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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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bam2fasta: symbol lookup error: bam2fasta: undefined symbol: _ZN6PacBio3CLI9InterfaceC1ESsSsSs #135

Closed niehu2018 closed 5 years ago

niehu2018 commented 5 years ago

Operating system Centos7

Package name bam2fasta

Conda environment

WARNING conda.core.prefix_data:_load_site_packages(272): Problem reading non-conda package record at lib/python2.7/site-packages/pyBigWig-0.2.8-py2.7-linux-x86_64.egg-info/PKG-INFO. Please verify that you still need this, and if so, that this is still installed correctly. Reinstalling this package may help.
# packages in environment at /anaconda2:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py27h08a7f0c_0    defaults
_r-mutex                  1.0.0               anacondar_1    defaults
alabaster                 0.7.10           py27he5a193a_0    defaults
alignqc                   2.0.5                    pypi_0    pypi
anaconda-client           1.6.14                   py27_0    defaults
anaconda-navigator        1.8.7                    py27_0    defaults
anaconda-project          0.8.2            py27h236b58a_0    defaults
ant                       1.9.9                         0    defaults
argparse                  1.4.0                    pypi_0    pypi
argtable2                 2.13                 h470a237_1    conda-forge
asn1crypto                0.24.0                   py27_0    defaults
astroid                   1.6.3                    py27_0    defaults
astropy                   2.0.6            py27h3010b51_1    defaults
attrs                     18.1.0                   py27_0    defaults
augustus                  3.2.2                         0    bioconda
avro                      1.8.0                    py27_0    bioconda
babel                     2.5.3                    py27_0    defaults
backports                 1.0              py27h63c9359_1    defaults
backports.functools_lru_cache 1.5                      py27_1    defaults
backports.shutil_get_terminal_size 1.0.0            py27h5bc021e_2    defaults
backports_abc             0.5              py27h7b3c97b_0    defaults
bam2fastx                 1.3.0                h4ef8376_6    bioconda
bamtools                  2.5.1                         0    bioconda
bbmap                     38.22                h470a237_0    bioconda
bcftools                  1.9                  ha228f0b_3    bioconda
beautifulsoup4            4.6.0            py27h3f86ba9_1    defaults
bedops                    2.4.35                        0    bioconda
bedtools                  2.27.1                        1    bioconda
binutils_impl_linux-64    2.28.1               had2808c_3    defaults
binutils_linux-64         7.2.0               had2808c_27    defaults
bioconductor-biobase      2.42.0           r351h14c3975_0    bioconda
bioconductor-biocgenerics 0.28.0                   r351_1    bioconda
bioconductor-biocparallel 1.16.2           r351h1c2f66e_1    bioconda
bioconductor-biostrings   2.50.1           r351h14c3975_0    bioconda
bioconductor-delayedarray 0.8.0            r351h14c3975_0    bioconda
bioconductor-genomeinfodb 1.18.1                   r351_0    bioconda
bioconductor-genomeinfodbdata 1.2.0                    r351_0    bioconda
bioconductor-genomicalignments 1.18.0           r351h14c3975_0    bioconda
bioconductor-genomicranges 1.34.0           r351h14c3975_0    bioconda
bioconductor-iranges      2.16.0           r351h14c3975_0    bioconda
bioconductor-noiseq       2.26.0                   r351_0    bioconda
bioconductor-rsamtools    1.34.0           r351hf484d3e_0    bioconda
bioconductor-s4vectors    0.20.1           r351h14c3975_0    bioconda
bioconductor-summarizedexperiment 1.12.0                   r351_0    bioconda
bioconductor-xvector      0.22.0           r351h14c3975_0    bioconda
bioconductor-zlibbioc     1.28.0           r351h14c3975_0    bioconda
bitarray                  0.8.1            py27h14c3975_1    defaults
bkcharts                  0.2              py27h241ae91_0    defaults
blas                      1.0                         mkl    defaults
blasr                     5.3.2                hac9d22c_4    bioconda
blasr_libcpp              5.3.1                hac9d22c_3    bioconda
blast                     2.5.0                hc0b0e79_3    bioconda
blaze                     0.11.3           py27h5f341da_0    defaults
bleach                    2.1.3                    py27_0    defaults
blosc                     1.14.3               hdbcaa40_0    defaults
bokeh                     0.12.16                  py27_0    defaults
boost                     1.67.0                   py27_4    defaults
boost-cpp                 1.64.0                        1    conda-forge
boto                      2.48.0           py27h9556ac2_1    defaults
bottleneck                1.2.1            py27h21b16a3_0    defaults
bowtie                    1.2.0                    py27_0    bioconda
bowtie2                   2.3.0                    py27_1    bioconda
busco                     3.0.2                    pypi_0    pypi
bwa                       0.7.15                        1    bioconda
bwidget                   1.9.11                        1    defaults
bx-python                 0.8.2            py27hebb334c_2    bioconda
bz2file                   0.98                     py27_0    defaults
bzip2                     1.0.6                h14c3975_5    defaults
ca-certificates           2019.3.9             hecc5488_0    conda-forge
cairo                     1.14.12              h8948797_3    defaults
cd-hit                    4.8.1                hdbcaa40_0    bioconda
cdecimal                  2.3              py27h14c3975_3    defaults
certifi                   2019.3.9                 py27_0    conda-forge
cffi                      1.11.5           py27h9745a5d_0    defaults
chardet                   3.0.4            py27hfa10054_1    defaults
click                     6.7              py27h4225b90_0    defaults
cloudpickle               0.5.3                    py27_0    defaults
clustalo                  1.2.4                hfc679d8_2    bioconda
clyent                    1.2.2            py27h7276e6c_1    defaults
collectl                  4.0.4                         2    bioconda
colorama                  0.3.9            py27h5cde069_0    defaults
conda                     4.6.13                   py27_0    conda-forge
conda-build               3.10.5                   py27_0    defaults
conda-env                 2.6.0                h36134e3_1    defaults
conda-verify              2.0.0            py27hf052a9d_0    defaults
configparser              3.5.0            py27h5117587_0    defaults
contextlib2               0.5.5            py27hbf4c468_0    defaults
cryptography              2.5              py27h9d9f1b6_1    conda-forge
curl                      7.64.0               h646f8bb_2    conda-forge
cutadapt                  1.16                     py27_1    bioconda
cycler                    0.10.0           py27hc7354d3_0    defaults
cython                    0.28.2           py27h14c3975_0    defaults
cytoolz                   0.9.0.1          py27h14c3975_0    defaults
dask                      0.17.5                   py27_0    defaults
dask-core                 0.17.5                   py27_0    defaults
datashape                 0.5.4            py27hf507385_0    defaults
dbus                      1.13.2               h714fa37_1    defaults
decorator                 4.3.0                    py27_0    defaults
deeptools                 3.2.1                      py_0    bioconda
deeptoolsintervals        0.1.7            py27h14c3975_1    bioconda
distributed               1.21.8                   py27_0    defaults
docutils                  0.14             py27hae222c1_0    defaults
entrypoints               0.2.3            py27h502b47d_2    defaults
enum34                    1.1.6            py27h99a27e9_1    defaults
et_xmlfile                1.0.1            py27h75840f5_0    defaults
expat                     2.2.5                he0dffb1_0    defaults
fastcache                 1.0.2            py27h14c3975_2    defaults
fastool                   0.1.4                ha92aebf_3    bioconda
fastp                     0.14.1                        0    bioconda
fastqc                    0.11.5                        1    bioconda
filelock                  3.0.4                    py27_0    defaults
flask                     1.0.2                    py27_1    defaults
flask-cors                3.0.4                    py27_0    defaults
fontconfig                2.13.0               h9420a91_0    defaults
freebayes                 1.2.0            py27h82df9c4_3    bioconda
freetype                  2.9.1             h94bbf69_1005    conda-forge
fribidi                   1.0.5                h7b6447c_0    defaults
funcsigs                  1.0.2            py27h83f16ab_0    defaults
functools32               3.2.3.2          py27h4ead58f_1    defaults
future                    0.16.0                   py27_2    conda-forge
futures                   3.2.0            py27h7b459c0_0    defaults
gatb                      1.4.1                hdfd8fe7_0    bioconda
gcc_impl_linux-64         7.2.0                habb00fd_3    defaults
gcc_linux-64              7.2.0               h550dcbe_27    defaults
get_terminal_size         1.0.0                haa9412d_0    defaults
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
gevent                    1.3.0            py27h14c3975_0    defaults
gfortran_impl_linux-64    7.2.0                hdf63c60_3    defaults
gfortran_linux-64         7.2.0               h550dcbe_27    defaults
giflib                    5.1.4             h14c3975_1001    conda-forge
git                       2.21.0          pl526h2882143_0    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
glob2                     0.6              py27hcea9cbd_0    defaults
gmap                      2018.03.25      pl526he4cf2ce_1    bioconda
gmp                       6.1.2                h6c8ec71_1    defaults
gmpy2                     2.0.8            py27h4cf3fa8_2    defaults
graphite2                 1.3.13               h23475e2_0    defaults
greenlet                  0.4.13           py27h14c3975_0    defaults
grin                      1.2.1                    py27_4    defaults
grunt                     1.0.4                         0    conda-forge
gsl                       2.4                  h14c3975_4    defaults
gst-plugins-base          1.14.0               hbbd80ab_1    defaults
gstreamer                 1.14.0               hb453b48_1    defaults
gxx_impl_linux-64         7.2.0                hdf63c60_3    defaults
gxx_linux-64              7.2.0               h550dcbe_27    defaults
h5py                      2.7.1            py27ha1f6525_2    defaults
harfbuzz                  1.9.0             he243708_1001    conda-forge
hdf5                      1.10.2               hba1933b_1    defaults
heapdict                  1.0.0                    py27_2    defaults
html5lib                  1.0.1            py27h5233db4_0    defaults
htop                      2.2.0             hf8c457e_1000    conda-forge
htslib                    1.9                  ha228f0b_6    bioconda
icu                       58.2                 h9c2bf20_1    defaults
idna                      2.6              py27h5722d68_1    defaults
imageio                   2.3.0                    py27_0    defaults
imagesize                 1.0.0                    py27_0    defaults
intel-openmp              2018.0.0                      8    defaults
intervene                 0.6.4           pyr332h24bf2e0_1    bioconda
ipaddress                 1.0.22                   py27_0    defaults
ipykernel                 4.8.2                    py27_0    defaults
ipython                   5.7.0                    py27_0    defaults
ipython_genutils          0.2.0            py27h89fb69b_0    defaults
ipywidgets                7.2.1                    py27_0    defaults
iso8601                   0.1.12                     py_1    conda-forge
isort                     4.3.4                    py27_0    defaults
isoseq3                   3.1.0                         0    bioconda
itsdangerous              0.24             py27hb8295c1_1    defaults
java-jdk                  8.0.92                        1    bioconda
jbig                      2.1                  hdba287a_0    defaults
jdcal                     1.4                      py27_0    defaults
jedi                      0.12.0                   py27_1    defaults
jellyfish                 2.2.10               h2d50403_0    bioconda
jemalloc                  5.1.0                hfc679d8_0    conda-forge
jinja2                    2.10             py27h4114e70_0    defaults
joblib                    0.11                     py27_0    defaults
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                2.6.0            py27h7ed5aa4_0    defaults
jupyter                   1.0.0                    py27_4    defaults
jupyter_client            5.2.3                    py27_0    defaults
jupyter_console           5.2.0            py27hc6bee7e_1    defaults
jupyter_core              4.4.0            py27h345911c_0    defaults
jupyterlab                0.32.1                   py27_0    defaults
jupyterlab_launcher       0.10.5                   py27_0    defaults
khmer                     2.1.2                    py27_0    bioconda
kiwisolver                1.0.1            py27hc15e7b5_0    defaults
krb5                      1.16.3            h05b26f9_1001    conda-forge
lazy-object-proxy         1.3.1            py27h682c727_0    defaults
libboost                  1.67.0               h46d08c1_4    defaults
libcurl                   7.64.0               h541490c_2    conda-forge
libdb                     6.1.26                        0    bioconda
libdeflate                1.0                  h470a237_0    bioconda
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1                hd88cf55_4    defaults
libgcc                    7.2.0                h69d50b8_2    defaults
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgd                     2.2.5                h5400f36_4    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    defaults
libiconv                  1.15                 h63c8f33_5    defaults
libopenblas               0.2.20               h9ac9557_7    defaults
libpng                    1.6.36            h84994c4_1000    conda-forge
libsodium                 1.0.16               h1bed415_0    defaults
libssh2                   1.8.0             h90d6eec_1004    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.9                he85c1e1_1    defaults
libtool                   2.4.6                h544aabb_3    defaults
libuuid                   1.0.3                h1bed415_2    defaults
libwebp                   0.5.2                         7    conda-forge
libxcb                    1.13                 h1bed415_1    defaults
libxml2                   2.9.8             h143f9aa_1005    conda-forge
libxscrnsaver-cos6-x86_64 1.2.2                h54af3ee_0    defaults
libxslt                   1.1.32            h4785a14_1002    conda-forge
lima                      1.9.0                         0    bioconda
llvmlite                  0.23.1           py27hdbcaa40_0    defaults
locket                    0.2.0            py27h73929a2_1    defaults
lordec                    0.9                  ha87ae23_0    bioconda
lxml                      4.1.1            py27hdd00cef_0    defaults
lzo                       2.10                 h49e0be7_2    defaults
macs2                     2.1.2                py27r351_0    bioconda/label/cf201901
make                      4.2.1             h14c3975_2004    conda-forge
markupsafe                1.0              py27h97b2822_1    defaults
matplotlib                2.2.3            py27h8a2030e_1    conda-forge
matplotlib-base           2.2.3            py27h60b886d_1    conda-forge
mccabe                    0.6.1            py27h0e7c7be_1    defaults
minimap2                  2.15                 ha92aebf_0    bioconda
mistune                   0.8.3            py27h14c3975_1    defaults
mkl                       2018.0.3                      1    defaults
mkl-service               1.1.2            py27hb2d42c5_4    defaults
mkl_fft                   1.0.10                   py27_0    conda-forge
mkl_random                1.0.1            py27h629b387_0    defaults
more-itertools            4.1.0                    py27_0    defaults
mpc                       1.0.3                hec55b23_5    defaults
mpfr                      3.1.5                h11a74b3_2    defaults
mpi                       1.0                     openmpi    conda-forge
mpmath                    1.0.0            py27h9669132_2    defaults
msgpack                   0.5.6                    pypi_0    pypi
msgpack-python            0.5.6            py27h6bb024c_0    defaults
multipledispatch          0.5.0                    py27_0    defaults
multiqc                   1.0.dev0                 pypi_0    pypi
muscle                    3.8.1551             h2d50403_3    bioconda
mysql-connector-c         6.1.6                         2    bioconda
mysqlclient               1.3.10                   py27_0    bioconda
navigator-updater         0.2.1                    py27_0    defaults
nbconvert                 5.3.1            py27he041f76_0    defaults
nbformat                  4.4.0            py27hed7f2b2_0    defaults
ncurses                   6.1               hf484d3e_1002    conda-forge
networkx                  2.1                      py27_0    defaults
nltk                      3.3.0                    py27_0    defaults
nose                      1.3.7            py27heec2199_2    defaults
notebook                  5.5.0                    py27_0    defaults
numba                     0.38.0           py27h637b7d7_0    defaults
numexpr                   2.6.8            py27hf8a1672_0    conda-forge
numpy                     1.15.4           py27h1d66e8a_0    defaults
numpy-base                1.15.4           py27h81de0dd_0    defaults
numpydoc                  0.8.0                    py27_0    defaults
odo                       0.5.1            py27h9170de3_0    defaults
olefile                   0.45.1                   py27_0    defaults
openblas                  0.3.3                ha44fe06_1    conda-forge
openjdk                   8.0.121                       1    defaults
openmpi                   3.1.3                h26a2512_0    conda-forge
openpyxl                  2.5.3                    py27_0    defaults
openssl                   1.1.1b               h14c3975_1    conda-forge
packaging                 17.1                     py27_0    defaults
pandas                    0.23.0           py27h637b7d7_0    defaults
pandoc                    1.19.2.1             hea2e7c5_1    defaults
pandocfilters             1.4.2            py27h428e1e5_1    defaults
pango                     1.42.4               h049681c_0    defaults
parafly                   r2013_01_21                   1    bioconda
parallel                  20160622                      1    bioconda
parso                     0.2.0                    py27_0    defaults
partd                     0.3.8            py27h4e55004_0    defaults
patchelf                  0.9                  hf79760b_2    defaults
path.py                   11.0.1                   py27_0    defaults
pathlib2                  2.3.2                    py27_0    defaults
patsy                     0.5.0                    py27_0    defaults
pbbam                     0.19.0               h6678c95_1    bioconda
pbccs                     3.4.1                         0    bioconda
pbcommand                 1.1.1            py27h24bf2e0_1    bioconda
pbcopper                  0.4.2                h3f2a3d2_1    bioconda
pbcore                    1.7.1                    py27_0    bioconda
pbcoretools               0.2.4                    py27_1    bioconda
pbmm2                     0.12.0               ha87ae23_0    bioconda
pcre                      8.42                 h439df22_0    defaults
pear                      0.9.6                he4cf2ce_4    bioconda
pep8                      1.7.1                    py27_0    defaults
perl                      5.26.2               h470a237_0    conda-forge
perl-app-cpanminus        1.7039                        2    bioconda
perl-capture-tiny         0.36                    pl526_2    bioconda
perl-carp                 1.38                    pl526_1    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-cpan-meta            2.120921                pl526_1    bioconda
perl-data-dumper          2.161                   pl526_2    bioconda
perl-db-file              1.835                         5    bioconda
perl-dbd-mysql            4.033           pl526h470a237_3    bioconda
perl-dbd-sqlite           1.56            pl526h14c3975_0    eumetsat
perl-dbi                  1.641                   pl526_1    bioconda
perl-devel-symdump        2.18                    pl526_1    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-extutils-cbuilder    0.280230                pl526_1    bioconda
perl-extutils-cppguess    0.12            pl526h2d50403_2    bioconda
perl-extutils-makemaker   7.34                    pl526_0    bioconda
perl-extutils-manifest    1.70                    pl526_2    bioconda
perl-extutils-parsexs     3.35                    pl526_0    bioconda
perl-file-find-rule       0.34                          2    bioconda
perl-file-path            2.12                    pl526_1    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-gd                   2.70            pl526he941832_0    bioconda
perl-gdgraph              1.54                    pl526_0    bioconda
perl-gdtextutil           0.86            pl526h470a237_4    bioconda
perl-getopt-long          2.50                    pl526_1    bioconda
perl-graph                0.9704                  pl526_1    bioconda
perl-io-gzip              0.20            pl526h1341992_2    bioconda
perl-ipc-cmd              1.02                    pl526_0    bioconda
perl-json-xs              3.04            pl526h2d50403_0    bioconda
perl-list-util            1.38                    pl526_1    bioconda
perl-locale-maketext-simple 0.21                    pl526_1    bioconda
perl-module-build         0.4224                  pl526_2    bioconda
perl-module-corelist      5.20180120              pl526_1    bioconda
perl-module-load          0.32                    pl526_1    bioconda
perl-module-load-conditional 0.68                    pl526_2    bioconda
perl-module-metadata      1.000019                pl526_1    bioconda
perl-number-compare       0.03                    pl526_2    bioconda
perl-params-check         0.38                    pl526_1    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-perl-ostype          1.010                   pl526_1    bioconda
perl-scalar-list-utils    1.45                          2    bioconda
perl-set-intervaltree     0.11                    pl526_1    bioconda
perl-test-more            1.001002                pl526_1    bioconda
perl-text-abbrev          1.02                    pl526_0    bioconda
perl-text-glob            0.11                    pl526_1    bioconda
perl-text-parsewords      3.29                    pl526_3    bioconda
perl-threaded             5.22.0                       10    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-uri                  1.71                    pl526_2    bioconda
perl-version              0.9924                  pl526_0    bioconda
perl-yaml                 1.24                          0    bioconda
pexpect                   4.5.0                    py27_0    defaults
phylip                    3.697                h470a237_0    bioconda
phyml                     3.3.20180621         h470a237_0    bioconda
pickleshare               0.7.4            py27h09770e1_0    defaults
pigz                      2.3                           0    defaults
pillow                    5.4.1           py27h00a061d_1000    conda-forge
pip                       10.0.1                   py27_0    defaults
pixman                    0.34.0               hceecf20_3    defaults
pkginfo                   1.4.2                    py27_1    defaults
plotly                    2.7.0                    py27_1    defaults
pluggy                    0.6.0            py27h1f4f128_0    defaults
ply                       3.11                     py27_0    defaults
prompt_toolkit            1.0.15           py27h1b593e1_0    defaults
psutil                    5.4.5            py27h14c3975_0    defaults
ptyprocess                0.5.2            py27h4ccb14c_0    defaults
py                        1.5.3                    py27_0    defaults
py-boost                  1.67.0           py27h04863e7_4    defaults
py2bit                    0.3.0                    py27_0    bioconda
pybedtools                0.8.0            py27he860b03_1    bioconda
pybigwig                  0.2.8                    py27_0    bioconda
pycairo                   1.10.0                   py27_0    defaults
pycodestyle               2.4.0                    py27_0    defaults
pycosat                   0.6.3            py27ha4109ae_0    defaults
pycparser                 2.18             py27hefa08c5_1    defaults
pycrypto                  2.6.1            py27h14c3975_8    defaults
pycurl                    7.43.0.2         py27h1ba5d50_0    defaults
pyflakes                  1.6.0            py27h904a57d_0    defaults
pygments                  2.2.0            py27h4a8b6f5_0    defaults
pylint                    1.8.4                    py27_0    defaults
pyodbc                    4.0.23           py27hf484d3e_0    defaults
pyopenssl                 18.0.0                   py27_0    defaults
pyparsing                 2.2.0            py27hf1513f8_1    defaults
pyqt                      5.6.0                    py27_2    defaults
pysam                     0.15.2           py27hb06f55c_2    bioconda
pysocks                   1.6.8                    py27_0    defaults
pytables                  3.4.3            py27h02b9ad4_2    defaults
pytest                    3.5.1                    py27_0    defaults
python                    2.7.15            h721da81_1007    conda-forge
python-dateutil           2.7.3                    py27_0    defaults
python-lzo                1.12            py27hb300a8c_1000    conda-forge
pytz                      2018.4                   py27_0    defaults
pywavelets                0.5.2            py27hecda097_0    defaults
pyyaml                    3.12             py27h2d70dd7_1    defaults
pyzmq                     17.0.0           py27h14c3975_1    defaults
qt                        5.6.3                h8bf5577_3    defaults
qtawesome                 0.4.4            py27hd7914c3_0    defaults
qtconsole                 4.3.1            py27hc444b0d_0    defaults
qtpy                      1.4.1                    py27_0    defaults
quast                     4.1                      py27_0    bioconda
r                         3.5.1                 r351_1000    conda-forge
r-assertthat              0.2.0           r351h6115d3f_1001    conda-forge
r-base                    3.5.1                h1e0a451_2    defaults
r-bh                      1.69.0_1         r351h6115d3f_0    conda-forge
r-bitops                  1.0_6           r351h96ca727_1002    conda-forge
r-boot                    1.3_20                r351_1000    conda-forge
r-cairo                   1.5_9            r351hc070d10_2    conda-forge
r-class                   7.3_15          r351h96ca727_1000    conda-forge
r-cli                     1.0.1           r351h6115d3f_1000    conda-forge
r-cluster                 2.0.7_1         r351ha65eedd_1000    conda-forge
r-codetools               0.2_16          r351h6115d3f_1000    conda-forge
r-colorspace              1.4_0            r351h96ca727_0    conda-forge
r-corrplot                0.84                  r351_1001    conda-forge
r-crayon                  1.3.4           r351h6115d3f_1001    conda-forge
r-digest                  0.6.18          r351h96ca727_1000    conda-forge
r-fansi                   0.4.0           r351h96ca727_1000    conda-forge
r-foreign                 0.8_71          r351h96ca727_1002    conda-forge
r-formatr                 1.5             r351h6115d3f_1001    conda-forge
r-futile.logger           1.4.3           r351h6115d3f_1001    conda-forge
r-futile.options          1.0.1           r351h6115d3f_1000    conda-forge
r-getopt                  1.20.2                r351_2001    conda-forge
r-ggplot2                 3.1.0           r351h6115d3f_1000    conda-forge
r-glue                    1.3.0           r351h14c3975_1002    conda-forge
r-gridextra               2.3             r351h6115d3f_1001    conda-forge
r-gtable                  0.2.0           r351h6115d3f_1001    conda-forge
r-kernsmooth              2.23_15         r351ha65eedd_1002    conda-forge
r-labeling                0.3             r351h6115d3f_1001    conda-forge
r-lambda.r                1.2.3           r351h6115d3f_1000    conda-forge
r-lattice                 0.20_38         r351h96ca727_1000    conda-forge
r-lazyeval                0.2.1           r351h96ca727_1002    conda-forge
r-magrittr                1.5             r351h6115d3f_1001    conda-forge
r-mass                    7.3_51.1        r351h96ca727_1000    conda-forge
r-matrix                  1.2_15          r351h96ca727_1000    conda-forge
r-matrixstats             0.54.0          r351h96ca727_1000    conda-forge
r-mgcv                    1.8_26          r351h96ca727_1000    conda-forge
r-munsell                 0.5.0           r351h6115d3f_1001    conda-forge
r-nlme                    3.1_137         r351ha65eedd_1000    conda-forge
r-nnet                    7.3_12          r351h96ca727_1002    conda-forge
r-pillar                  1.3.1           r351h6115d3f_1000    conda-forge
r-pkgconfig               2.0.2           r351h6115d3f_1001    conda-forge
r-plyr                    1.8.4           r351h29659fb_1002    conda-forge
r-r6                      2.4.0            r351h6115d3f_0    conda-forge
r-rcolorbrewer            1.1_2           r351h6115d3f_1001    conda-forge
r-rcpp                    1.0.0           r351h29659fb_1000    conda-forge
r-rcurl                   1.95_4.11        r351h96ca727_0    defaults
r-recommended             3.5.1                 r351_1001    conda-forge
r-reshape2                1.4.3           r351h29659fb_1003    conda-forge
r-rlang                   0.3.1            r351h96ca727_0    conda-forge
r-rpart                   4.1_13          r351h96ca727_1002    conda-forge
r-scales                  1.0.0           r351h29659fb_1001    conda-forge
r-snow                    0.4_3           r351h6115d3f_1000    conda-forge
r-spatial                 7.3_11          r351h96ca727_1002    conda-forge
r-stringi                 1.2.4           r351h29659fb_1001    conda-forge
r-stringr                 1.4.0            r351h6115d3f_0    conda-forge
r-survival                2.43_3          r351h96ca727_1000    conda-forge
r-tibble                  2.0.1            r351h96ca727_0    conda-forge
r-upsetr                  1.3.3                 r351_1001    conda-forge
r-utf8                    1.1.4           r351h96ca727_1000    conda-forge
r-viridislite             0.3.0           r351h6115d3f_1001    conda-forge
r-withr                   2.1.2           r351h6115d3f_1000    conda-forge
r-xml                     3.98_1.16       r351h96ca727_1000    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
recalladapters            7.1.0                         0    bioconda
regex                     2016.06.24               py27_1    bioconda
requests                  2.18.4           py27hc5b0589_1    defaults
rmats                     4.0.2            py27h24bf2e0_0    bioconda
rope                      0.10.7           py27hfe459b0_0    defaults
rpy2                      2.6.0                    pypi_0    pypi
ruamel_yaml               0.15.35          py27h14c3975_1    defaults
salmon                    0.12.0               h86b0361_1    bioconda
sambamba                  0.6.6                         1    bioconda
samtools                  1.9                  h91753b0_5    bioconda
scandir                   1.7              py27h14c3975_0    defaults
scikit-image              0.13.1           py27h14c3975_1    defaults
scikit-learn              0.19.1           py27hedc7406_0    defaults
scipy                     1.1.0            py27hc49cb51_0    defaults
screed                    1.0                        py_1    bioconda
seaborn                   0.8.1            py27h633ea1e_0    defaults
send2trash                1.5.0                    py27_0    defaults
seq-tools                 1.0.10                   pypi_0    pypi
seqkit                    0.8.1                         2    bioconda
setuptools                39.1.0                   py27_0    defaults
sicer                     1.1              py27h24bf2e0_3    bioconda
simplegeneric             0.8.1                    py27_2    defaults
simplejson                3.8.1                    py27_0    bioconda
singledispatch            3.4.0.3          py27h9bcb476_0    defaults
sip                       4.19.8           py27hf484d3e_0    defaults
six                       1.11.0           py27h5f960f1_1    defaults
slclust                   02022010                      2    bioconda
snappy                    1.1.7                hbae5bb6_3    defaults
snowballstemmer           1.2.1            py27h44e2768_0    defaults
sortedcollections         0.6.1                    py27_0    defaults
sortedcontainers          1.5.10                   py27_0    defaults
soupsieve                 1.9.1                    py27_0    conda-forge
sphinx                    1.7.4                    py27_0    defaults
sphinxcontrib             1.0              py27h1512b58_1    defaults
sphinxcontrib-websupport  1.0.1            py27hf906f22_1    defaults
splicegrapher             0.2.6                    pypi_0    pypi
spyder                    3.2.8                    py27_0    defaults
sqlalchemy                1.2.7            py27h6b74fdf_0    defaults
sqlite                    3.26.0               h7b6447c_0    defaults
ssl_match_hostname        3.5.0.1          py27h4ec10b9_2    defaults
star                      2.6.0c                        0    bioconda
statsmodels               0.9.0            py27h3010b51_0    defaults
subprocess32              3.5.0            py27h14c3975_0    defaults
sympy                     1.1.1            py27hc28188a_0    defaults
system                    5.8                           2    defaults
tapis                     0.3.1                    pypi_0    pypi
tbb                       2019.3            h6bb024c_1000    conda-forge
tblib                     1.3.2            py27h51fe5ba_0    defaults
terminado                 0.8.1                    py27_1    defaults
testpath                  0.3.1            py27hc38d2c4_0    defaults
tk                        8.6.9             h84994c4_1000    conda-forge
tktable                   2.10                 h14c3975_0    defaults
toolz                     0.9.0                    py27_0    defaults
tornado                   5.0.2                    py27_0    defaults
traitlets                 4.3.2            py27hd6ce930_0    defaults
transdecoder              5.3.0                         0    bioconda
trim-galore               0.4.5                         2    bioconda
trimmomatic               0.38                          0    bioconda
typing                    3.6.4                    py27_0    defaults
ucsc-blat                 357                           1    bioconda
umap-learn                0.2.3                    py27_0    conda-forge
unicodecsv                0.14.1           py27h5062da9_0    defaults
unixodbc                  2.3.6                h1bed415_0    defaults
urllib3                   1.22             py27ha55213b_0    defaults
viewbs                    0.1.6                         0    xie186
wcwidth                   0.1.7            py27h9e3e1ab_0    defaults
webencodings              0.5.1            py27hff10b21_1    defaults
werkzeug                  0.14.1                   py27_0    defaults
wget                      1.19.5               h20c2e04_0    defaults
wheel                     0.31.1                   py27_0    defaults
widgetsnbextension        3.2.1                    py27_0    defaults
wrapt                     1.10.11          py27h04f6869_0    defaults
xlrd                      1.1.0            py27ha77178f_1    defaults
xlsxwriter                1.0.4                    py27_0    defaults
xlwt                      1.3.0            py27h3d85d97_0    defaults
xopen                     0.3.2                    py27_0    bioconda
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4                h14c3975_4    defaults
yaml                      0.1.7                had09818_2    defaults
zeromq                    4.2.5                h439df22_0    defaults
zict                      0.1.3            py27h12c336c_0    defaults
zlib                      1.2.11               ha838bed_2    defaults

Describe the bug bam2fasta failed to run

Error message

$ bam2fasta 
bam2fasta: symbol lookup error: bam2fasta: undefined symbol: _ZN6PacBio3CLI9InterfaceC1ESsSsSs

To Reproduce

Expected behavior

pb-cdunn commented 5 years ago

Missing symbol:

PacBio::CLI::Interface::Interface(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)

That's in pbcopper. You have:

pbbam                     0.19.0               h6678c95_1    bioconda
pbcopper                  0.4.2                h3f2a3d2_1    bioconda

Latest:

pbbam                     0.23.0               h88345a9_0    bioconda
pbcopper                  0.4.2                h3f2a3d2_1    bioconda

Hmmm. I'm not sure what's wrong, but try conda update --all.

niehu2018 commented 5 years ago

I update pbbam from 0.19.0 to 0.23.0 using conda, then the problem is solved. Thanks!