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Ismael Olea olea Sus Labores S.L. Almería (Spain) http://olea.org/diario/ Add a Bio

olea/lemarios 128

Lemarios y listas de palabras del español

HackLab-Almeria/hacklab-almeria.github.io 16

Web en producción del HackLab Almería

olea/LuCAS-cvs 4

Antiguo repo CVS usado en LuCAS

Elvirarp92/iaph-json-to-csv 1

A script to parse JSON data from the Instituto Andaluz de Patrimonio Histórico (Andalusian Institute for Historical Heritage) public API and convert it to CSV.

inchocordero/granadaton 1

Segundo hackatón de periodismo de datos granaíno

olea/acoustid-fingerprinter 1

GUI application for submitting audio fingerprints to Acoustid

olea/LuCAS-web 1

Antigua web de TLDP-ES/LuCAS

olea/minetest-bower 1

A package manager for Minetest.

olea/odoo-libro-de-practicas 1

Manual de prácticas con Odoo

issue commentqgis/QGIS

Popped Out Panels Can't be Re-docked

Same bug here. QGIS 3.20.3 (from Flathub) + Fedora 34 + GNOME Shell + Wayland.

qgib

comment created time in 4 days

push eventolea/lemarios

Ismael Olea

commit sha e4f3043c6d7c15e454d43e6e62dfba0c68378ecf

Update README.md grafiquito guay.

view details

push time in a month

fork olea/labelImg

🖍️ LabelImg is a graphical image annotation tool and label object bounding boxes in images

https://youtu.be/p0nR2YsCY_U

fork in a month

issue commentearnaud/MetaShARK-v2

Reporting: container can't be build with podman

the error message does not seem to be linked to a permission issue. I led few researches about it, and it seems to be linked to the filesystem sanity (maybe hardware).

I don't have a real evidence but I don't think so. This happens always and only when EDIorg components rebuild htmltools. Maybe this should be better reported and EDIorg issue tracker or the htmltools one.

Anyhow, I opened this issue more as a knowledge base entry than a MetaShARK error report :)

olea

comment created time in 2 months

issue commentearnaud/MetaShARK-v2

Reporting: container can't be build with podman

Hi ! Just discovering your issue (sorry), but I do not know Podman either. Same as Yvan ;)

Don't worry. Just wanted to explain the case for future others finding same problem.

olea

comment created time in 2 months

issue closedearnaud/MetaShARK_docker

Error compiling htmltools when building the image

Hi:

When building the docker image it can't finish the htmltools instalation. Building with docker build -t metashark .

* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c template.c -o template.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o htmltools.so init.o template.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-htmltools/00new/htmltools/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
mv: cannot overwrite non-directory '/usr/local/lib/R/site-library/htmltools' with directory '/usr/local/lib/R/site-library/00LOCK-htmltools/00new/htmltools'
ERROR:   moving to final location failed
* restoring previous ‘/usr/local/lib/R/site-library/htmltools’
Error in i.p(...) : 
  (converted from warning) installation of package ‘htmltools’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
Error: error building at STEP "RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.0.0")'": error while running runtime: exit status 1

Application data:

$ git info --no-config

## Remote URLs:

origin	git@github.com:earnaud/MetaShARK_docker.git (fetch)
origin	git@github.com:earnaud/MetaShARK_docker.git (push)

## Remote Branches:

  origin/HEAD -> origin/master
  origin/master
  origin/stable

## Local Branches:

* master

## Most Recent Commit:

commit 9e3b50dcbaece50236ae9dafb580ed675576e49e
Author: Elie Ker Arno <earnaud@outlook.com>

    MetaShARK updated

No configuration changes:

$ git diff .

Using Fedora Linux 32. I'm very familiar with Linux application compiling but not with R ecosystem.

Could you please provide some advice?

closed time in 2 months

olea

issue commentearnaud/MetaShARK_docker

Error compiling htmltools when building the image

Not sure if it was the same problem than https://github.com/earnaud/MetaShARK-v2/issues/163, but close this anyway.

olea

comment created time in 2 months

issue openedearnaud/MetaShARK-v2

Reporting: container can't be build with podman

Hi:

Probably this issue is not very important for the project but I think is appropriate to report. I've been trying to build the Metashark container using podman. Probably you know Podman is a container technology compatible with OCI. Podman is designed to be used in userspace and it's expected to be 100% compatible with docker syntax and CLI. Being well integrated in my Fedora Linux it was the obvious tool to build Metashark. But found out this not work. I'm finding a problem building htmltools as a dependency of the modules EDIorg/EMLassemblyline and EDIorg/taxonomyCleanr.

This is the error log:


trying URL 'https://cran.rstudio.com/src/contrib/xfun_0.25.tar.gz'
Content type 'application/x-gzip' length 112755 bytes (110 KB)
==================================================
downloaded 110 KB

* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
mv: cannot remove '/usr/local/lib/R/site-library/htmltools/Meta': Input/output error
mv: cannot remove '/usr/local/lib/R/site-library/htmltools/R': Input/output error
mv: cannot remove '/usr/local/lib/R/site-library/htmltools/help': Input/output error
mv: cannot remove '/usr/local/lib/R/site-library/htmltools/html': Input/output error
mv: cannot remove '/usr/local/lib/R/site-library/htmltools/libs': Input/output error
ERROR: cannot remove earlier installation, is it in use?
* removing ‘/usr/local/lib/R/site-library/htmltools’
* restoring previous ‘/usr/local/lib/R/site-library/htmltools’
Error in i.p(...) : 
  (converted from warning) installation of package ‘htmltools’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
Error: error building at STEP "RUN Rscript -e 'remotes::install_github("EDIorg/EMLassemblyline@ad838f970ee259eda7f96d6a0bbe7f9fa509c66e")'": error while running runtime: exit status 1

OTOH, the line RUN Rscript -e 'remotes::install_version("htmltools",upgrade="never", version = "0.5.1.1")' works as expected.

I've tried to diagnose what is really happening but I don't know about the R build system to deep into this. @jesmg suspects this htmltools building trouble is caused by some kind of UID mismatch Docker admits but it's OCI incompatible.

I post this just for the record.

Configuration details:

$ cat /etc/fedora-release 
Fedora release 33 (Thirty Three)
$ rpm -q podman
podman-3.2.3-2.fc33.x86_64
$ git info --no-config

## Remote URLs:

origin	https://github.com/earnaud/MetaShARK-v2 (fetch)
origin	https://github.com/earnaud/MetaShARK-v2 (push)

## Remote Branches:

  origin/HEAD -> origin/master
  origin/dev
  origin/dev-metafin
  origin/master
  origin/sd-annotations
  origin/server
  origin/server-dev

## Local Branches:

* dev
  master

## Most Recent Commit:

commit 404a9d4aa32b6ace46efded5d8cad629320fc93d
Author: Elie Ker Arno <earnaud@outlook.com>

    Update description file and associated files

created time in 2 months

startedearnaud/MetaShARK_docker

started time in 2 months

startedEDIorg/EMLassemblyline

started time in 2 months

startedearnaud/MetaShARK-v2

started time in 2 months

issue openedwetneb/openrefine-wikibase

ModuleNotFoundError: No module named 'config'

Hi:

I can't run a docker instance in my Fedora 32 system. I follow the build instructions (just using podman instead of docker):

git clone https://github.com/wetneb/openrefine-wikibase
cd openrefine-wikibase/
cp config_docker.py config.py
podman-compose up

and everything builds but the openrefine-wikibase container can't run:

[...]
podman start -a openrefine-wikibase_reconcile_1
podman start -a openrefine-wikibase_redis_1
1:C 22 Aug 2021 17:41:08.310 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
1:C 22 Aug 2021 17:41:08.310 # Redis version=6.2.5, bits=64, commit=00000000, modified=0, pid=1, just started
1:C 22 Aug 2021 17:41:08.310 # Warning: no config file specified, using the default config. In order to specify a config file use redis-server /path/to/redis.conf
1:M 22 Aug 2021 17:41:08.311 * monotonic clock: POSIX clock_gettime
1:M 22 Aug 2021 17:41:08.313 * Running mode=standalone, port=6379.
1:M 22 Aug 2021 17:41:08.313 # Server initialized
1:M 22 Aug 2021 17:41:08.313 # WARNING overcommit_memory is set to 0! Background save may fail under low memory condition. To fix this issue add 'vm.overcommit_memory = 1' to /etc/sysctl.conf and then reboot or run the command 'sysctl vm.overcommit_memory=1' for this to take effect.
1:M 22 Aug 2021 17:41:08.314 * Ready to accept connections
Traceback (most recent call last):
  File "app.py", line 11, in <module>
    from wdreconcile.engine import ReconcileEngine
  File "/openrefine-wikibase/wdreconcile/engine.py", line 1, in <module>
    import config
ModuleNotFoundError: No module named 'config'
1

I've tried some python configuration experiment without success, the expected result as I really don't know.

What I'm doing wrong?

Thanks

created time in 2 months

issue commentOpenRefine/OpenRefine

Socket timeout too low for reconciliation operations

I think I'm having the same problem with Wikidata:

13:06:22.601 [    refine-standard-recon] Failed to batch recon with load:
{"q0":{"query":"175236","type":"Q473972","properties":[{"pid":"P4762","v":"175236"}],"type_strict":"should"},"q1":{"query":"175243","type":"Q473972","properties":[{"pid":"P4762","v":"175243"}],"type_strict":"should"},"q2":{"query":"195298","type":"Q473972","properties":[{"pid":"P4762","v":"195298"}],"type_strict":"should"},"q3":{"query":"151229","type":"Q473972","properties":[{"pid":"P4762","v":"151229"}],"type_strict":"should"},"q4":{"query":"555515435","type":"Q473972","properties":[{"pid":"P4762","v":"555515435"}],"type_strict":"should"},"q5":{"query":"175382","type":"Q473972","properties":[{"pid":"P4762","v":"175382"}],"type_strict":"should"},"q6":{"query":"175372","type":"Q473972","properties":[{"pid":"P4762","v":"175372"}],"type_strict":"should"},"q7":{"query":"175198","type":"Q473972","properties":[{"pid":"P4762","v":"175198"}],"type_strict":"should"},"q8":{"query":"555515449","type":"Q473972","properties":[{"pid":"P4762","v":"555515449"}],"type_strict":"should"},"q9":{"query":"555551123","type":"Q473972","properties":[{"pid":"P4762","v":"555551123"}],"type_strict":"should"}} (300337ms)
java.net.SocketTimeoutException: Read timed out
        at java.net.SocketInputStream.socketRead0(Native Method)
        at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
        at java.net.SocketInputStream.read(SocketInputStream.java:171)
        at java.net.SocketInputStream.read(SocketInputStream.java:141)
        at sun.security.ssl.SSLSocketInputRecord.read(SSLSocketInputRecord.java:457)
        at sun.security.ssl.SSLSocketInputRecord.bytesInCompletePacket(SSLSocketInputRecord.java:68)
        at sun.security.ssl.SSLSocketImpl.readApplicationRecord(SSLSocketImpl.java:1095)
        at sun.security.ssl.SSLSocketImpl.access$200(SSLSocketImpl.java:72)
        at sun.security.ssl.SSLSocketImpl$AppInputStream.read(SSLSocketImpl.java:815)
        at org.apache.http.impl.io.SessionInputBufferImpl.streamRead(SessionInputBufferImpl.java:137)
        at org.apache.http.impl.io.SessionInputBufferImpl.fillBuffer(SessionInputBufferImpl.java:153)
        at org.apache.http.impl.io.SessionInputBufferImpl.readLine(SessionInputBufferImpl.java:282)
        at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:138)
        at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:56)
        at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:259)
        at org.apache.http.impl.DefaultBHttpClientConnection.receiveResponseHeader(DefaultBHttpClientConnection.java:163)
        at org.apache.http.impl.conn.CPoolProxy.receiveResponseHeader(CPoolProxy.java:165)
        at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:273)
        at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:125)
        at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:272)
        at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:185)
        at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
        at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:111)
        at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:108)
        at com.google.refine.model.recon.StandardReconConfig.batchRecon(StandardReconConfig.java:478)
        at com.google.refine.operations.recon.ReconOperation$ReconProcess.run(ReconOperation.java:282)
        at java.lang.Thread.run(Thread.java:748)

and

13:12:17.364 [    refine-standard-recon] Failed to batch recon with load:
{"q0":{"query":"151065","type":"Q473972","properties":[{"pid":"P4762","v":"151065"}],"limit":2,"type_strict"
:"should"},"q1":{"query":"195196","type":"Q473972","properties":[{"pid":"P4762","v":"195196"}],"limit":2,"ty
pe_strict":"should"},"q2":{"query":"195316","type":"Q473972","properties":[{"pid":"P4762","v":"195316"}],"li
mit":2,"type_strict":"should"},"q3":{"query":"195395","type":"Q473972","properties":[{"pid":"P4762","v":"195
395"}],"limit":2,"type_strict":"should"},"q4":{"query":"64519","type":"Q473972","properties":[{"pid":"P4762"
,"v":"64519"}],"limit":2,"type_strict":"should"},"q5":{"query":"555515311","type":"Q473972","properties":[{"
pid":"P4762","v":"555515311"}],"limit":2,"type_strict":"should"},"q6":{"query":"555641519","type":"Q473972",
"properties":[{"pid":"P4762","v":"555641519"}],"limit":2,"type_strict":"should"},"q7":{"query":"195180","typ
e":"Q473972","properties":[{"pid":"P4762","v":"195180"}],"limit":2,"type_strict":"should"},"q8":{"query":"55
5515387","type":"Q473972","properties":[{"pid":"P4762","v":"555515387"}],"limit":2,"type_strict":"should"},"
q9":{"query":"555515266","type":"Q473972","properties":[{"pid":"P4762","v":"555515266"}],"limit":2,"type_strict":"should"}} (153521ms)
org.apache.http.NoHttpResponseException: wikidata.reconci.link:443 failed to respond
        at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:141)
        at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:56)
        at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:259)
        at org.apache.http.impl.DefaultBHttpClientConnection.receiveResponseHeader(DefaultBHttpClientConnection.java:163)
        at org.apache.http.impl.conn.CPoolProxy.receiveResponseHeader(CPoolProxy.java:165)
        at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:273)
        at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:125)
        at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:272)
        at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:185)
        at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
        at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:111)
        at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
        at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:108)
        at com.google.refine.model.recon.StandardReconConfig.batchRecon(StandardReconConfig.java:478)
        at com.google.refine.operations.recon.ReconOperation$ReconProcess.run(ReconOperation.java:282)
        at java.lang.Thread.run(Thread.java:748)

The difference is the second case OR seems to resume the conciliation task but, with the first. sessions hangs indefinitely. In any case I got no error message.

I'm using wikidata.reconci.link service.

wetneb

comment created time in 2 months