# Import pygmt error after jupyterlab installation

**URL:** https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117
**Category:** PyGMT Q&A
**Tags:** gmt
**Created:** [September 22, 2021, 7:08am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117 "2021-09-22T07:08:34Z")
**Posts on this page:** 13
**Page:** 1

<div class="post-metadata">

### Author: ![kradorl](https://avatars.discourse-cdn.com/v4/letter/k/50afbb/32.png) [@kradorl](https://forum.generic-mapping-tools.org/u/kradorl)
#### Post date: [September 22, 2021, 7:08am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/1 "2021-09-22T07:08:34Z")

</div>

Hi All,

Using the command `conda create --name pygmt --channel conda-forge pygmt`, I installed the pygmt and when I `import pygmt` it looked fine to me.

> PyGMT information:  
> version: v0.4.1  
> System information:  
> python: 3.9.7 | packaged by conda-forge | (default, Sep 14 2021, 01:18:03) [Clang 11.1.0]  
> executable: /Users/lli/opt/anaconda3/envs/pygmt/bin/python  
> machine: macOS-11.6-x86\_64-i386-64bit  
> Dependency information:  
> numpy: 1.21.2  
> pandas: 1.3.3  
> xarray: 0.19.0  
> netCDF4: 1.5.7  
> packaging: 21.0  
> ghostscript: 9.54.0  
> gmt: 6.2.0  
> GMT library information:  
> binary dir: /Users/lli/opt/anaconda3/envs/pygmt/bin  
> cores: 8  
> grid layout: rows  
> library path: /Users/lli/opt/anaconda3/envs/pygmt/lib/libgmt.dylib  
> padding: 2  
> plugin dir: /Users/lli/opt/anaconda3/envs/pygmt/lib/gmt/plugins  
> share dir: /Users/lli/opt/anaconda3/envs/pygmt/share/gmt  
> version: 6.2.0

After jupyterlab installation with `conda install jupyterlab`, I am getting an ImportError. Here is the full traceback:

```python-traceback
> Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/ __init__.py", line 57, in <module>
    _begin()
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/session_management.py", line 16, in begin
    with Session() as lib:
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 185, in __enter__
    self.create("pygmt-session")
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 332, in create
    c_create_session = self.get_libgmt_func(
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 284, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/loading.py", line 59, in load_libgmt
    raise GMTCLibNotFoundError("\n".join(error_msg))
pygmt.exceptions.GMTCLibNotFoundError: Error loading GMT shared library at '/Users/lli/opt/anaconda3/envs/pygmt/lib/libgmt.dylib'.
dlopen(/Users/lli/opt/anaconda3/envs/pygmt/lib/libgmt.dylib, 6): Symbol not found: _libiconv
  Referenced from: /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
  Expected in: /usr/lib/libiconv.2.dylib
 in /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
Error loading GMT shared library at 'libgmt.dylib'.
dlopen(libgmt.dylib, 6): Symbol not found: _libiconv
  Referenced from: /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
  Expected in: /usr/lib/libiconv.2.dylib
 in /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib

```

---

<div class="post-metadata">

### Author: ![jldavis](https://avatars.discourse-cdn.com/v4/letter/j/3bc359/32.png) [@jldavis](https://forum.generic-mapping-tools.org/u/jldavis)
#### Post date: [October 25, 2021, 8:04pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/2 "2021-10-25T20:04:29Z")

</div>

Did you figure this out? I have the same problem. Thanks.

---

<div class="post-metadata">

### Author: ![weiji14](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/weiji14/32/33_2.png) [@weiji14](https://forum.generic-mapping-tools.org/u/weiji14)
#### Post date: [October 26, 2021, 12:38am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/3 "2021-10-26T00:38:36Z")

</div>

Could be a few things. Did you do `conda activate pygmt` before `conda install jupyterlab`? Just want to make sure that you installed `jupyterlab` into the correct virtual environment.

Otherwise, the error message you posted could be because libspatialite or libgmt got corrupted during the download or extraction process. Try doing a clean reinstall of PyGMT, like so:

```bash
conda deactivate
conda clean --all
conda create --name pygmt --channel conda-forge pygmt jupyterlab
conda activate pygmt
python -c "import pygmt; pygmt.show_versions()"
jupyter lab --no-browser

```

---

<div class="post-metadata">

### Author: ![EJFielding](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/ejfielding/32/82_2.png) [@EJFielding](https://forum.generic-mapping-tools.org/u/EJFielding)
#### Post date: [November 1, 2021, 4:57am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/4 "2021-11-01T04:57:27Z")

</div>

I tried installing `pygmt` with `conda` and have a somewhat similar problem with `libgmt` not loading. I tried doing the `conda clean --all` and reinstalled pygmt, but I get the same error:

```auto
python -c "import pygmt; pygmt.show_versions()"
dyld: Library not loaded: @rpath/libgeos_c.1.dylib
  Referenced from: /Users/fielding/anaconda3/envs/pygmt/lib/libgmt.6.2.0.dylib
  Reason: Incompatible library version: libgmt.6.dylib requires version 16.0.0 or later, but libgeos_c.1.dylib provides version 1.0.0
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/ __init__.py", line 70, in <module>
    _begin()
  File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/session_management.py", line 16, in begin
    with Session() as lib:
  File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 183, in __enter__
    self.create("pygmt-session")
  File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 329, in create
    c_create_session = self.get_libgmt_func(
  File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 281, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/loading.py", line 59, in load_libgmt
    raise GMTCLibNotFoundError("\n".join(error_msg))
pygmt.exceptions.GMTCLibNotFoundError: Error loading GMT shared library at 'libgmt.dylib'.
dlopen(libgmt.dylib, 6): Library not loaded: @rpath/libgeos_c.1.dylib
  Referenced from: /Users/fielding/anaconda3/envs/pygmt/lib/libgmt.6.2.0.dylib
  Reason: Incompatible library version: libgmt.dylib requires version 16.0.0 or later, but libgeos_c.1.dylib provides version 1.0.0

```

I am on a Mac running macOS 10.15.7 in case that matters.

---

<div class="post-metadata">

### Author: ![weiji14](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/weiji14/32/33_2.png) [@weiji14](https://forum.generic-mapping-tools.org/u/weiji14)
#### Post date: [November 1, 2021, 8:41am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/5 "2021-11-01T08:41:03Z")

</div>

Hi @EJFielding, yes we’re aware that there’s a problem with GEOS 3.10.0 from conda-forge on macOS (see bug report at [https://github.com/GenericMappingTools/pygmt/issues/1600](https://github.com/GenericMappingTools/pygmt/issues/1600)). Could you try downgrading to GEOS 3.9 using `conda install -c conda-forge geos=3.9` and see if it works?

Edit: We’re attempting to fix this problem by rebuilding the GMT conda-forge package for GEOS 3.10.0 at [https://github.com/conda-forge/gmt-feedstock/pull/169](https://github.com/conda-forge/gmt-feedstock/pull/169).

---

<div class="post-metadata">

### Author: ![kradorl](https://avatars.discourse-cdn.com/v4/letter/k/50afbb/32.png) [@kradorl](https://forum.generic-mapping-tools.org/u/kradorl)
#### Post date: [November 2, 2021, 7:53am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/6 "2021-11-02T07:53:18Z")

</div>

> [@kradorl](#):
>
> `/usr/lib/libiconv.2.dylib`

The problem still exists after a clean install of PyGMT.  
When I remove jupyterlab, it works. It likes PyGMT can find libiconv.2.dylib in `~/anaconda3/envs/pygmt/lib`, but cannot find libiconv.2.dylib in `/usr/lib` after jupyterlab installation.

How do I force PyGMT use this `~/anaconda3/envs/pygmt/lib/libiconv.2.dylib` version?

Some additional information that may or may not be useful.  
MacOS 11.6.

```auto
# packages in environment at ~/opt/anaconda3/envs/pygmt:
#
# Name Version Build Channel
anyio 3.3.4 py39h6e9494a_0 conda-forge
aom 3.2.0 he49afe7_2 conda-forge
appnope 0.1.2 py39h6e9494a_2 conda-forge
argon2-cffi 21.1.0 py39h89e85a6_0 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 21.2.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
boost-cpp 1.74.0 hff03dee_4 conda-forge
brotlipy 0.7.0 py39h89e85a6_1001 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.18.1 h0d85af4_0 conda-forge
ca-certificates 2021.10.8 h033912b_0 conda-forge
cairo 1.16.0 he43a7df_1008 conda-forge
certifi 2021.10.8 py39h6e9494a_1 conda-forge
cffi 1.14.6 py39he338e87_1 conda-forge
cfitsio 3.470 h01dc385_7 conda-forge
cftime 1.5.1.1 py39hc89836e_0 conda-forge
chardet 4.0.0 py39h6e9494a_2 conda-forge
charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge
cryptography 35.0.0 py39h209aa08_1 conda-forge
curl 7.79.1 hf45b732_1 conda-forge
dcw-gmt 2.0.0 h694c41f_0 conda-forge
debugpy 1.4.1 py39h9fcab8e_0 conda-forge
decorator 5.1.0 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.4.1 he49afe7_0 conda-forge
ffmpeg 4.4.0 h79e7b16_7 conda-forge
fftw 3.3.10 nompi_h4024a70_101 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.1 h10f422b_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h4cff582_1 conda-forge
freexl 1.0.6 h0d85af4_0 conda-forge
fribidi 1.0.10 hbcb3906_0 conda-forge
gdal 3.3.3 py39he7e3f19_0 conda-forge
geos 3.9.1 he49afe7_2 conda-forge
geotiff 1.7.0 hb0faedc_3 conda-forge
gettext 0.19.8.1 hd1a6beb_1008 conda-forge
ghostscript 9.54.0 he49afe7_1 conda-forge
giflib 5.2.1 hbcb3906_2 conda-forge
glib 2.70.0 hcf210ce_1 conda-forge
glib-tools 2.70.0 hcf210ce_1 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
gmt 6.2.0 h5ea12c9_2 conda-forge
gnuplot 5.4.1 h561275a_2 conda-forge
gnutls 3.6.13 h756fd2b_1 conda-forge
graphicsmagick 1.3.36 hc3d8c12_0 conda-forge
graphite2 1.3.13 h2e338ed_1001 conda-forge
gshhg-gmt 2.3.7 h694c41f_1003 conda-forge
harfbuzz 3.0.0 h159f659_1 conda-forge
hdf4 4.2.15 hefd3b78_3 conda-forge
hdf5 1.12.1 nompi_h2f0ef1a_101 conda-forge
icu 68.2 he49afe7_0 conda-forge
idna 3.1 pyhd3deb0d_0 conda-forge
importlib-metadata 4.8.1 py39h6e9494a_1 conda-forge
ipykernel 6.4.2 py39h71a6800_0 conda-forge
ipython 7.29.0 py39h71a6800_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jbig 2.1 h0d85af4_2003 conda-forge
jedi 0.18.0 py39h6e9494a_3 conda-forge
jinja2 3.0.2 pyhd8ed1ab_0 conda-forge
jpeg 9d hbcb3906_0 conda-forge
json-c 0.15 hcb556a6_0 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.1.2 pyhd8ed1ab_0 conda-forge
jupyter_client 7.0.6 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.1 py39h6e9494a_0 conda-forge
jupyter_server 1.11.2 pyhd8ed1ab_0 conda-forge
jupyterlab 3.2.1 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_server 2.8.2 pyhd8ed1ab_0 conda-forge
kealib 1.4.14 ha22a8b1_3 conda-forge
krb5 1.19.2 hcfbf3a7_2 conda-forge
lame 3.100 h35c211d_1001 conda-forge
lcms2 2.12 h577c468_0 conda-forge
lerc 3.0 he49afe7_0 conda-forge
libblas 3.9.0 12_osx64_openblas conda-forge
libcblas 3.9.0 12_osx64_openblas conda-forge
libclang 11.1.0 default_he082bbe_1 conda-forge
libcurl 7.79.1 hf45b732_1 conda-forge
libcxx 12.0.1 habf9029_0 conda-forge
libdap4 3.20.6 h3e144a0_2 conda-forge
libdeflate 1.8 h0d85af4_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libffi 3.4.2 he49afe7_4 conda-forge
libgd 2.3.3 h311d3fc_0 conda-forge
libgdal 3.3.3 h053b6da_0 conda-forge
libgfortran 5.0.0 9_3_0_h6c81a4c_23 conda-forge
libgfortran5 9.3.0 h6c81a4c_23 conda-forge
libglib 2.70.0 hf1fb8c0_1 conda-forge
libiconv 1.16 haf1e3a3_0 conda-forge
libkml 1.3.0 h8fd9edb_1014 conda-forge
liblapack 3.9.0 12_osx64_openblas conda-forge
libllvm11 11.1.0 hd011deb_2 conda-forge
libnetcdf 4.8.1 nompi_h6609ca0_101 conda-forge
libnghttp2 1.43.0 h6f36284_1 conda-forge
libopenblas 0.3.18 openmp_h3351f45_0 conda-forge
libpng 1.6.37 h7cec526_2 conda-forge
libpq 13.3 hea3049e_2 conda-forge
librttopo 1.1.0 h5413771_6 conda-forge
libsodium 1.0.18 hbcb3906_1 conda-forge
libspatialite 5.0.1 hfc891e7_9 conda-forge
libssh2 1.10.0 h52ee1ee_2 conda-forge
libtiff 4.3.0 hd146c10_2 conda-forge
libvpx 1.11.0 he49afe7_3 conda-forge
libwebp 1.2.1 h28dabe5_0 conda-forge
libwebp-base 1.2.1 h0d85af4_0 conda-forge
libxml2 2.9.12 h93ec3fd_0 conda-forge
libzip 1.8.0 h8b0c345_1 conda-forge
libzlib 1.2.11 h9173be1_1013 conda-forge
llvm-openmp 12.0.1 hda6cdc1_1 conda-forge
lz4-c 1.9.3 he49afe7_1 conda-forge
markupsafe 2.0.1 py39h89e85a6_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py39h89e85a6_1004 conda-forge
mysql-common 8.0.27 h694c41f_1 conda-forge
mysql-libs 8.0.27 h115446f_1 conda-forge
nbclassic 0.3.4 pyhd8ed1ab_0 conda-forge
nbclient 0.5.4 pyhd8ed1ab_0 conda-forge
nbconvert 6.2.0 py39h6e9494a_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h2e338ed_4 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
netcdf4 1.5.8 nompi_py39he7d1c46_100 conda-forge
nettle 3.6 hedd7734_0 conda-forge
notebook 6.4.5 pyha770c72_0 conda-forge
nspr 4.32 hcd9eead_0 conda-forge
nss 3.71 h31e2bf1_0 conda-forge
numpy 1.21.3 py39h7eed0ac_0 conda-forge
openh264 2.1.1 hfd3ada9_0 conda-forge
openjpeg 2.4.0 h6e7aa92_1 conda-forge
openssl 1.1.1l h0d85af4_0 conda-forge
packaging 21.0 pyhd8ed1ab_0 conda-forge
pandas 1.3.4 py39h4d6be9b_0 conda-forge
pandoc 2.16 h0d85af4_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.48.10 h056538c_2 conda-forge
parso 0.8.2 pyhd8ed1ab_0 conda-forge
pcre 8.45 he49afe7_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 hbcb3906_0 conda-forge
poppler 21.09.0 h9573804_3 conda-forge
poppler-data 0.4.11 hd8ed1ab_0 conda-forge
postgresql 13.3 he8fe76e_2 conda-forge
proj 8.1.1 h1512c50_2 conda-forge
prometheus_client 0.12.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.21 pyha770c72_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.10.0 pyhd8ed1ab_0 conda-forge
pygmt 0.5.0 pyhd8ed1ab_1 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.4 pyhd8ed1ab_0 conda-forge
pyrsistent 0.17.3 py39h89e85a6_2 conda-forge
pysocks 1.7.1 py39h6e9494a_3 conda-forge
python 3.9.7 h1248fe1_3_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pyzmq 22.3.0 py39h7fec2f1_0 conda-forge
qt 5.12.9 h126340a_4 conda-forge
readline 8.1 h05e3726_0 conda-forge
requests 2.26.0 pyhd8ed1ab_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 58.4.0 py39h6e9494a_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.2.0 py39h6e9494a_1 conda-forge
sqlite 3.36.0 h23a322b_2 conda-forge
svt-av1 0.8.7 he49afe7_1 conda-forge
terminado 0.12.1 py39h6e9494a_0 conda-forge
testpath 0.5.0 pyhd8ed1ab_0 conda-forge
tiledb 2.3.4 h8370e7a_0 conda-forge
tk 8.6.11 h5dbffcc_1 conda-forge
tornado 6.1 py39h89e85a6_2 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
tzcode 2021e h0d85af4_0 conda-forge
tzdata 2021e he74cb21_0 conda-forge
urllib3 1.26.7 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 0.57.0 py39h6e9494a_4 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
x264 1!161.3030 h0d85af4_1 conda-forge
x265 3.5 h940c156_1 conda-forge
xarray 0.19.0 pyhd8ed1ab_1 conda-forge
xerces-c 3.2.3 h379762d_3 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
zeromq 4.3.4 he49afe7_1 conda-forge
zipp 3.6.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h9173be1_1013 conda-forge
zstd 1.5.0 h582d3a0_0 conda-forge

```

---

<div class="post-metadata">

### Author: ![weiji14](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/weiji14/32/33_2.png) [@weiji14](https://forum.generic-mapping-tools.org/u/weiji14)
#### Post date: [November 2, 2021, 10:18pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/7 "2021-11-02T22:18:11Z")

</div>

Hi @kradori. could you post the full error that you are getting with `libiconv.2.dylib` not found? Also, just to clarify, PyGMT/GMT should not be picking up `libiconv.2.dylib` from `/usr/lib`, it should be using the `~/anaconda3/envs/pygmt/lib/libiconv.2.dylib` (as you probably know already).

My guess is that your jupyterlab was installed outside of the pygmt virtual environment, but just to be sure, can you try the following (adapted from [No module issue when importing pygmt](https://flint.soest.hawaii.edu/t/no-module-issue-when-importing-pygmt/1769/10)):

```bash
conda env remove -n pygmt
conda clean --all

conda create --name pygmt --channel conda-forge pygmt jupyterlab
conda activate pygmt

jupyterlab --no-browser

```

This should install `jupyterlab` **inside** the pygmt virtual environment. Given that this is a recurring issue with people using jupyter and pygmt, we might try to clarify this on the installation page.

---

<div class="post-metadata">

### Author: ![kradorl](https://avatars.discourse-cdn.com/v4/letter/k/50afbb/32.png) [@kradorl](https://forum.generic-mapping-tools.org/u/kradorl)
#### Post date: [November 3, 2021, 2:31am UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/8 "2021-11-03T02:31:35Z")

</div>

Hi, @weiji14.

I do not think this is a virtual environment problem. I installed jupyter in PyGMT environment.  
The import error occurred only after jupyter installation (not import PyGMT error in jupyter).

If I install PyGMT without jupyterlab,

```auto
conda env remove -n pygmt
conda clean --all
conda create --name pygmt --channel conda-forge pygmt geos=3.9
conda activate pygmt
python -c "import pygmt; pygmt.show_versions()"

```

It works.

```python
  version: v0.5.0
System information:
  python: 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 20:33:18) [Clang 11.1.0]
  executable: /Users/lli/opt/anaconda3/envs/pygmt/bin/python
  machine: macOS-11.6-x86_64-i386-64bit
Dependency information:
  numpy: 1.21.3
  pandas: 1.3.4
  xarray: 0.19.0
  netCDF4: 1.5.8
  packaging: 21.0
  ghostscript: 9.54.0
  gmt: 6.2.0
GMT library information:
  binary dir: /Users/lli/opt/anaconda3/envs/pygmt/bin
  cores: 8
  grid layout: rows
  library path: /Users/lli/opt/anaconda3/envs/pygmt/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/lli/opt/anaconda3/envs/pygmt/lib/gmt/plugins
  share dir: /Users/lli/opt/anaconda3/envs/pygmt/share/gmt
  version: 6.2.0

```

If I install PyGMT with jupyterlab,

```auto
conda env remove -n pygmt
conda clean --all
conda create --name pygmt --channel conda-forge pygmt geos=3.9 jupyterlab
conda activate pygmt
python -c "import pygmt; pygmt.show_versions()"

```

This is the error.

```python
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/ __init__.py", line 57, in <module>
    _begin()
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/session_management.py", line 16, in begin
    with Session() as lib:
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 185, in __enter__
    self.create("pygmt-session")
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 332, in create
    c_create_session = self.get_libgmt_func(
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 284, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/Users/lli/opt/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/loading.py", line 59, in load_libgmt
    raise GMTCLibNotFoundError("\n".join(error_msg))
pygmt.exceptions.GMTCLibNotFoundError: Error loading GMT shared library at '/Users/lli/opt/anaconda3/envs/pygmt/lib/libgmt.dylib'.
dlopen(/Users/lli/opt/anaconda3/envs/pygmt/lib/libgmt.dylib, 6): Symbol not found: _libiconv
  Referenced from: /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
  Expected in: /usr/lib/libiconv.2.dylib
 in /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
Error loading GMT shared library at 'libgmt.dylib'.
dlopen(libgmt.dylib, 6): Symbol not found: _libiconv
  Referenced from: /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
  Expected in: /usr/lib/libiconv.2.dylib
 in /Users/lli/opt/anaconda3/envs/pygmt/lib/libspatialite.7.dylib
```

---

<div class="post-metadata">

### Author: ![weiji14](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/weiji14/32/33_2.png) [@weiji14](https://forum.generic-mapping-tools.org/u/weiji14)
#### Post date: [November 3, 2021, 8:13pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/9 "2021-11-03T20:13:48Z")

</div>

Hmm, you might be on to another dependency related bug. Unfortunately I don’t have a macOS computer to reproduce this. @maxrjones could you test and see if the same `libiconv` error appears?

Oh and btw everyone, we fixed the GEOS 3.10 issue, so no need to pin to GEOS 3.9 anymore.

---

<div class="post-metadata">

### Author: ![maxrjones](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/maxrjones/32/2698_2.png) [@maxrjones](https://forum.generic-mapping-tools.org/u/maxrjones)
#### Post date: [November 3, 2021, 9:28pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/10 "2021-11-03T21:28:41Z")

</div>

No, I am not able to reproduce this error on macOS.

For my installations, libspatialite.7.dylib references libiconv.2.dylib in the same /opt/anaconda3/env/pygmt/lib/ directory, not /usr/lib/. I’m not sure what about the jupterlab installation is breaking the reference.

---

<div class="post-metadata">

### Author: ![kradorl](https://avatars.discourse-cdn.com/v4/letter/k/50afbb/32.png) [@kradorl](https://forum.generic-mapping-tools.org/u/kradorl)
#### Post date: [November 4, 2021, 12:18pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/11 "2021-11-04T12:18:53Z")

</div>

FYI. I try to install PyGMT on another MAC and can not reproduce my issue on MacOS 10.15.6. It seems to potentially occur on MacOS 11.6.

---

<div class="post-metadata">

### Author: ![maxrjones](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/maxrjones/32/2698_2.png) [@maxrjones](https://forum.generic-mapping-tools.org/u/maxrjones)
#### Post date: [November 4, 2021, 4:04pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/12 "2021-11-04T16:04:50Z")

</div>

I am also on MacOS 11.6 and did not receive the same error. This particular issue is often unique to specific environments and difficult to reproduce (e.g., [https://newbedev.com/libiconv-or-iconv-undefined-symbol-on-mac-osx](https://newbedev.com/libiconv-or-iconv-undefined-symbol-on-mac-osx)).

---

<div class="post-metadata">

### Author: ![EJFielding](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/ejfielding/32/82_2.png) [@EJFielding](https://forum.generic-mapping-tools.org/u/EJFielding)
#### Post date: [November 4, 2021, 4:48pm UTC](https://forum.generic-mapping-tools.org/t/import-pygmt-error-after-jupyterlab-installation/2117/13 "2021-11-04T16:48:17Z")

</div>

I waited until the dust settled and I ran `conda update gmt` today. It updated a lot of packages. Now `PyGMT` runs on my Mac!

```auto
PyGMT information:
  version: v0.5.0
System information:
  python: 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 20:33:18) [Clang 11.1.0]
  executable: /Users/fielding/anaconda3/envs/pygmt/bin/python
  machine: macOS-10.15.7-x86_64-i386-64bit
Dependency information:
  numpy: 1.21.3
  pandas: 1.3.4
  xarray: 0.19.0
  netCDF4: 1.5.8
  packaging: 21.0
  ghostscript: 9.54.0
  gmt: 6.2.0
GMT library information:
  binary dir: /Users/fielding/anaconda3/envs/pygmt/bin
  cores: 16
  grid layout: rows
  library path: /Users/fielding/anaconda3/envs/pygmt/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/fielding/anaconda3/envs/pygmt/lib/gmt/plugins
  share dir: /Users/fielding/anaconda3/envs/pygmt/share/gmt
  version: 6.2.0

```