:00:22 0:00:02 282k 0 0 515k 0 0:00:25 0:00:23 0:00:02 268k 0 0 516k 0 0:00:25 0:00:24 0:00:01 343k 0 0 518k 0 0:00:24 0:00:24 --:--:-- 418k is a tool for working with Clojure projects. tasks are available: Check syntax and warn on reflection. Write the classpath of the current project to output-file. Remove all files from project's target-path. Compile Clojure source into .class files. Build jar and deploy to remote repository. Show details about dependencies. Higher-order task to perform other tasks in succession. Display a list of tasks or help for a given task or subtask. Install current project to the local repository. Package up all the project's files into a jar file. Compile Java source files. Generate scaffolding for a new project based on a template. DEPRECATED. Please use the :user profile instead. Write a pom.xml file to disk for Maven interoperability. Start a repl session either with the current project or standalone. Run only the test namespaces which failed last time around. Run the project's -main function. Search remote maven repositories for matching jars. List all available profiles or display one if given an argument. Run the project's tests. Run a task without nesting the project's JVM inside Leiningen's. Package up the project files and all dependencies into a jar file. Upgrade Leiningen to specified version or latest stable. Print version for Leiningen and the current JVM. Apply the given task with the profile(s) specified. lein help $TASK for details. also: readme, faq, tutorial, news, sample, profiles, deploying, mixed-source, templates, and copying.

[localhost] run: rm -rf /home/pedrosoi/tmp/cloudbiolinux INFO: Custom install for 'leiningen' end time: 2013-02-06 08:29:40.600416; duration: 0:00:30.327443 INFO: Custom install for 'leiningen' end time: 2013-02-06 08:29:40.600416; duration: 0:00:30.327443 INFO: Custom install for 'cortex_var' start time: 2013-02-06 08:29:40.600716 INFO: Custom install for 'cortex_var' start time: 2013-02-06 08:29:40.600716 INFO: Custom install for 'cortex_var' start time: 2013-02-06 08:29:40.600716 DBG [fabfile.py]: Import cortex_var DBG [fabfile.py]: Import cortex_var DBG [fabfile.py]: Import cortex_var [localhost] run: echo $TMPDIR [localhost] out: [localhost] out: [localhost] run: echo $HOME [localhost] out: /home/pedrosoi [localhost] out:

[localhost] run: mkdir -p /home/pedrosoi/tmp/cloudbiolinux [localhost] run: wget --no-check-certificate -O CORTEX_release_v1.0.5.14.tgz 'http://downloads.sourceforge.net/project/cortexassembler/cortex_var/latest/CORTEX_release_v1.0.5.14.tgz' [localhost] out: --2013-02-06 08:29:41-- http://downloads.sourceforge.net/project/cortexassembler/cortex_var/latest/CORTEX_release_v1.0.5.14.tgz [localhost] out: Resolving downloads.sourceforge.net... 216.34.181.59 [localhost] out: Connecting to downloads.sourceforge.net|216.34.181.59|:80... connected. [localhost] out: HTTP request sent, awaiting response... 302 Found [localhost] out: Location: http://netcologne.dl.sourceforge.net/project/cortexassembler/cortex_var/latest/CORTEX_release_v1.0.5.14.tgz [following] [localhost] out: --2013-02-06 08:29:41-- http://netcologne.dl.sourceforge.net/project/cortexassembler/cortex_var/latest/CORTEX_release_v1.0.5.14.tgz [localhost] out: Resolving netcologne.dl.sourceforge.net... 78.35.24.46, 2001:4dd0:1234:6::5f [localhost] out: Connecting to netcologne.dl.sourceforge.net|78.35.24.46|:80... connected. [localhost] out: HTTP request sent, awaiting response... 200 OK [localhost] out: Length: 30656942 (29M) [application/x-gzip] [localhost] out: Saving to: “CORTEX_release_v1.0.5.14.tgz” [localhost] out: [localhost] out: [localhost] out: 0% [ ] 0 --.-K/s
[localhost] out: 1% [ ] 379,225 1.64M/s
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[localhost] out: 100%[==========================================================================>] 30,656,942 2.03M/s in 22s
[localhost] out: [localhost] out: 2013-02-06 08:30:04 (1.32 MB/s) - “CORTEX_release_v1.0.5.14.tgz” saved [30656942/30656942] [localhost] out: [localhost] out:

[localhost] run: tar --pax-option='delete=SCHILY.,delete=LIBARCHIVE.' -xzpf CORTEX_releasev1.0.5.14.tgz [localhost] run: sed -i.bak -r -e 's/-L\/full\/path\/\S/-L\/home\/pedrosoi\/APP\/bcbio_nextgen\/install_directory\/lib/g' Makefile [localhost] run: sed -i.bak -r -e 's/^IDIRGSL=.$/IDIR_GSL=\/home\/pedrosoi\/APP\/bcbio_nextgen\/install_directory\/include/g' Makefile [localhost] run: sed -i.bak -r -e 's/^IDIR_GSL_ALSO=.$/IDIR_GSL_ALSO=\/home\/pedrosoi\/APP\/bcbio_nextgen\/install_directory\/include\/gsl/g' Makefile [localhost] run: make clean [localhost] out: Making clean in doc [localhost] out: make[1]: Entering directory /home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/doc' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory `/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: test -z "gsl-ref.dvi gsl-ref.pdf gsl-ref.ps gsl-ref.html" \ [localhost] out: || rm -rf gsl-ref.dvi gsl-ref.pdf gsl-ref.ps gsl-ref.html [localhost] out: rm -rf .libs _libs [localhost] out: rm -rf gsl-ref.aux gsl-ref.cp gsl-ref.cps gsl-ref.fn gsl-ref.fns \ [localhost] out: gsl-ref.ky gsl-ref.kys gsl-ref.log gsl-ref.pg gsl-ref.pgs \ [localhost] out: gsl-ref.tmp gsl-ref.toc gsl-ref.tp gsl-ref.tps gsl-ref.vr \ [localhost] out: gsl-ref.vrs [localhost] out: rm -f .lo [localhost] out: rm -f vti.tmp [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/doc' [localhost] out: Making clean in bspline [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/bspline' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslbspline.la " || rm -f libgslbspline.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/bspline' [localhost] out: Making clean in wavelet [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/wavelet' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslwavelet.la " || rm -f libgslwavelet.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/wavelet' [localhost] out: Making clean in cdf [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/cdf' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslcdf.la" || rm -f libgslcdf.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/cdf' [localhost] out: Making clean in deriv [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/deriv' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslderiv.la" || rm -f libgslderiv.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/deriv' [localhost] out: Making clean in diff [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/diff' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgsldiff.la" || rm -f libgsldiff.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/diff' [localhost] out: Making clean in ntuple [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ntuple' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: test -z "test.dat" || rm -f test.dat [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslntuple.la" || rm -f libgslntuple.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ntuple' [localhost] out: Making clean in monte [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/monte' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmonte.la " || rm -f libgslmonte.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/monte' [localhost] out: Making clean in multimin [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multimin' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmultimin.la " || rm -f libgslmultimin.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multimin' [localhost] out: Making clean in min [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/min' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmin.la " || rm -f libgslmin.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/min' [localhost] out: Making clean in multiroots [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multiroots' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmultiroots.la " || rm -f libgslmultiroots.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multiroots' [localhost] out: Making clean in roots [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/roots' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslroots.la " || rm -f libgslroots.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/roots' [localhost] out: Making clean in ode-initval2 [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ode-initval2' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslodeiv2.la " || rm -f libgslodeiv2.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ode-initval2' [localhost] out: Making clean in ode-initval [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ode-initval' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslodeiv.la " || rm -f libgslodeiv.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ode-initval' [localhost] out: Making clean in histogram [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/histogram' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: test -z "test.txt test.dat" || rm -f test.txt test.dat [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslhistogram.la " || rm -f libgslhistogram.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/histogram' [localhost] out: Making clean in interpolation [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/interpolation' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslinterpolation.la " || rm -f libgslinterpolation.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/interpolation' [localhost] out: Making clean in integration [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/integration' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslintegration.la" || rm -f libgslintegration.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/integration' [localhost] out: Making clean in sum [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/sum' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslsum.la " || rm -f libgslsum.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/sum' [localhost] out: Making clean in siman [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/siman' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: test -z "siman_test.out" || rm -f siman_test.out [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslsiman.la" || rm -f libgslsiman.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f siman_tsp [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/siman' [localhost] out: Making clean in statistics [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/statistics' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslstatistics.la" || rm -f libgslstatistics.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/statistics' [localhost] out: Making clean in multifit [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multifit' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmultifit.la " || rm -f libgslmultifit.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multifit' [localhost] out: Making clean in fit [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/fit' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslfit.la " || rm -f libgslfit.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/fit' [localhost] out: Making clean in poly [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/poly' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslpoly.la " || rm -f libgslpoly.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/poly' [localhost] out: Making clean in fft [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/fft' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslfft.la " || rm -f libgslfft.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/fft' [localhost] out: Making clean in randist [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/randist' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslrandist.la" || rm -f libgslrandist.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/randist' [localhost] out: Making clean in rng [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/rng' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: test -z "test.dat" || rm -f test.dat [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslrng.la " || rm -f libgslrng.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/rng' [localhost] out: Making clean in qrng [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/qrng' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslqrng.la " || rm -f libgslqrng.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/qrng' [localhost] out: Making clean in dht [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/dht' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgsldht.la " || rm -f libgsldht.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/dht' [localhost] out: Making clean in specfunc [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/specfunc' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslspecfunc.la " || rm -f libgslspecfunc.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/specfunc' [localhost] out: Making clean in eigen [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/eigen' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgsleigen.la " || rm -f libgsleigen.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/eigen' [localhost] out: Making clean in linalg [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/linalg' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgsllinalg.la " || rm -f libgsllinalg.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/linalg' [localhost] out: Making clean in blas [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/blas' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslblas.la" || rm -f libgslblas.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/blas' [localhost] out: Making clean in cblas [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/cblas' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: test -z "libgslcblas.la" || rm -f libgslcblas.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -rf .libs _libs [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/cblas' [localhost] out: Making clean in ieee-utils [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ieee-utils' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslieeeutils.la " || rm -f libgslieeeutils.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/ieee-utils' [localhost] out: Making clean in sort [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/sort' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslsort.la" || rm -f libgslsort.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/sort' [localhost] out: Making clean in multiset [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multiset' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmultiset.la" || rm -f libgslmultiset.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/multiset' [localhost] out: Making clean in combination [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/combination' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslcombination.la " || rm -f libgslcombination.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/combination' [localhost] out: Making clean in permutation [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/permutation' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslpermutation.la " || rm -f libgslpermutation.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/permutation' [localhost] out: Making clean in matrix [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/matrix' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test test_static [localhost] out: test -z "test.txt test.dat" || rm -f test.txt test.dat [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslmatrix.la " || rm -f libgslmatrix.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/matrix' [localhost] out: Making clean in vector [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/vector' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test test_static [localhost] out: test -z "test.txt test.dat" || rm -f test.txt test.dat [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslvector.la " || rm -f libgslvector.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/vector' [localhost] out: Making clean in block [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/block' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: test -z "test.txt test.dat" || rm -f test.txt test.dat [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslblock.la " || rm -f libgslblock.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/block' [localhost] out: Making clean in cheb [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/cheb' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslcheb.la " || rm -f libgslcheb.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/cheb' [localhost] out: Making clean in complex [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/complex' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslcomplex.la " || rm -f libgslcomplex.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/complex' [localhost] out: Making clean in const [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/const' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/const' [localhost] out: Making clean in err [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/err' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslerr.la" || rm -f libgslerr.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/err' [localhost] out: Making clean in test [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/test' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgsltest.la" || rm -f libgsltest.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/test' [localhost] out: Making clean in sys [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/sys' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -f test [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libgslsys.la " || rm -f libgslsys.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] out: make[1]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/sys' [localhost] out: Making clean in utils [localhost] out: make[1]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15/utils' [localhost] out: make[2]: Entering directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: make[2]: Leaving directory/home/pedrosoi/tmp/cloudbiolinux/CORTEX_release_v1.0.5.14/libs/gsl-1.15' [localhost] out: rm -rf .libs _libs [localhost] out: test -z "libutils.la" || rm -f libutils.la [localhost] out: rm -f "./so_locations" [localhost] out: rm -f .o [localhost] out: rm -f .lo [localhost] ou

chapmanb commented 11 years ago

Inti; It looks like the log you posted was too long and the actual error got cut off. I don't need the full log, only the last lines with the error will work great.

In general, one of the issues with --nosudo installs is that the installer can't install system libraries required for compilation. I know cortex requires the GNU scientific library, so if that is available on your cluster as a module including it may fix the problem.

Another option I'll kick around is creating a "lite" version of the 3rd party installs that leaves out tricky compilations that are not strictly necessary. cortex_var is a variant caller choice but not required if you don't want to run it. I'll give this some thought about the best way to do it.

Happy to answer more specifically about this issue if you can paste the error. Thanks again.

chapmanb commented 10 years ago

Closing old report, since cortex no longer installed by default.

chapmanb / bcbb

issue compiling cortex #72