Comments (6)
Hi, Eric,
We tried and were not able to replicate this problem using computers in
locations. We will look into any adjustments that might remedy this
situation. For now, would you mind downloading this file and add to the
folder if this problem persists? Thank you.
Benli
On Thu, Feb 25, 2016 at 5:55 AM, Eric Deveaud [email protected]
wrote:
hello,
while trying to build a docker image for RDPTools I have a problem with
the donload of the classifier training set that timesoutsee:
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz
[untar] Expanding: /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz into /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classesBUILD FAILED
/local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build.xml:112: Error while expanding /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz
java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)wget of the same url gives:
wget http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
--2016-02-25 http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz--2016-02-25 11:43:38-- http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
Resolving rdp.cme.msu.edu... 35.8.164.79
Connecting to rdp.cme.msu.edu|35.8.164.79|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 149530230 (143M) [application/x-gzip]
Saving to: 'data.tgz'61% [================================> ] 91,435,408 255KB/s in 3m 30s
2016-02-25 11:47:08 (425 KB/s) - Connection closed at byte 91435408. Retrying.
seems to me that the the get method used does not honour timeout nor the
retrybest regards
Eric
—
Reply to this email directly or view it on GitHub
#10.
RDP Staff
Ribosomal Database Project
Center for Microbial Ecology
Michigan State University
567 Wilson Rd. Room 2225 A
East Lansing, MI 48824
(517) 353-3842
from rdptools.
currently I was abble to build using the following
get externaly the data.tgz (wget)
host data.tgz in localhost web server
and patch classifier/build.xml to use localhost instead of rdp.cme.msu.edu
sed -i -e 's,http://rdp.cme.msu.edu/download,http://localhost|' classifier/build.xml
it's more or less what you suggested.
2 suggestion to fix the build process
- (hard way) check the get method used while building in order to see if it can handle timeouts
- (easy way) what you suggested. remove training data download from the build process and document that user must download the files by their own.
regards
Eric
from rdptools.
Hi, Eric,
Thank you for the suggestions. We will look into the options to get it
fixed.
Benli
On Sat, Feb 27, 2016 at 6:22 AM, Eric Deveaud [email protected]
wrote:
currently I was abble to build using the following
get externaly the data.tgz (wget)
host data.tgz in localhost web server
and patch classifier/build.xml to use localhost instead of rdp.cme.msu.edused -i -e 's,http://rdp.cme.msu.edu/download,http://localhost|' classifier/build.xml
it's more or less what you suggested.
2 suggestion to fix the build process
- (hard way) check the get method used while building in order to see if
it can handle timeouts- (easy way) what you suggested. remove training data download from the
build process and document that user must download the files by their own.regards
Eric
—
Reply to this email directly or view it on GitHub
#10 (comment).
RDP Staff
Ribosomal Database Project
Center for Microbial Ecology
Michigan State University
567 Wilson Rd. Room 2225 A
East Lansing, MI 48824
(517) 353-3842
from rdptools.
back at this.
I had to make a fresh install RDPtools.
here is some output from wget
make[1]: Entering directory `/inst/RDPTools/RDPTools-2.0.2'
# java builder//installer tries to download data file and timeout
# donwload externaly
test -d /src/RDPTools/RDPTools-2.0.2/classifier/build/classes || mkdir -m 2775 -p /src/RDPTools/RDPTools-2.0.2/classifier/build/classes
test -f /src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz || \
wget --tries=5 -c http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz -O /src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz
--2016-07-07 18:02:02-- http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
Resolving rdp.cme.msu.edu... 35.8.164.79
Connecting to rdp.cme.msu.edu|35.8.164.79|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.
--2016-07-07 18:03:33-- (try: 2) http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
Connecting to rdp.cme.msu.edu|35.8.164.79|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 181332714 (173M) [application/x-gzip]
Saving to: `/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz'
0% [ ] 302,632 101K/s in 47s
2016-07-07 18:04:22 (6.26 KB/s) - Connection closed at byte 302632. Retrying.
--2016-07-07 18:04:24-- (try: 3) http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
Connecting to rdp.cme.msu.edu|35.8.164.79|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 181332714 (173M), 181030082 (173M) remaining [application/x-gzip]
Saving to: `/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz'
100%[=======================================================================================>] 181,332,714 5.31M/s in 36s
2016-07-07 18:05:00 (4.81 MB/s) - `/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz' saved [181332714/181332714]
from rdptools.
Cannot download the traindata either. Can you copy the traindata somewhere or fix the URL ??
from rdptools.
Same problem here as of 14/05/2024
from rdptools.
Related Issues (20)
- RDP training using custom trainset
- Build failed HOT 7
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- Do not create output files on error
- Installation problem: the 'make' command HOT 1
- make command issue HOT 3
- rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz not available
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