Mercurial > repos > frogs > frogs_3_1_0

annotate test-data/references/18-phylo_structure.log @ 0:59bc96331073 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
1 ## Application
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
2 Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py (version : 3.1)
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
3 Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py --varExp EnvType --ordination-method MDS --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/18-phylo_structure.html --log-file res/18-phylo_structure.log
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
4
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
5 ########################################################################################################
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
6 # Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
7 [1] "Rmarkdown version: 1.10"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
8 [1] "Phyloseq version: 1.19.1")
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
9 Command:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
10 Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_structure.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/18-phylo_structure.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620190.28_24114_rmarkdown.stderr
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
11
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
12 Execution:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
13 start: 08 Feb 2019 11:03:14
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
14 end: 08 Feb 2019 11:03:27
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
15
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
16 ## Application
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
17 Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py (version : 3.1)
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
18 Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py --varExp EnvType --ordination-method MDS --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/18-phylo_structure.html --log-file res/18-phylo_structure.log
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
19
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
20 ########################################################################################################
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
21 # Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
22 [1] "Rmarkdown version: 1.10"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
23 [1] "Phyloseq version: 1.19.1")
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
24 Command:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
25 Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_structure.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/18-phylo_structure.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623069.52_25554_rmarkdown.stderr
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
26
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
27 Execution:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
28 start: 08 Feb 2019 11:51:12
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
29 end: 08 Feb 2019 11:51:24
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff changeset
30