<div dir="ltr">Thank you Jmarie, <div><br></div><div>Working now. </div><div><br></div><div>My mistake was trying to run the R notebooks from jupyter lab without using your Docker command. </div><div><br></div><div>All the best,</div><div>j<br><div><br></div></div><div class="gmail_extra"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><br></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Jun 5, 2018 at 4:47 PM, Jean-Marie Burel (Staff) <span dir="ltr"><<a href="mailto:j.burel@dundee.ac.uk" target="_blank">j.burel@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif">
<div>Hi Josh</div>
<div><br>
</div>
<div>We pushed the version we used for the Users meeting to DockerHub</div>
<div><br>
</div>
<div>Could you try:</div>
<div><span style="font-family:Menlo;font-size:11px;background-color:rgb(255,255,255)">docker pull openmicroscopy/training-<wbr>notebooks:0.1.0</span></div>
<div>and run that image?</div>
<div><br>
</div>
<div>I have just tried it again and I could run everything without problem</div>
<div><br>
</div>
<div>Cheers</div>
<div>Jmarie</div>
<div><br>
</div>
<span id="m_-1919030408454571912OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span>ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-devel-bounces@lists.<wbr>openmicroscopy.org.uk</a>> on behalf of Joshua S Titlow <<a href="mailto:joshua.titlow@bioch.ox.ac.uk" target="_blank">joshua.titlow@bioch.ox.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.<wbr>openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 5 June 2018 at 13:06<br>
<span style="font-weight:bold">To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.<wbr>openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-devel] Missing packages in R-omero installation with Docker<br>
</div><div><div class="h5">
<div><br>
</div>
<div>
<div>
<div dir="ltr">Thanks for making an R notebook with OMERO support!
<div><br>
</div>
<div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
I installed the notebook with the <a href="https://github.com/ome/training-notebooks" target="_blank">
Docker workflow on Github</a> but still seem to be missing packages:</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
<div><img src="cid:ii_ji1m0y6n1_163cfbd0d0b41beb" width="562" height="145"><br>
</div>
I thought the idea was that libraries/dependencies would be installed through the Docker image.</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
<br>
</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Installation
 with the Docker file went smooth:</span><br>
</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
<br>
</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
> cloned the repository to my machine</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
> docker build -t training-notebooks .</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
> docker run -it -p 8888:8888 training-notebook</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
<br>
</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
Any ideas?</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
Thanks!</div>
<span class="m_-1919030408454571912gmail-m_-6271941052498847771HOEnZb" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#888888">
<div>j</div>
</font></span></div>
</div>
</div>
</div>
</div></div></span><br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>

<br>______________________________<wbr>_________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.<wbr>openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">http://lists.openmicroscopy.<wbr>org.uk/mailman/listinfo/ome-<wbr>devel</a><br>
<br></blockquote></div><br></div></div>