[med-svn] [circos] 02/06: New upstream version 0.69.5+dfsg
Andreas Tille
tille at debian.org
Tue Jul 18 08:28:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository circos.
commit 910f53db19061f1307712c7ba05584f699467f98
Author: Andreas Tille <tille at debian.org>
Date: Tue Jul 18 08:45:04 2017 +0200
New upstream version 0.69.5+dfsg
---
CHANGES | 5 +-
example/run.out | 773 ++++++++++++++++++++++----------------------
lib/Circos.pm | 4 +-
lib/Circos/Configuration.pm | 10 +-
lib/Circos/Error.pm | 144 ++++-----
5 files changed, 470 insertions(+), 466 deletions(-)
diff --git a/CHANGES b/CHANGES
index ed75134..4091fa2 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1267,11 +1267,14 @@ Added a commented chrM to data/karyotype/karyotype.human.hg38.txt to complement
Fixed text track so that r0 can be changed using rules.
-17 Jan 2016 v0.69-4
+17 Jan 2017 v0.69-4
Fixed harmless warning in heatmap legend output.
Fixed bug that was displaying ideogram labels at the wrong position when chromosomes_radius was used to change ideogram radius.
+2 May 2017 v0.69-5
+
+Removed error due to __ in configuration file. The use of __ for setting values was deprecated for a while now.
diff --git a/example/run.out b/example/run.out
index 4a85ead..c4b2e44 100644
--- a/example/run.out
+++ b/example/run.out
@@ -1,389 +1,390 @@
-debuggroup summary 0.15s welcome to circos v0.69-4 21 Dec 2016 on Perl 5.010000
+debuggroup summary 0.15s welcome to circos v0.69-4 17 Dec 2016 on Perl 5.010000
debuggroup summary 0.15s current working directory /home/martink/work/circos/svn/example
debuggroup summary 0.15s command ../bin/circos -conf etc/circos.conf -debug_group summary,timer
debuggroup summary 0.15s loading configuration from file etc/circos.conf
-debuggroup summary 0.18s found conf file etc/circos.conf
-debuggroup summary 1.04s debug will appear for these features: summary,timer
-debuggroup summary 1.04s bitmap output image ./circos.png
-debuggroup summary 1.04s SVG output image ./circos.svg
-debuggroup summary 1.04s parsing karyotype and organizing ideograms
-debuggroup summary 1.52s karyotype has 66 chromosomes of total size 8,540,079,869
-debuggroup summary 1.55s applying global and local scaling
-debuggroup summary 1.70s allocating image, colors and brushes
-debuggroup summary 9.80s drawing 24 ideograms of total size 3,344,416,167
-debuggroup summary 9.80s drawing highlights and ideograms
-debuggroup summary 12.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/link.conf
-debuggroup summary 12.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/link.conf
-debuggroup summary 12.72s process track_0 link /home/martink/work/circos/svn/example/data/rn.bundle.txt
-debuggroup summary 13.52s process track_1 link /home/martink/work/circos/svn/example/data/mm.bundle.txt
-debuggroup summary 13.69s drawing link track_0 z 0
-debuggroup summary 14.59s drawing link track_1 z 0
-debuggroup summary 14.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/highlight.conf
-debuggroup summary 14.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/highlight.conf
-debuggroup summary 14.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/text.conf
-debuggroup summary 14.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.77s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/histogram.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/histogram.conf
-debuggroup summary 14.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
-debuggroup summary 14.80s processing track_0 highlight /home/martink/work/circos/svn/example/data/highlights.txt
-debuggroup summary 14.80s processing track_1 highlight /home/martink/work/circos/svn/example/data/highlights.txt
-debuggroup summary 14.84s processing track_2 text /home/martink/work/circos/svn/example/data/genes.txt
-debuggroup summary 15.86s processing track_3 heatmap /home/martink/work/circos/svn/example/data/heatmap.hs.mm.20e6.txt
-debuggroup summary 15.93s processing track_4 heatmap /home/martink/work/circos/svn/example/data/heatmap.hs.rn.20e6.txt
-debuggroup summary 16.00s processing track_5 heatmap /home/martink/work/circos/svn/example/data/heatmap.hs.mm.10e6.txt
-debuggroup summary 16.14s processing track_6 heatmap /home/martink/work/circos/svn/example/data/heatmap.hs.rn.10e6.txt
-debuggroup summary 16.29s processing track_7 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.1.txt
-debuggroup summary 16.36s processing track_8 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.2.txt
-debuggroup summary 16.43s processing track_9 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.3.txt
-debuggroup summary 16.48s processing track_10 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.4.txt
-debuggroup summary 16.52s processing track_11 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.5.txt
-debuggroup summary 16.56s processing track_12 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.6.txt
-debuggroup summary 16.60s processing track_13 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.7.txt
-debuggroup summary 16.64s processing track_14 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.8.txt
-debuggroup summary 16.69s processing track_15 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.9.txt
-debuggroup summary 16.75s processing track_16 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.10.txt
-debuggroup summary 16.80s processing track_17 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.11.txt
-debuggroup summary 16.84s processing track_18 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.12.txt
-debuggroup summary 16.88s processing track_19 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.13.txt
-debuggroup summary 16.92s processing track_20 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.14.txt
-debuggroup summary 16.97s processing track_21 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.15.txt
-debuggroup summary 17.01s processing track_22 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.16.txt
-debuggroup summary 17.06s processing track_23 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.17.txt
-debuggroup summary 17.10s processing track_24 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.18.txt
-debuggroup summary 17.15s processing track_25 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.19.txt
-debuggroup summary 17.19s processing track_26 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.20.txt
-debuggroup summary 17.23s processing track_27 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.21.txt
-debuggroup summary 17.27s processing track_28 heatmap /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.22.txt
-debuggroup summary 17.33s processing track_29 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.1.txt
-debuggroup summary 17.39s processing track_30 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.2.txt
-debuggroup summary 17.44s processing track_31 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.3.txt
-debuggroup summary 17.49s processing track_32 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.4.txt
-debuggroup summary 17.54s processing track_33 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.5.txt
-debuggroup summary 17.59s processing track_34 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.6.txt
-debuggroup summary 17.64s processing track_35 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.7.txt
-debuggroup summary 17.70s processing track_36 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.8.txt
-debuggroup summary 17.75s processing track_37 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.9.txt
-debuggroup summary 17.80s processing track_38 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.10.txt
-debuggroup summary 17.85s processing track_39 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.11.txt
-debuggroup summary 17.90s processing track_40 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.12.txt
-debuggroup summary 17.96s processing track_41 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.13.txt
-debuggroup summary 18.01s processing track_42 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.14.txt
-debuggroup summary 18.06s processing track_43 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.15.txt
-debuggroup summary 18.11s processing track_44 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.16.txt
-debuggroup summary 18.18s processing track_45 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.17.txt
-debuggroup summary 18.23s processing track_46 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.18.txt
-debuggroup summary 18.29s processing track_47 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.19.txt
-debuggroup summary 18.34s processing track_48 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.20.txt
-debuggroup summary 18.40s processing track_49 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.21.txt
-debuggroup summary 18.45s processing track_50 heatmap /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.22.txt
-debuggroup summary 18.51s processing track_51 scatter /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.1.txt
-debuggroup summary 18.57s processing track_52 scatter /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.2.txt
-debuggroup summary 18.64s processing track_53 scatter /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.3.txt
-debuggroup summary 18.70s processing track_54 scatter /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.4.txt
-debuggroup summary 18.77s processing track_55 scatter /home/martink/work/circos/svn/example/data/heatmap.rn.5e6.hs.5.txt
-debuggroup summary 18.83s processing track_56 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.1.txt
-debuggroup summary 18.88s processing track_57 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.2.txt
-debuggroup summary 18.94s processing track_58 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.3.txt
-debuggroup summary 18.99s processing track_59 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.4.txt
-debuggroup summary 19.04s processing track_60 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.5.txt
-debuggroup summary 19.09s processing track_61 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.6.txt
-debuggroup summary 19.14s processing track_62 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.7.txt
-debuggroup summary 19.20s processing track_63 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.8.txt
-debuggroup summary 19.25s processing track_64 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.9.txt
-debuggroup summary 19.30s processing track_65 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.10.txt
-debuggroup summary 19.35s processing track_66 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.11.txt
-debuggroup summary 19.40s processing track_67 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.12.txt
-debuggroup summary 19.46s processing track_68 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.13.txt
-debuggroup summary 19.51s processing track_69 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.14.txt
-debuggroup summary 19.56s processing track_70 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.15.txt
-debuggroup summary 19.61s processing track_71 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.16.txt
-debuggroup summary 19.66s processing track_72 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.17.txt
-debuggroup summary 19.71s processing track_73 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.18.txt
-debuggroup summary 19.77s processing track_74 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.19.txt
-debuggroup summary 19.82s processing track_75 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.20.txt
-debuggroup summary 19.87s processing track_76 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.21.txt
-debuggroup summary 19.92s processing track_77 scatter /home/martink/work/circos/svn/example/data/heatmap.mm.5e6.hs.22.txt
-debuggroup summary 19.97s processing track_78 histogram /home/martink/work/circos/svn/example/data/heatmap.hs.mm.20e6.txt
-debuggroup summary 20.04s processing track_79 scatter /home/martink/work/circos/svn/example/data/heatmap.hs.mm.5e6.txt
-debuggroup summary 20.31s processing track_80 histogram /home/martink/work/circos/svn/example/data/heatmap.hs.rn.20e6.txt
-debuggroup summary 20.38s processing track_81 scatter /home/martink/work/circos/svn/example/data/heatmap.hs.rn.5e6.txt
-debuggroup summary 20.64s drawing track_0 highlight z 0 highlights.txt
-debuggroup summary 20.64s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 20.70s drawing track_1 highlight z 0 highlights.txt
-debuggroup summary 20.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 20.74s drawing track_2 text z 0 genes.txt
-debuggroup summary 20.81s placing text track data/genes.txt
-debuggroup summary 20.81s ... see progress with -debug_group text
-debuggroup summary 20.81s ... see placement summary with -debug_group textplace
-debuggroup summary 58.13s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 60.15s drawing track_3 heatmap z 0 heatmap.hs.mm.20e6.txt
-debuggroup summary 60.17s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 60.34s drawing track_4 heatmap z 0 heatmap.hs.rn.20e6.txt
-debuggroup summary 60.36s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 60.52s drawing track_5 heatmap z 0 heatmap.hs.mm.10e6.txt
-debuggroup summary 60.54s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 60.85s drawing track_6 heatmap z 0 heatmap.hs.rn.10e6.txt
-debuggroup summary 60.88s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.16s drawing track_7 heatmap z 0 heatmap.mm.5e6.hs.1.txt
-debuggroup summary 61.17s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.22s drawing track_8 heatmap z 0 heatmap.mm.5e6.hs.2.txt
-debuggroup summary 61.22s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.27s drawing track_9 heatmap z 0 heatmap.mm.5e6.hs.3.txt
-debuggroup summary 61.28s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.32s drawing track_10 heatmap z 0 heatmap.mm.5e6.hs.4.txt
-debuggroup summary 61.33s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.37s drawing track_11 heatmap z 0 heatmap.mm.5e6.hs.5.txt
-debuggroup summary 61.38s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.43s drawing track_12 heatmap z 0 heatmap.mm.5e6.hs.6.txt
-debuggroup summary 61.43s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.48s drawing track_13 heatmap z 0 heatmap.mm.5e6.hs.7.txt
-debuggroup summary 61.48s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.53s drawing track_14 heatmap z 0 heatmap.mm.5e6.hs.8.txt
-debuggroup summary 61.53s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.58s drawing track_15 heatmap z 0 heatmap.mm.5e6.hs.9.txt
-debuggroup summary 61.58s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.63s drawing track_16 heatmap z 0 heatmap.mm.5e6.hs.10.txt
-debuggroup summary 61.63s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.68s drawing track_17 heatmap z 0 heatmap.mm.5e6.hs.11.txt
-debuggroup summary 61.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.73s drawing track_18 heatmap z 0 heatmap.mm.5e6.hs.12.txt
-debuggroup summary 61.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.78s drawing track_19 heatmap z 0 heatmap.mm.5e6.hs.13.txt
-debuggroup summary 61.79s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.83s drawing track_20 heatmap z 0 heatmap.mm.5e6.hs.14.txt
-debuggroup summary 61.84s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.88s drawing track_21 heatmap z 0 heatmap.mm.5e6.hs.15.txt
-debuggroup summary 61.89s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.93s drawing track_22 heatmap z 0 heatmap.mm.5e6.hs.16.txt
-debuggroup summary 61.93s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 61.98s drawing track_23 heatmap z 0 heatmap.mm.5e6.hs.17.txt
-debuggroup summary 61.99s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.03s drawing track_24 heatmap z 0 heatmap.mm.5e6.hs.18.txt
-debuggroup summary 62.04s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.08s drawing track_25 heatmap z 0 heatmap.mm.5e6.hs.19.txt
-debuggroup summary 62.09s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.13s drawing track_26 heatmap z 0 heatmap.mm.5e6.hs.20.txt
-debuggroup summary 62.14s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.18s drawing track_27 heatmap z 0 heatmap.mm.5e6.hs.21.txt
-debuggroup summary 62.18s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.23s drawing track_28 heatmap z 0 heatmap.mm.5e6.hs.22.txt
-debuggroup summary 62.23s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.27s drawing track_29 heatmap z 0 heatmap.rn.5e6.hs.1.txt
-debuggroup summary 62.28s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.34s drawing track_30 heatmap z 0 heatmap.rn.5e6.hs.2.txt
-debuggroup summary 62.35s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.40s drawing track_31 heatmap z 0 heatmap.rn.5e6.hs.3.txt
-debuggroup summary 62.40s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.46s drawing track_32 heatmap z 0 heatmap.rn.5e6.hs.4.txt
-debuggroup summary 62.46s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.52s drawing track_33 heatmap z 0 heatmap.rn.5e6.hs.5.txt
-debuggroup summary 62.52s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.58s drawing track_34 heatmap z 0 heatmap.rn.5e6.hs.6.txt
-debuggroup summary 62.58s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.63s drawing track_35 heatmap z 0 heatmap.rn.5e6.hs.7.txt
-debuggroup summary 62.64s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.69s drawing track_36 heatmap z 0 heatmap.rn.5e6.hs.8.txt
-debuggroup summary 62.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.75s drawing track_37 heatmap z 0 heatmap.rn.5e6.hs.9.txt
-debuggroup summary 62.76s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.81s drawing track_38 heatmap z 0 heatmap.rn.5e6.hs.10.txt
-debuggroup summary 62.82s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.87s drawing track_39 heatmap z 0 heatmap.rn.5e6.hs.11.txt
-debuggroup summary 62.87s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.93s drawing track_40 heatmap z 0 heatmap.rn.5e6.hs.12.txt
-debuggroup summary 62.93s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 62.99s drawing track_41 heatmap z 0 heatmap.rn.5e6.hs.13.txt
-debuggroup summary 62.99s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.04s drawing track_42 heatmap z 0 heatmap.rn.5e6.hs.14.txt
-debuggroup summary 63.05s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.10s drawing track_43 heatmap z 0 heatmap.rn.5e6.hs.15.txt
-debuggroup summary 63.11s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.16s drawing track_44 heatmap z 0 heatmap.rn.5e6.hs.16.txt
-debuggroup summary 63.17s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.22s drawing track_45 heatmap z 0 heatmap.rn.5e6.hs.17.txt
-debuggroup summary 63.23s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.28s drawing track_46 heatmap z 0 heatmap.rn.5e6.hs.18.txt
-debuggroup summary 63.29s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.34s drawing track_47 heatmap z 0 heatmap.rn.5e6.hs.19.txt
-debuggroup summary 63.34s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.40s drawing track_48 heatmap z 0 heatmap.rn.5e6.hs.20.txt
-debuggroup summary 63.40s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.45s drawing track_49 heatmap z 0 heatmap.rn.5e6.hs.21.txt
-debuggroup summary 63.46s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.51s drawing track_50 heatmap z 0 heatmap.rn.5e6.hs.22.txt
-debuggroup summary 63.51s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.57s drawing track_51 scatter z 0 heatmap.rn.5e6.hs.1.txt orient out
-debuggroup summary 63.57s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.64s drawing track_52 scatter z 0 heatmap.rn.5e6.hs.2.txt orient out
-debuggroup summary 63.64s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.71s drawing track_53 scatter z 0 heatmap.rn.5e6.hs.3.txt orient out
-debuggroup summary 63.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.78s drawing track_54 scatter z 0 heatmap.rn.5e6.hs.4.txt orient out
-debuggroup summary 63.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.84s drawing track_55 scatter z 0 heatmap.rn.5e6.hs.5.txt orient out
-debuggroup summary 63.85s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.91s drawing track_56 scatter z 0 heatmap.mm.5e6.hs.1.txt orient out
-debuggroup summary 63.92s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.95s drawing track_57 scatter z 0 heatmap.mm.5e6.hs.2.txt orient out
-debuggroup summary 63.95s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 63.98s drawing track_58 scatter z 0 heatmap.mm.5e6.hs.3.txt orient out
-debuggroup summary 63.99s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.02s drawing track_59 scatter z 0 heatmap.mm.5e6.hs.4.txt orient out
-debuggroup summary 64.02s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.06s drawing track_60 scatter z 0 heatmap.mm.5e6.hs.5.txt orient out
-debuggroup summary 64.06s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.09s drawing track_61 scatter z 0 heatmap.mm.5e6.hs.6.txt orient out
-debuggroup summary 64.10s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.13s drawing track_62 scatter z 0 heatmap.mm.5e6.hs.7.txt orient out
-debuggroup summary 64.13s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.16s drawing track_63 scatter z 0 heatmap.mm.5e6.hs.8.txt orient out
-debuggroup summary 64.17s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.20s drawing track_64 scatter z 0 heatmap.mm.5e6.hs.9.txt orient out
-debuggroup summary 64.20s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.23s drawing track_65 scatter z 0 heatmap.mm.5e6.hs.10.txt orient out
-debuggroup summary 64.24s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.27s drawing track_66 scatter z 0 heatmap.mm.5e6.hs.11.txt orient out
-debuggroup summary 64.27s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.30s drawing track_67 scatter z 0 heatmap.mm.5e6.hs.12.txt orient out
-debuggroup summary 64.31s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.34s drawing track_68 scatter z 0 heatmap.mm.5e6.hs.13.txt orient out
-debuggroup summary 64.34s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.37s drawing track_69 scatter z 0 heatmap.mm.5e6.hs.14.txt orient out
-debuggroup summary 64.38s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.41s drawing track_70 scatter z 0 heatmap.mm.5e6.hs.15.txt orient out
-debuggroup summary 64.41s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.44s drawing track_71 scatter z 0 heatmap.mm.5e6.hs.16.txt orient out
-debuggroup summary 64.45s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.48s drawing track_72 scatter z 0 heatmap.mm.5e6.hs.17.txt orient out
-debuggroup summary 64.48s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.51s drawing track_73 scatter z 0 heatmap.mm.5e6.hs.18.txt orient out
-debuggroup summary 64.52s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.55s drawing track_74 scatter z 0 heatmap.mm.5e6.hs.19.txt orient out
-debuggroup summary 64.55s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.58s drawing track_75 scatter z 0 heatmap.mm.5e6.hs.20.txt orient out
-debuggroup summary 64.59s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.62s drawing track_76 scatter z 0 heatmap.mm.5e6.hs.21.txt orient out
-debuggroup summary 64.62s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.65s drawing track_77 scatter z 0 heatmap.mm.5e6.hs.22.txt orient out
-debuggroup summary 64.65s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 64.68s drawing track_78 histogram z 0 heatmap.hs.mm.20e6.txt orient out
-debuggroup summary 64.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 65.40s drawing track_79 scatter z 0 heatmap.hs.mm.5e6.txt orient out
-debuggroup summary 65.46s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 65.96s drawing track_80 histogram z 0 heatmap.hs.rn.20e6.txt orient in
-debuggroup summary 65.97s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup summary 66.37s drawing track_81 scatter z 0 heatmap.hs.rn.5e6.txt orient in
-debuggroup summary 66.42s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
-debuggroup timer 68.09s report circos 67.943 s
-debuggroup timer 68.09s report color 7.546 s
-debuggroup timer 68.09s report colordefinitions 0.169 s
-debuggroup timer 68.09s report colorfetch 0.175 s
-debuggroup timer 68.09s report colorlists 6.803 s
-debuggroup timer 68.09s report colorlookups 0.007 s
-debuggroup timer 68.09s report colortransparency 0.348 s
-debuggroup timer 68.09s report dataparams 1.638 s
-debuggroup timer 68.09s report datarules 3.291 s
-debuggroup timer 68.09s report graphic_png_polygon 0.875 s
-debuggroup timer 68.09s report graphic_slice 2.536 s
-debuggroup timer 68.09s report graphic_slice_polygon_coord 0.437 s
-debuggroup timer 68.09s report graphic_slice_polygon_svg 0.883 s
-debuggroup timer 68.09s report graphic_slice_preprocess 0.218 s
-debuggroup timer 68.09s report highlights 0.000 s
-debuggroup timer 68.09s report ideograms_draw 2.885 s
-debuggroup timer 68.09s report ideograms_processing 0.025 s
-debuggroup timer 68.09s report ideograms_ticks_draw 2.225 s
-debuggroup timer 68.09s report ideograms_zoom 0.149 s
-debuggroup timer 68.09s report io 0.800 s
-debuggroup timer 68.09s report karyotype 0.483 s
-debuggroup timer 68.09s report parameter_seek 4.867 s
-debuggroup timer 68.09s report track_heatmap 2.187 s
-debuggroup timer 68.09s report track_highlight 0.065 s
-debuggroup timer 68.09s report track_histogram 0.699 s
-debuggroup timer 68.09s report track_preprocess 0.631 s
-debuggroup timer 68.09s report track_scatter 1.363 s
-debuggroup timer 68.09s report track_text_ashift 28.267 s
-debuggroup timer 68.09s report track_text_ashiftiter 13.979 s
-debuggroup timer 68.09s report track_text_draw 1.845 s
-debuggroup timer 68.09s report track_text_place 37.320 s
-debuggroup timer 68.09s report track_text_preashift 7.846 s
-debuggroup timer 68.09s report track_text_preprocess 0.594 s
-debuggroup timer 68.09s report track_text_refine 0.004 s
-debuggroup timer 68.09s report unitconvert 0.052 s
-debuggroup timer 68.09s report unitconvert_decision 0.004 s
-debuggroup timer 68.09s report unitconvert_delegate 0.015 s
-debuggroup timer 68.09s report unitparse 0.184 s
+debuggroup summary 0.15s found conf file etc/circos.conf
+debuggroup summary 0.63s debug will appear for these features: summary,timer
+debuggroup summary 0.63s bitmap output image ./circos.png
+debuggroup summary 0.63s SVG output image ./circos.svg
+debuggroup summary 0.63s parsing karyotype and organizing ideograms
+debuggroup summary 0.95s karyotype has 66 chromosomes of total size 8,540,079,869
+debuggroup summary 0.97s applying global and local scaling
+debuggroup summary 1.12s allocating image, colors and brushes
+debuggroup summary 2.02s drawing 24 ideograms of total size 3,344,416,167
+debuggroup summary 2.02s drawing highlights and ideograms
+debuggroup summary 4.80s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/link.conf
+debuggroup summary 4.80s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/link.conf
+debuggroup summary 4.80s process track_0 link /home/martink/work/circos/svn/example/data/rn.bundle.txt
+debuggroup summary 5.56s process track_1 link /home/martink/work/circos/svn/example/data/mm.bundle.txt
+debuggroup summary 5.72s drawing link track_0 z 0
+debuggroup summary 6.59s drawing link track_1 z 0
+debuggroup summary 6.67s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/highlight.conf
+debuggroup summary 6.67s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/highlight.conf
+debuggroup summary 6.67s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/text.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.69s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.70s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.71s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/heatmap.conf
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+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.73s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
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+debuggroup summary 6.74s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/scatter.conf
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+debuggroup summary 53.13s drawing track_37 heatmap z 0 heatmap.rn.5e6.hs.9.txt
+debuggroup summary 53.13s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.19s drawing track_38 heatmap z 0 heatmap.rn.5e6.hs.10.txt
+debuggroup summary 53.19s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.24s drawing track_39 heatmap z 0 heatmap.rn.5e6.hs.11.txt
+debuggroup summary 53.25s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.30s drawing track_40 heatmap z 0 heatmap.rn.5e6.hs.12.txt
+debuggroup summary 53.31s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.36s drawing track_41 heatmap z 0 heatmap.rn.5e6.hs.13.txt
+debuggroup summary 53.37s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.42s drawing track_42 heatmap z 0 heatmap.rn.5e6.hs.14.txt
+debuggroup summary 53.43s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.48s drawing track_43 heatmap z 0 heatmap.rn.5e6.hs.15.txt
+debuggroup summary 53.49s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.54s drawing track_44 heatmap z 0 heatmap.rn.5e6.hs.16.txt
+debuggroup summary 53.54s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.60s drawing track_45 heatmap z 0 heatmap.rn.5e6.hs.17.txt
+debuggroup summary 53.60s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.65s drawing track_46 heatmap z 0 heatmap.rn.5e6.hs.18.txt
+debuggroup summary 53.66s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.71s drawing track_47 heatmap z 0 heatmap.rn.5e6.hs.19.txt
+debuggroup summary 53.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.77s drawing track_48 heatmap z 0 heatmap.rn.5e6.hs.20.txt
+debuggroup summary 53.78s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.83s drawing track_49 heatmap z 0 heatmap.rn.5e6.hs.21.txt
+debuggroup summary 53.83s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.88s drawing track_50 heatmap z 0 heatmap.rn.5e6.hs.22.txt
+debuggroup summary 53.89s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 53.94s drawing track_51 scatter z 0 heatmap.rn.5e6.hs.1.txt orient out
+debuggroup summary 53.95s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.01s drawing track_52 scatter z 0 heatmap.rn.5e6.hs.2.txt orient out
+debuggroup summary 54.02s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.09s drawing track_53 scatter z 0 heatmap.rn.5e6.hs.3.txt orient out
+debuggroup summary 54.09s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.15s drawing track_54 scatter z 0 heatmap.rn.5e6.hs.4.txt orient out
+debuggroup summary 54.16s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.22s drawing track_55 scatter z 0 heatmap.rn.5e6.hs.5.txt orient out
+debuggroup summary 54.22s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.29s drawing track_56 scatter z 0 heatmap.mm.5e6.hs.1.txt orient out
+debuggroup summary 54.29s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.32s drawing track_57 scatter z 0 heatmap.mm.5e6.hs.2.txt orient out
+debuggroup summary 54.33s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.36s drawing track_58 scatter z 0 heatmap.mm.5e6.hs.3.txt orient out
+debuggroup summary 54.37s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.40s drawing track_59 scatter z 0 heatmap.mm.5e6.hs.4.txt orient out
+debuggroup summary 54.40s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.43s drawing track_60 scatter z 0 heatmap.mm.5e6.hs.5.txt orient out
+debuggroup summary 54.44s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.47s drawing track_61 scatter z 0 heatmap.mm.5e6.hs.6.txt orient out
+debuggroup summary 54.47s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.50s drawing track_62 scatter z 0 heatmap.mm.5e6.hs.7.txt orient out
+debuggroup summary 54.51s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.54s drawing track_63 scatter z 0 heatmap.mm.5e6.hs.8.txt orient out
+debuggroup summary 54.54s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.57s drawing track_64 scatter z 0 heatmap.mm.5e6.hs.9.txt orient out
+debuggroup summary 54.58s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.61s drawing track_65 scatter z 0 heatmap.mm.5e6.hs.10.txt orient out
+debuggroup summary 54.61s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.64s drawing track_66 scatter z 0 heatmap.mm.5e6.hs.11.txt orient out
+debuggroup summary 54.65s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.68s drawing track_67 scatter z 0 heatmap.mm.5e6.hs.12.txt orient out
+debuggroup summary 54.68s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.71s drawing track_68 scatter z 0 heatmap.mm.5e6.hs.13.txt orient out
+debuggroup summary 54.72s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.75s drawing track_69 scatter z 0 heatmap.mm.5e6.hs.14.txt orient out
+debuggroup summary 54.75s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.78s drawing track_70 scatter z 0 heatmap.mm.5e6.hs.15.txt orient out
+debuggroup summary 54.79s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.82s drawing track_71 scatter z 0 heatmap.mm.5e6.hs.16.txt orient out
+debuggroup summary 54.82s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.85s drawing track_72 scatter z 0 heatmap.mm.5e6.hs.17.txt orient out
+debuggroup summary 54.86s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.89s drawing track_73 scatter z 0 heatmap.mm.5e6.hs.18.txt orient out
+debuggroup summary 54.89s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.92s drawing track_74 scatter z 0 heatmap.mm.5e6.hs.19.txt orient out
+debuggroup summary 54.93s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.96s drawing track_75 scatter z 0 heatmap.mm.5e6.hs.20.txt orient out
+debuggroup summary 54.96s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 54.99s drawing track_76 scatter z 0 heatmap.mm.5e6.hs.21.txt orient out
+debuggroup summary 55.00s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 55.03s drawing track_77 scatter z 0 heatmap.mm.5e6.hs.22.txt orient out
+debuggroup summary 55.03s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 55.06s drawing track_78 histogram z 0 heatmap.hs.mm.20e6.txt orient out
+debuggroup summary 55.08s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 55.78s drawing track_79 scatter z 0 heatmap.hs.mm.5e6.txt orient out
+debuggroup summary 55.84s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 56.33s drawing track_80 histogram z 0 heatmap.hs.rn.20e6.txt orient in
+debuggroup summary 56.35s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup summary 56.74s drawing track_81 scatter z 0 heatmap.hs.rn.5e6.txt orient in
+debuggroup summary 56.79s found conf file /home/martink/work/circos/svn/bin/../etc/tracks/axis.conf
+debuggroup timer 58.46s report circos 58.315 s
+debuggroup timer 58.46s report color 0.727 s
+debuggroup timer 58.46s report colorcache 0.006 s
+debuggroup timer 58.46s report colordefinitions 0.162 s
+debuggroup timer 58.46s report colorfetch 0.173 s
+debuggroup timer 58.46s report colorlists 0.011 s
+debuggroup timer 58.46s report colorlookups 0.006 s
+debuggroup timer 58.46s report colortransparency 0.335 s
+debuggroup timer 58.46s report dataparams 1.552 s
+debuggroup timer 58.47s report datarules 3.180 s
+debuggroup timer 58.47s report graphic_png_polygon 0.873 s
+debuggroup timer 58.47s report graphic_slice 2.522 s
+debuggroup timer 58.47s report graphic_slice_polygon_coord 0.434 s
+debuggroup timer 58.47s report graphic_slice_polygon_svg 0.876 s
+debuggroup timer 58.47s report graphic_slice_preprocess 0.217 s
+debuggroup timer 58.47s report highlights 0.000 s
+debuggroup timer 58.47s report ideograms_draw 2.776 s
+debuggroup timer 58.47s report ideograms_processing 0.024 s
+debuggroup timer 58.47s report ideograms_ticks_draw 2.142 s
+debuggroup timer 58.47s report ideograms_zoom 0.144 s
+debuggroup timer 58.47s report io 0.589 s
+debuggroup timer 58.47s report karyotype 0.314 s
+debuggroup timer 58.47s report parameter_seek 4.705 s
+debuggroup timer 58.47s report track_heatmap 2.191 s
+debuggroup timer 58.47s report track_highlight 0.063 s
+debuggroup timer 58.47s report track_histogram 0.696 s
+debuggroup timer 58.47s report track_preprocess 0.637 s
+debuggroup timer 58.47s report track_scatter 1.365 s
+debuggroup timer 58.47s report track_text_ashift 27.520 s
+debuggroup timer 58.47s report track_text_ashiftiter 13.467 s
+debuggroup timer 58.47s report track_text_draw 1.850 s
+debuggroup timer 58.47s report track_text_place 36.211 s
+debuggroup timer 58.47s report track_text_preashift 7.526 s
+debuggroup timer 58.47s report track_text_preprocess 0.574 s
+debuggroup timer 58.47s report track_text_refine 0.004 s
+debuggroup timer 58.47s report unitconvert 0.051 s
+debuggroup timer 58.47s report unitconvert_decision 0.004 s
+debuggroup timer 58.47s report unitconvert_delegate 0.015 s
+debuggroup timer 58.47s report unitparse 0.186 s
diff --git a/lib/Circos.pm b/lib/Circos.pm
index 76702d9..8cb581c 100644
--- a/lib/Circos.pm
+++ b/lib/Circos.pm
@@ -1,7 +1,7 @@
package Circos;
-our $VERSION = "0.69-4";
-our $VERSION_DATE = "17 Dec 2016";
+our $VERSION = "0.69-5";
+our $VERSION_DATE = "2 May 2017";
=pod
diff --git a/lib/Circos/Configuration.pm b/lib/Circos/Configuration.pm
index bb85fd7..d8aeaa9 100644
--- a/lib/Circos/Configuration.pm
+++ b/lib/Circos/Configuration.pm
@@ -643,7 +643,6 @@ sub repopulateconfiguration {
sub parse_field {
my ($str,$key,$parent_node_name,$node,$curr) = @_;
- my $delim = "__";
if(! defined $str) {
printdumper($node);
@@ -665,10 +664,11 @@ sub parse_field {
# conf(LEAF,LEAF,...)
$str = parse_conf_fn($str,$node,$curr);
- # this is going to be deprecated
- if( $str =~ /$delim([^_].+?)$delim/g ) {
- fatal_error("configuration","deprecated","__FIELD__","var(FIELD)");
- }
+ # this is now totally deprecated
+ # my $delim = "__";
+ #if( $str =~ /$delim([^_].+?)$delim/g ) {
+ #error("configuration","deprecated","__FIELD__","var(FIELD)");
+ #}
$str = eval_conf($str) if $str !~ /var\s*\(/ && (! defined $parent_node_name || $parent_node_name ne "rule");
diff --git a/lib/Circos/Error.pm b/lib/Circos/Error.pm
index fa3a820..b680c18 100644
--- a/lib/Circos/Error.pm
+++ b/lib/Circos/Error.pm
@@ -323,63 +323,63 @@ $ERROR{support} =
};
sub error {
- my ($cat,$errorid, at args) = @_;
- my $error_text = $ERROR{$cat}{$errorid};
- if(! defined $error_text) {
- fatal_error("system","bad_error_name",$cat,$errorid);
- }
- if($error_text =~ /file\((.*)\)/) {
- my $file = Circos::Utils::locate_file(file=>$1,name=>"error file",return_undef=>1);
- if($file && open(F,$file)) {
- $error_text = join("",<F>);
- close(F);
- } else {
- $error_text = "...error text from [$1] could not be read...";
- }
- }
- my (@text,$format);
- my $undef_text = Circos::Configuration::fetch_conf("debug_undef_text") || "_undef_";
- @args = map { defined $_ ? $_ : $undef_text } @args;
- if($cat eq "warning") {
- if(Circos::Configuration::fetch_conf("paranoid")) {
- @text = ("WARNING *** "
- .
- ($GROUPERROR{$cat} ? uc $GROUPERROR{$cat} : $EMPTY_STR)
- .
- sprintf($error_text, at args));
- #$format = 1;
- } else {
- printdebug_group("!circoswarning",uc $GROUPERROR{$cat},sprintf($error_text, at args));
- return;
- }
- } else {
- @text = ("*** CIRCOS ERROR ***",
- sprintf(" cwd: %s",cwd()),
- sprintf(" command: %s",join(" ",$0,$main::OPT{"_argv"})),
- $GROUPERROR{$cat} ? uc $GROUPERROR{$cat} : $EMPTY_STR,
- sprintf($error_text, at args),
- $ERROR{support}{googlegroup},
- "",
- "Stack trace:",
- );
- $format = 1;
- }
- if($format) {
- my @text_fmt;
- for my $t (@text) {
- for my $line (split(/\n/, $t)) {
- if ($line =~ /^\s/) {
- push @text_fmt, Text::Format->new({leftMargin=>6,columns=>80,firstIndent=>0})->paragraphs($line);
- } else {
- push @text_fmt, Text::Format->new({leftMargin=>2,columns=>80,firstIndent=>0})->paragraphs($line);
- }
+ my ($cat,$errorid, at args) = @_;
+ my $error_text = $ERROR{$cat}{$errorid};
+ if(! defined $error_text) {
+ fatal_error("system","bad_error_name",$cat,$errorid);
+ }
+ if($error_text =~ /file\((.*)\)/) {
+ my $file = Circos::Utils::locate_file(file=>$1,name=>"error file",return_undef=>1);
+ if($file && open(F,$file)) {
+ $error_text = join("",<F>);
+ close(F);
+ } else {
+ $error_text = "...error text from [$1] could not be read...";
+ }
+ }
+ my (@text,$format);
+ my $undef_text = Circos::Configuration::fetch_conf("debug_undef_text") || "_undef_";
+ @args = map { defined $_ ? $_ : $undef_text } @args;
+ if($cat eq "warning") {
+ if(Circos::Configuration::fetch_conf("paranoid")) {
+ @text = ("WARNING *** "
+ .
+ ($GROUPERROR{$cat} ? uc $GROUPERROR{$cat} : $EMPTY_STR)
+ .
+ sprintf($error_text, at args));
+ #$format = 1;
+ } else {
+ printdebug_group("!circoswarning",uc $GROUPERROR{$cat},sprintf($error_text, at args));
+ return;
+ }
+ } else {
+ @text = ("*** CIRCOS ERROR ***",
+ sprintf(" cwd: %s",cwd()),
+ sprintf(" command: %s",join(" ",$0,$main::OPT{"_argv"})),
+ $GROUPERROR{$cat} ? uc $GROUPERROR{$cat} : $EMPTY_STR,
+ sprintf($error_text, at args),
+ $ERROR{support}{googlegroup},
+ "",
+ "Stack trace:",
+ );
+ $format = 1;
+ }
+ if($format) {
+ my @text_fmt;
+ for my $t (@text) {
+ for my $line (split(/\n/, $t)) {
+ if ($line =~ /^\s/) {
+ push @text_fmt, Text::Format->new({leftMargin=>6,columns=>80,firstIndent=>0})->paragraphs($line);
+ } else {
+ push @text_fmt, Text::Format->new({leftMargin=>2,columns=>80,firstIndent=>0})->paragraphs($line);
}
}
- print "\n" . join("\n", @text_fmt);
- } else {
- print join(" ", at text)."\n";
- }
+ }
+ print "\n" . join("\n", @text_fmt);
+ } else {
+ print join(" ", at text)."\n";
}
+}
sub fake_error {
my $error_path = shift;
@@ -396,31 +396,31 @@ sub fake_error {
exit;
} elsif (! $name) {
printinfo("The following errors are available for category [$cat]");
- for my $name (sort keys %{$ERROR{$cat}}) {
+ for my $name (sort keys %{$ERROR{$cat}}) {
printinfo(" ",$name);
- }
- exit;
- } elsif (! $cat) {
- my $found;
- printinfo("The following categories contain the error ID [$name]");
- for my $thiscat (sort keys %ERROR) {
- for my $thisname (sort keys %{$ERROR{$thiscat}}) {
- if($name eq $thisname) {
- printinfo($thiscat,$name);
- $found = 1;
}
+ exit;
+ } elsif (! $cat) {
+ my $found;
+ printinfo("The following categories contain the error ID [$name]");
+ for my $thiscat (sort keys %ERROR) {
+ for my $thisname (sort keys %{$ERROR{$thiscat}}) {
+ if($name eq $thisname) {
+ printinfo($thiscat,$name);
+ $found = 1;
+ }
}
+ }
+ printinfo("Could not find error name [$name] in any error category") if ! $found;
+ exit;
+ } else {
+ fatal_error($cat,$name, map { 0 } (1..10) );
}
- printinfo("Could not find error name [$name] in any error category") if ! $found;
- exit;
- } else {
- fatal_error($cat,$name, map { 0 } (1..10) );
- }
}
sub fatal_error {
- error(@_);
- confess;
+ error(@_);
+ confess;
}
1;
--
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