search

conda / conda

A system-level, binary package and environment manager running on all major operating systems and platforms.
https://docs.conda.io/projects/conda/
Other
6.37k stars 1.65k forks source link

"x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lcrypto" #7578

Closed flopezo closed 2 years ago

flopezo commented 6 years ago

I'm submitting a...

Current Behavior

I installed the conda compiler tools and am trying to compile a third-party program:

conda install cmake curl libcurl gcc_linux-64 gxx_linux-64 gfortran_linux-64 libgcc-ng libgcc openmp openssl isl cloog mpc mpfr
source activate root
cmake -DINSTALL_PREFIX=/path/to/build ..
make -j MP

However, I'm getting the linkage errors below:

.../miniconda2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lcrypto
.../miniconda2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lcurl
.../miniconda2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lssl

Steps to Reproduce

Expected Behavior

Environment Information

`conda info`

``` active environment : None user config file : /home/username/.condarc populated config files : /home/username/.condarc conda version : 4.5.8 conda-build version : not installed python version : 2.7.14.final.0 base environment : /home/username/miniconda2 (writable) channel URLs : https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch https://conda.anaconda.org/r/linux-64 https://conda.anaconda.org/r/noarch package cache : /home/username/miniconda2/pkgs /home/username/.conda/pkgs envs directories : /home/username/miniconda2/envs /home/username/.conda/envs platform : linux-64 user-agent : conda/4.5.8 requests/2.18.4 CPython/2.7.14 Linux/3.10.0-862.3.3.el7.x86_64 centos/7 glibc/2.17 UID:GID : 3269:50000 netrc file : None offline mode : False ```

`conda config --show-sources`

``` ==> /home/username/.condarc <== channels: - bioconda - conda-forge - defaults - r ```

`conda list --show-channel-urls`

``` # packages in environment at /home/username/miniconda2: # # Name Version Build Channel abyss 2.1.0 h09b0a5c_0 bioconda appdirs 1.4.3 py_1 conda-forge argtable2 2.13 1 conda-forge armadillo 8.500.0 blas_openblash45cfd7e_202 [blas_openblas] conda-forge arpack 3.5.0 blas_openblas_202 [blas_openblas] conda-forge asn1crypto 0.24.0 py27_0 defaults assembly-stats 1.0.1 0 bioconda backports 1.0 py27_1 conda-forge backports.functools_lru_cache 1.5 py27_0 conda-forge backports_abc 0.5 py27_0 conda-forge bamtools 2.4.1 1 bioconda bcftools 1.8 1 bioconda beagle-lib 2.1.2 7 bioconda beast2 2.4.5 0 bioconda bfc r181 2 bioconda binutils_impl_linux-64 2.28.1 had2808c_3 anaconda binutils_linux-64 7.2.0 had2808c_27 anaconda bioawk 1.0 ha92aebf_3 bioconda bioconductor-biobase 2.38.0 r3.4.1_0 bioconda bioconductor-biocgenerics 0.24.0 r3.4.1_0 bioconda bioconductor-edger 3.20.7 r3.4.1_0 bioconda bioconductor-limma 3.34.9 r3.4.1_0 bioconda bioconductor-qvalue 2.10.0 r3.4.1_0 bioconda biopython 1.70 np112py27_1 bioconda blas 1.0 mkl defaults blast 2.7.1 boost1.64_3 bioconda blat 36 0 bioconda boost 1.64.0 py27_4 conda-forge boost-cpp 1.64.0 1 conda-forge bowtie 1.2.2 py27pl5.22.0_0 bioconda bowtie2 2.3.4.1 py27pl5.22.0_0 bioconda bwa 0.7.17 pl5.22.0_2 bioconda bzip2 1.0.6 1 conda-forge ca-certificates 2018.4.16 0 conda-forge cairo 1.14.10 0 conda-forge capnproto 0.6.1 0 conda-forge cd-hit 4.6.8 0 bioconda certifi 2018.4.16 py27_0 anaconda cffi 1.11.5 py27h9745a5d_0 defaults chardet 3.0.4 py27hfa10054_1 defaults click 6.7 py_1 conda-forge cloog 0.18.1 0 defaults cmake 3.12.0 h011004d_0 conda-forge collectl 4.0.4 pl5.22.0_3 bioconda colorama 0.3.9 colormath 3.0.0 py_2 conda-forge conda 4.5.8 py27_1 conda-forge conda-env 2.6.0 h36134e3_1 defaults crb-blast 0.6.6 0 bioconda cryptography 2.2.2 py27h14c3975_0 defaults curl 7.60.0 0 conda-forge cycler 0.10.0 py27_0 conda-forge cython 0.28.2 py27_0 conda-forge dbus 1.11.0 0 conda-forge decorator 4.3.0 py_0 conda-forge diamond 0.9.21 1 bioconda dlcpar 1.0 py27_0 bioconda docopt 0.6.2 py27_0 conda-forge emboss 6.5.7 4 bioconda enum34 1.1.6 py27h99a27e9_1 defaults ete3 3.1.1 exonerate 2.4.0 0 bioconda expat 2.2.5 0 conda-forge fasta3 36.3.8 2 bioconda fastme 2.1.5 0 bioconda fastool 0.1.4 2 bioconda fastqc 0.11.7 pl5.22.0_1 bioconda fasttree 2.1.10 0 bioconda font-ttf-ubuntu 0.83 h8b1ccd4_0 defaults fontconfig 2.12.6 0 conda-forge freetype 2.8.1 0 conda-forge ftputil 3.2 py27_0 bioconda functools32 3.2.3.2 py27_2 conda-forge future 0.16.0 py27_0 conda-forge futures 3.2.0 py27h7b459c0_0 defaults gawk 4.2.1 h14c3975_0 anaconda gcc_impl_linux-64 7.2.0 habb00fd_3 anaconda gcc_linux-64 7.2.0 h550dcbe_27 defaults gclib 0.0.1 4 bioconda genometools 1.2.1 py27_0 bioconda gettext 0.19.8.1 0 conda-forge gffcompare 0.10.1 0 bioconda gffread 0.9.9 0 bioconda gfortran_impl_linux-64 7.2.0 hdf63c60_3 defaults gfortran_linux-64 7.2.0 h550dcbe_27 defaults giflib 5.1.4 0 conda-forge glib 2.55.0 0 conda-forge gmap 2018.03.25 pl5.22.0_0 bioconda gmp 6.1.2 0 conda-forge gnuplot 5.0.3 4 bioconda gnutls 3.5.17 0 conda-forge graphite2 1.3.11 0 conda-forge graphviz 2.38.0 7 conda-forge gsl 2.1 2 conda-forge gst-plugins-base 1.8.0 0 conda-forge gstreamer 1.8.0 1 conda-forge gxx_impl_linux-64 7.2.0 hdf63c60_3 anaconda gxx_linux-64 7.2.0 h550dcbe_27 defaults harfbuzz 1.7.6 0 conda-forge hdf5 1.8.17 11 conda-forge hisat2 2.1.0 py27pl5.22.0_0 bioconda hmmer 3.1b2 3 bioconda hyphy 2.3.12 h5466e78_1 bioconda icu 58.2 0 conda-forge idna 2.6 py27h5722d68_1 defaults infernal 1.1.2 0 bioconda intel-openmp 2018.0.0 8 defaults ipaddress 1.0.22 py27_0 defaults iqtree 1.5.5 1 bioconda isl 0.19 0 conda-forge java-jdk 8.0.92 1 bioconda jellyfish 2.2.6 0 bioconda jemalloc 4.5.0 0 bioconda jinja2 2.10 py27_0 conda-forge jpeg 9c h470a237_0 conda-forge kallisto 0.44.0 hdf51.8.17_1 bioconda kat 2.3.1 boost1.64_2 bioconda kmc 3.0.1 noasmlib_2 bioconda krb5 1.14.6 0 conda-forge lapack 3.6.0 2 bioconda lastz 1.0.4 1 bioconda leveldb 1.18 0 conda-forge libcurl 7.60.0 h1ad7b7a_0 defaults libdb 6.1.26 0 bioconda libdeflate 0.8 0 bioconda libedit 3.1.20170329 haf1bffa_0 conda-forge libffi 3.2.1 hd88cf55_4 defaults libgcc 7.2.0 h69d50b8_2 defaults libgcc-ng 7.2.0 hdf63c60_3 defaults libgd 2.2.5 3 conda-forge libgfortran 3.0.0 1 defaults libgfortran-ng 7.2.0 hdf63c60_3 defaults libiconv 1.15 0 conda-forge libidn11 1.33 0 conda-forge libopenblas 0.2.20 h9ac9557_7 defaults libpng 1.6.34 0 conda-forge libssh2 1.8.0 h5b517e9_2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 defaults libtiff 4.0.9 0 conda-forge libtool 2.4.6 0 conda-forge libuuid 1.0.3 1 conda-forge libuv 1.20.3 0 conda-forge libwebp 0.5.2 7 conda-forge libxcb 1.13 0 conda-forge libxml2 2.9.8 0 conda-forge libxslt 1.1.29 4 conda-forge llvm-meta 6.0.0 0 conda-forge lzstring 1.0.3 py27_0 conda-forge m4 1.4.18 0 conda-forge mafft 7.313 0 bioconda make 4.2.1 h470a237_0 conda-forge maker 2.31.9 3 bioconda mako 1.0.7 py_1 conda-forge markdown 2.6.11 py_0 conda-forge markupsafe 1.0 py27_0 conda-forge mash 2.0 gsl2.2_2 bioconda mashmap 2.0 gsl2.2_1 bioconda matplotlib 2.1.0 py27h09aba24_0 defaults mcl 14.137 2 bioconda miniasm 0.2 0 bioconda minimap2 2.11 ha92aebf_0 bioconda mkl 2018.0.2 1 defaults mkl_fft 1.0.2 py27_0 conda-forge mkl_random 1.0.1 py27_0 conda-forge mmtf-python 1.0.2 py27_0 bioconda mpc 1.1.0 hb705a9b_6 conda-forge mpfr 4.0.1 h16a7912_0 conda-forge mpi 1.0 openmpi conda-forge mpi4py 2.0.0 py27_2 defaults mpich2 1.4.1p1 0 defaults msgpack-python 0.5.6 py27h2d50403_2 conda-forge multiqc 1.5 py27_0 bioconda mysql 5.7.20 0 conda-forge mysql-connector-c 6.1.6 2 bioconda mysql-python 1.2.5 py27_0 defaults mysqlclient 1.3.10 py27_0 bioconda ncurses 6.1 0 conda-forge nettle 3.3 0 conda-forge networkx 2.0 py27_1 conda-forge nlopt 2.4.2 py27_2 conda-forge numpy 1.12.1 py27h9378851_1 defaults numpy-base 1.14.3 py27h0ea5e3f_1 defaults ocl-icd 2.2.9 h470a237_4 conda-forge olefile 0.45.1 py27_0 conda-forge openblas 0.2.20 7 conda-forge openjdk 8.0.121 1 defaults openmp 6.0.0 1 conda-forge openmpi 3.1.0 h26a2512_3 conda-forge openssl 1.0.2o 0 conda-forge paml 4.9 1 bioconda pandoc 2.2.1 0 conda-forge pango 1.40.14 0 conda-forge parafly r2013_01_21 1 bioconda parallel 20170422 pl5.22.0_0 bioconda pcre 8.39 0 conda-forge perl 5.22.0.1 0 conda-forge perl-aceperl 1.92 0 bioconda perl-acme-damn 0.08 pl5.22.0_0 bioconda perl-algorithm-munkres 0.08 0 bioconda perl-app-cpanminus 1.7043 pl5.22.0_0 bioconda perl-appconfig 1.71 0 bioconda perl-archive-tar 2.18 pl5.22.0_2 bioconda perl-array-compare 2.11 0 bioconda perl-bio-asn1-entrezgene 1.72 1 bioconda perl-bio-featureio 1.6.905 0 bioconda perl-bio-phylo 0.58 0 bioconda perl-bio-samtools 1.43 0 bioconda perl-bioperl 1.6.924 pl5.22.0_7 bioconda perl-bioperl-core 1.6.924 pl5.22.0_2 bioconda perl-bioperl-run 1.006900 2 bioconda perl-bit-vector 7.4 0 bioconda perl-carp 1.38 pl5.22.0_0 bioconda perl-cgi 4.22 3 bioconda perl-class-inspector 1.28 0 bioconda perl-class-method-modifiers 2.11 1 bioconda perl-clone 0.38 0 bioconda perl-common-sense 3.74 0 bioconda perl-compress-raw-bzip2 2.069 1 bioconda perl-compress-raw-zlib 2.069 3 bioconda perl-convert-binary-c 0.78 0 bioconda perl-convert-binhex 1.125 0 bioconda perl-crypt-rc4 2.02 0 bioconda perl-data-dumper 2.161 pl5.22.0_0 bioconda perl-data-stag 0.14 0 bioconda perl-db-file 1.835 5 bioconda perl-dbd-mysql 4.033 2 bioconda perl-dbd-pg 3.5.3 0 bioconda perl-dbd-sqlite 1.50 1 bioconda perl-dbi 1.641 pl5.22.0_0 bioconda perl-devel-globaldestruction 0.13 1 bioconda perl-digest-hmac 1.03 pl5.22.0_1 bioconda perl-digest-perl-md5 1.9 0 bioconda perl-email-date-format 1.005 0 bioconda perl-encode-locale 1.05 pl5.22.0_4 bioconda perl-error 0.17024 0 bioconda perl-exporter 5.72 pl5.22.0_0 bioconda perl-exporter-tiny 0.042 1 bioconda perl-extutils-makemaker 7.24 pl5.22.0_1 bioconda perl-file-copy-recursive 0.38 1 bioconda perl-file-find-rule 0.34 1 bioconda perl-file-listing 6.04 0 bioconda perl-file-sharedir 1.102 3 bioconda perl-file-sharedir-install 0.10 3 bioconda perl-file-slurp-tiny 0.004 0 bioconda perl-file-sort 1.01 pl5.22.0_1 bioconda perl-file-which 1.20 0 bioconda perl-font-afm 1.20 0 bioconda perl-forks 0.36 pl5.22.0_2 bioconda perl-gd 2.56 5 bioconda perl-graph 0.9704 0 bioconda perl-graphviz 2.20 1 bioconda perl-html-element-extended 1.18 0 bioconda perl-html-entities-numbered 0.04 0 bioconda perl-html-formatter 2.14 0 bioconda perl-html-parser 3.72 pl5.22.0_1 bioconda perl-html-tableextract 2.13 0 bioconda perl-html-tagset 3.20 pl5.22.0_1 bioconda perl-html-tidy 1.56 1 bioconda perl-html-tree 5.03 0 bioconda perl-html-treebuilder-xpath 0.14 0 bioconda perl-http-cookies 6.01 0 bioconda perl-http-daemon 6.01 0 bioconda perl-http-date 6.02 pl5.22.0_1 bioconda perl-http-message 6.11 0 bioconda perl-http-negotiate 6.01 0 bioconda perl-image-info 1.38 0 bioconda perl-image-size 3.300 0 bioconda perl-inline 0.80 0 bioconda perl-inline-c 0.76 0 bioconda perl-io-all 0.86 0 bioconda perl-io-compress 2.069 pl5.22.0_2 bioconda perl-io-html 1.001 pl5.22.0_1 bioconda perl-io-prompt 0.997004 pl5.22.0_0 bioconda perl-io-sessiondata 1.03 0 bioconda perl-io-socket-ssl 2.024 0 bioconda perl-io-string 1.08 pl5.22.0_1 bioconda perl-io-stringy 2.111 0 bioconda perl-io-tty 1.12 0 bioconda perl-io-zlib 1.10 1 bioconda perl-ipc-run 0.94 0 bioconda perl-jcode 2.07 0 bioconda perl-json 2.90 1 bioconda perl-json-xs 2.34 0 bioconda perl-libwww-perl 6.15 0 bioconda perl-libxml-perl 0.08 0 bioconda perl-list-moreutils 0.15 pl5.22.0_0 bioconda perl-lwp-mediatypes 6.02 pl5.22.0_1 bioconda perl-lwp-protocol-https 6.06 2 bioconda perl-lwp-simple 6.15 3 bioconda perl-mailtools 2.14 0 bioconda perl-math-cdf 0.1 3 bioconda perl-math-derivative 0.04 0 bioconda perl-math-random 0.72 0 bioconda perl-math-spline 0.02 0 bioconda perl-mime-base64 3.15 pl5.22.0_0 bioconda perl-mime-lite 3.030 0 bioconda perl-mime-tools 5.507 0 bioconda perl-mime-types 2.12 0 bioconda perl-mldbm 2.05 0 bioconda perl-module-build 0.4224 pl5.22.0_0 bioconda perl-module-runtime 0.014 1 bioconda perl-moo 2.001000 1 bioconda perl-net-http 6.09 0 bioconda perl-net-ssleay 1.84 pl5.22.0_0 bioconda perl-ntlm 1.09 1 bioconda perl-number-compare 0.03 pl5.22.0_1 bioconda perl-ole-storage_lite 0.19 0 bioconda perl-parse-recdescent 1.967013 0 bioconda perl-pathtools 3.73 0 bioconda perl-pdf-api2 2.025 2 bioconda perl-pegex 0.61 0 bioconda perl-perl-unsafe-signals 0.03 0 bioconda perl-perlio-gzip 0.19 pl5.22.0_2 bioconda perl-postscript 0.06 0 bioconda perl-role-tiny 2.000001 1 bioconda perl-scalar-list-utils 1.45 2 bioconda perl-set-scalar 1.29 0 bioconda perl-soap-lite 1.19 0 bioconda perl-sort-naturally 1.03 0 bioconda perl-spreadsheet-parseexcel 0.65 0 bioconda perl-spreadsheet-writeexcel 2.40 0 bioconda perl-statistics-descriptive 3.0612 0 bioconda perl-sub-exporter-progressive 0.001011 1 bioconda perl-svg 2.64 0 bioconda perl-svg-graph 0.02 0 bioconda perl-sys-sigaction 0.23 pl5.22.0_0 bioconda perl-task-weaken 1.04 0 bioconda perl-template-toolkit 2.26 0 bioconda perl-termreadkey 2.32 0 bioconda perl-test-leaktrace 0.16 pl5.22.0_0 bioconda perl-test-more 1.001002 pl5.22.0_0 bioconda perl-test-pod 1.51 0 bioconda perl-text-glob 0.11 pl5.22.0_0 bioconda perl-text-soundex 3.05 0 bioconda perl-threaded 5.22.0 10 bioconda perl-tie-ixhash 1.23 pl5.22.0_1 bioconda perl-timedate 2.30 0 bioconda perl-tree-dag_node 1.29 0 bioconda perl-type-tiny 1.000005 0 bioconda perl-unicode-map 0.112 0 bioconda perl-uri 1.71 pl5.22.0_1 bioconda perl-want 0.29 pl5.22.0_0 bioconda perl-www-robotrules 6.02 0 bioconda perl-xml-dom 1.45 0 bioconda perl-xml-dom-xpath 0.14 0 bioconda perl-xml-filter-buffertext 1.01 0 bioconda perl-xml-libxml 2.0124 0 bioconda perl-xml-libxslt 1.94 0 bioconda perl-xml-namespacesupport 1.11 0 bioconda perl-xml-parser 2.44 4 bioconda perl-xml-regexp 0.04 0 bioconda perl-xml-sax 0.99 0 bioconda perl-xml-sax-base 1.08 0 bioconda perl-xml-sax-expat 0.51 0 bioconda perl-xml-sax-writer 0.56 0 bioconda perl-xml-simple 2.22 0 bioconda perl-xml-twig 3.49 0 bioconda perl-xml-writer 0.625 0 bioconda perl-xml-xpath 1.33 0 bioconda perl-xml-xpathengine 0.14 0 bioconda perl-xsloader 0.22 pl5.22.0_0 bioconda perl-yaml 1.24 0 bioconda perl-yaml-libyaml 0.66 pl5.22.0_0 bioconda phyphy 0.4.2 pigz 2.3.4 0 conda-forge pillow 5.1.0 py27_0 conda-forge pilon 1.22 py27_0 bioconda pip 9.0.3 py27_0 conda-forge pixman 0.34.0 2 conda-forge plyvel 1.0.4 postgresql 10.3 py27_0 conda-forge prank v.170427 0 bioconda pycosat 0.6.3 py27ha4109ae_0 defaults pycparser 2.18 py27hefa08c5_1 defaults pyopenssl 17.5.0 py27hcee3be0_0 defaults pyparsing 2.2.0 py27_0 conda-forge pyqt 5.6.0 py27_5 conda-forge pysocks 1.6.8 py27_0 defaults python 2.7.14 ha6fc286_23 defaults python-dateutil 2.3 py27_0 bioconda pytools 2018.5.2 py_0 conda-forge pytz 2018.4 py_0 conda-forge pyyaml 3.12 py27_1 conda-forge qt 5.6.2 7 conda-forge r-assertthat 0.2.0 r3.4.1_0 conda-forge r-base 3.4.1 4 conda-forge r-cli 1.0.0 r3.4.1_0 conda-forge r-cluster 2.0.6 r3.4.1_0 r r-colorspace 1.3_2 r3.4.1_0 conda-forge r-crayon 1.3.4 r3.4.1_0 conda-forge r-dichromat 2.0_0 r3.4.1_0 conda-forge r-digest 0.6.15 r3.4.1_0 conda-forge r-ggplot2 2.2.1 r3.4.1_0 conda-forge r-glue 1.2.0 r3.4.1_0 conda-forge r-gtable 0.2.0 r3.4.1_0 conda-forge r-labeling 0.3 r3.4.1_0 conda-forge r-lattice 0.20_34 r3.4.1_0 conda-forge r-lazyeval 0.2.1 r3.4.1_0 conda-forge r-locfit 1.5_9.1 r3.4.1_0 conda-forge r-magrittr 1.5 r3.4.1_0 conda-forge r-mass 7.3_48 r3.4.1_0 conda-forge r-munsell 0.5.0 r341_0 conda-forge r-pillar 1.2.2 r341_0 conda-forge r-plyr 1.8.4 r3.4.1_0 conda-forge r-r6 2.2.2 r3.4.1_0 conda-forge r-rcolorbrewer 1.1_2 r3.4.1_0 conda-forge r-rcpp 0.12.15 r3.4.1_0 conda-forge r-reshape2 1.4.3 r3.4.1_0 conda-forge r-rlang 0.2.1 r341_0 conda-forge r-scales 0.5.0 r3.4.1_0 conda-forge r-stringi 1.1.7 r3.4.1_1 conda-forge r-stringr 1.3.0 r3.4.1_0 conda-forge r-tibble 1.4.2 r3.4.1_0 conda-forge r-utf8 1.1.3 r3.4.1_0 conda-forge r-viridislite 0.3.0 r3.4.1_0 conda-forge raxml 8.2.10 0 bioconda readline 7.0 haf1bffa_1 conda-forge recon 1.08 0 bioconda rename 1.600 pl5.22.0_0 bioconda repeatscout 1.0.5 0 bioconda reportlab 3.4.0 py27_0 defaults requests 2.18.4 py27hc5b0589_1 defaults rhash 1.3.4 0 conda-forge ruamel_yaml 0.15.35 py27h14c3975_1 defaults ruby 2.2.3 0 bioconda samtools 1.9 h46bd0b3_0 bioconda scipy 1.1.0 py27hfc37229_0 defaults seqkit 0.8.0 1 bioconda seqmagick 0.6.1 py27_0 bioconda seqtk 1.2 1 bioconda setuptools 39.0.1 py27_0 defaults sga 0.10.15 bamtools2.4.1_2 bioconda simplejson 3.8.1 py27_0 bioconda singledispatch 3.4.0.3 py27_0 conda-forge sip 4.18 py27_1 conda-forge six 1.11.0 py27h5f960f1_1 defaults slclust 02022010 2 bioconda snap 2013_11_29 0 bioconda snappy 1.1.7 1 conda-forge spades 3.11.1 py27_zlib1.2.11_1 bioconda sparsehash 2.0.2 0 bioconda spectra 0.0.11 py_0 conda-forge sqlite 3.20.1 hb898158_2 anaconda sra-tools 2.8.2 0 bioconda stringtie 1.3.3 py27_3 bioconda subprocess32 3.5.1 py27_0 conda-forge superlu 5.2.1 blas_openblas_202 [blas_openblas] conda-forge tbb 2018_20171205 0 conda-forge termcolor 1.1.0 tidyp 1.04 0 bioconda tk 8.6.7 hc745277_3 defaults tldr 0.4.4 tornado 5.0.2 py27_0 conda-forge transdecoder 5.2.0 pl5.22.0_0 bioconda trf 4.09 0 bioconda trimmomatic 0.36 5 bioconda trinity 2.5.1 1 bioconda trinotate 3.1.1 pl5.22.0_0 bioconda trnascan-se 2.0 pl5.22.0_0 bioconda ucsc-pslcdnafilter 357 1 bioconda unicodecsv 0.14.1 py27_0 conda-forge urllib3 1.22 py27ha55213b_0 defaults wheel 0.31.0 py27_0 defaults xmltodict 0.9.2 py27_0 bioconda xorg-fixesproto 5.0 1 conda-forge xorg-inputproto 2.3.2 1 conda-forge xorg-kbproto 1.0.7 1 conda-forge xorg-libx11 1.6.5 0 conda-forge xorg-libxau 1.0.8 3 conda-forge xorg-libxdmcp 1.1.2 3 conda-forge xorg-libxext 1.3.3 2 conda-forge xorg-libxfixes 5.0.3 2 conda-forge xorg-libxi 1.7.8 2 conda-forge xorg-libxtst 1.2.3 0 conda-forge xorg-recordproto 1.14.2 1 conda-forge xorg-xextproto 7.3.0 1 conda-forge xorg-xproto 7.0.31 6 conda-forge xz 5.2.3 0 conda-forge yaml 0.1.7 had09818_2 defaults zlib 1.2.11 h470a237_3 conda-forge ```

nehaljwani commented 5 years ago

@flopezo Try passing -Wl,--sysroot=/ to LDFLAGS ?

mingwandroid commented 5 years ago

Why would that help? Our sysroot is not at /

Try -L$CONDA_PREFIX/lib -Wl,-rpath,$CONDA_PREFIX/lib -Wl,rpath-link,$CONDA-PREFIX/lib

You should check some some of our cmake using recipes though. You haven't passed nearly enough options.

Also you haven't given us anything useful we can work with. What third party program? How are we meant to reproduce this?

nehaljwani commented 5 years ago

From the output, it seemed that OP is trying to link against openssl and curl libraries and has probably been installed via the system package manager. (Assuming OP is just trying to use the Anaconda Compilers for normal compilation and not creation of a conda package)

mingwandroid commented 5 years ago

Given the conda install command line I disagree.

nehaljwani commented 5 years ago

Oh right. Sorry, didn't notice that. @flopezo please ignore my comment.

meishiue commented 5 years ago

Hello, I have the same problem here with an other flag : -lz What I have in my terminal is "/home/msk/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld: cannot find -lz" I have this problem with a program named meme-suite (http://meme-suite.org). When i try compile files with Makefile it can't finish because of this error.

I installed ld with "conda install -c conda-forge binutils" Do you have any idea ?

github-actions[bot] commented 2 years ago

Hi there, thank you for your contribution to Conda!

This issue has been automatically marked as stale because it has not had recent activity. It will be closed automatically if no further activity occurs.

If you would like this issue to remain open please:

  1. Verify that you can still reproduce the issue in the latest version of Conda

  2. Comment that the issue is still reproducible and include:

    • What version of Conda you reproduced the issue on
    • What OS and version you reproduced the issue on
    • What steps you followed to reproduce the issue

  3. It would also be helpful to have the output of the following commands available:

    • conda info
    • conda config --show-sources
    • conda list --show-channel-urls

NOTE: If this issue was closed prematurely, please leave a comment and we will gladly reopen the issue.

In case this issue was originally about a project that is covered by the Anaconda issue tracker (e.g. Anaconda, Miniconda, packages built by Anaconda, Inc. like Anaconda Navigator etc), please reopen the issue there again.

Thanks!

github-actions[bot] commented 2 years ago

Hi again!

This issue has been closed since it has not had recent activity. Please don't hesitate to leave a comment if that was done prematurely.

Thank you for your contribution.