I want to use leptonica. So I download and make and make check.
But when I use command make check, there is one FAIL.
How to solve it? I searched the similar problem in stackoverflow but I couldn't find.
////////////////////////////////////////////////
//////////////// iomisc_reg ///////////////
////////////////////////////////////////////////
leptonica-1.78.0 : libjpeg 6b (libjpeg-turbo 1.2.90) : libpng 1.5.13 : libtiff 4.0.3 : zlib 1.2.7
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Failure in iomisc_reg: value comparison for index 38
difference = 68.000000 but allowed delta = 0.000000
Time: 0.337 sec
I want 0 FAIL but the actual resuls are below.
leptonica 1.78.0: prog/test-suite.log
TOTAL: 125
PASS: 124
SKIP: 0
XFAIL: 0
FAIL: 1
XPASS: 0
ERROR: 0
.. contents:: :depth: 2
## FAIL: iomisc_reg
leptonica-1.78.0 : libjpeg 6b (libjpeg-turbo 1.2.90) : libpng 1.5.13 : libtiff 4.0.3 : zlib 1.2.7
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Info in pixReadStreamPng: not stripping 16 --> 8 in png reading
Failure in iomisc_reg: value comparison for index 38
difference = 68.000000 but allowed delta = 0.000000
Time: 0.337 sec
Related
The 'mdat box' of Mp4 file may at the last of file. I want to know the position of 'mdat' box using 'ffmpeg' or 'ffprobe'.
Mp4 consists of 'ftyp', 'moov' and 'mdat' BOX. each BOX consists of "BoxHeader" and "BoxData". "BoxHeader" consists of "BoxSize(4Byte)", "BoxType(4Byte)", "BoxLargesize(8Byte, only have when box size exceeding the range of 4Byte expression, then the value of BoxSize is 1)".
In program, you could first read 8 Byte and know the size of 'ftyp box', then seek the size and read 8 Byte to know if the next box is 'moov box'. If not 'moov', it shoud be 'mdat box', then seek cross 'mdat box' to find 'mdat box'...
But I want to use 'ffprobe' to find the position of 'moov'. I use 'ffprobe -v trace demo.mp4', and output is like below
[mov,mp4,m4a,3gp,3g2,mj2 # 0x7fc8fd000e00] Format mov,mp4,m4a,3gp,3g2,mj2 probed with size=2048 and score=100
[mov,mp4,m4a,3gp,3g2,mj2 # 0x7fc8fd000e00] type:'ftyp' parent:'root' sz: 28 8 41044500
[mov,mp4,m4a,3gp,3g2,mj2 # 0x7fc8fd000e00] ISO: File Type Major Brand: mp42
[mov,mp4,m4a,3gp,3g2,mj2 # 0x7fc8fd000e00] type:'moov' parent:'root' sz: 17943 36 41044500
[mov,mp4,m4a,3gp,3g2,mj2 # 0x7fc8fd000e00] type:'mvhd' parent:'moov' sz: 108 8 17935
I want to know the meaning of type:'ftyp' parent:'root' sz: 28 8 41044500:
type:'ftyp' parent:'root'is easy to know, sz: 28 8 41044500 is really make me confused, I guess 28 is size of ftyp box,but the meaning of 8 41044500 is what?
Could you explain the meaning of sz: 28 8 41044500, and where could find the doc?
Consider
type:'mvhd' parent:'moov' sz: 108 8 17935
type and parent represent the type of the current and parent box respectively.
There are three values for sz (size).
The first value, 108 represents the total size of the current box, including the header.
The second value, 8, represents the starting offset of the box data relative to the start of the box header. This is needed because box size can be 8 bytes and box type can have a UUID, in which case, may be up to 20 bytes long. This offset will be non-zero even if the box has no data e.g. free.
The third value, 17935, is the data size of the parent box.
I started my project with the NCBI standalone BLAST and used the -outfmt 17 option. For my purpose that formatting is extremely helpful. However, I had to change to Biopython and I'm now using qblast to align my sequences to the NCBI NT database. Can I save/convert the qblast XML in a format which is comparable to the NCBI BLAST standalone -outfmt 17 format?
Thank you very much for your help!
Cheers,
Philipp
I'm going to assume you meant -outfmt 7 and you need an output with columns.
from Bio.Blast import NCBIWWW, NCBIXML
# This is the BLASTN query which returns an XML handler in a StringIO
r = NCBIWWW.qblast(
"blastn",
"nr",
"ACGGGGTCTCGAAAAAAGGAGAATGGGATGAGAAGGATATATGGGTAGTGTCATTTTTTAACTTGCAGAT" +
"TTCATCCTAGTCTTCCAGTTATCGTTTCCTAGCACTCCATGTTCCCAAGATAGTGTCACCACCCCAAGGA" +
"CTCTCTCTCATTTTCTTTGCCTGGGCCCTCTTTCTACTGAGGAGTCGTGGCCTTCCATCAGTAGAAGCCG",
expect=1E-5)
# Now we read that XML extracting the info
for record in NCBIXML.parse(r):
for alignment in record.alignments:
for hsp in alignment.hsps:
cols = "{}\t" * 10
print(cols.format(hsp.positives / hsp.align_length,
hsp.align_length,
hsp.align_length - hsp.positives,
hsp.gaps,
hsp.query_start,
hsp.query_end,
hsp.sbjct_start,
hsp.sbjct_end,
hsp.expect,
hsp.score))
Outputs something like:
1 210 0 0 1 210 89250 89459 8.73028e-102 420.0
0 206 19 2 5 210 46259 46462 5.16461e-73 314.0
1 210 0 0 1 210 68822 69031 8.73028e-102 420.0
0 206 19 2 5 210 25825 26028 5.16461e-73 314.0
1 210 0 0 1 210 65887 66096 8.73028e-102 420.0
...
I'm using stackprof to profile a sinatra application which uses Active Record. When I inspect the output of the generated files, I get the following:
[vagrant#localhost vagrant]$ bin/stackprof tmp/stackprof-cpu-5754-1468440335.dump --text --limit 10
==================================
Mode: cpu(1000)
Samples: 146 (1.35% miss rate)
GC: 7 (4.79%)
==================================
TOTAL (pct) SAMPLES (pct) FRAME
19 (13.0%) 18 (12.3%) ActiveSupport::Subscriber#start
10 (6.8%) 10 (6.8%) ActiveRecord::Timestamp#current_time_from_proper_timezone
13 (8.9%) 9 (6.2%) Logger#add
285 (195.2%) 5 (3.4%) Statsd#time
5 (3.4%) 5 (3.4%) block in ActiveRecord::ConnectionAdapters::AbstractMysqlAdapter#execute
6 (4.1%) 5 (3.4%) ActiveRecord::LazyAttributeHash#[]
12 (8.2%) 5 (3.4%) ActiveSupport::Subscriber#finish
4 (2.7%) 4 (2.7%) ActiveRecord::Relation#initialize_copy
6 (4.1%) 4 (2.7%) block (2 levels) in Class#class_attribute
3 (2.1%) 3 (2.1%) Logger::Formatter#format_datetime
When I subscribe and log the notifications, they are simply AR query notifications, which I don't care about at the moment.
It also appears that ActiveSupport::Subscribers / notifications are a performance bottleneck. Is there a way to disable turn these via an ActiveSupport configuration?
I am using:
Firefox 30
selenium-server-standalone-2.43.1.jar
Xvfb
Ubuntu Headless
Lineman grunt spec-e2e
I am able to run Xvfb, Firefox, and lineman grunt spec-e2e with no errors.
On all terminals I run export DISPLAY=:10
I run Xvfb :10 -ac in one terminal with no issues, I see:
Initializing built-in extension Generic Event Extension
Initializing built-in extension SHAPE
Initializing built-in extension MIT-SHM
Initializing built-in extension XInputExtension
Initializing built-in extension XTEST
Initializing built-in extension BIG-REQUESTS
Initializing built-in extension SYNC
Initializing built-in extension XKEYBOARD
Initializing built-in extension XC-MISC
Initializing built-in extension SECURITY
Initializing built-in extension XINERAMA
Initializing built-in extension XFIXES
Initializing built-in extension RENDER
Initializing built-in extension RANDR
Initializing built-in extension COMPOSITE
Initializing built-in extension DAMAGE
Initializing built-in extension MIT-SCREEN-SAVER
Initializing built-in extension DOUBLE-BUFFER
Initializing built-in extension RECORD
Initializing built-in extension DPMS
Initializing built-in extension Present
Initializing built-in extension DRI3
Initializing built-in extension X-Resource
Initializing built-in extension XVideo
Initializing built-in extension XVideo-MotionCompensation
Initializing built-in extension SELinux
Initializing built-in extension GLX
[dix] Could not init font path element /usr/share/fonts/X11/cyrillic, removing from list!
On a separate terminal, I run Firefox:
one#node ~/github/load-balancer-service/app/js/loadbalancer/controllers $ firefox
(process:16020): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed
Xlib: extension "RANDR" missing on display ":10".
Finally, in lineman I run (with a additional session of lineman run also):
one#node ~/github/load-balancer-service $ lineman grunt spec-e2e
Running "spec-e2e" task
Starting selenium standalone server...
Selenium standalone server started at http://10.14.13.161:42182/wd/hub
one#node ~/github/load-balancer-service $
But the issue I am having is there is no output going to the terminal window that is running firefox. When I run the spec-e2e, I do see the Xvfb terminal window have this output:
6 XSELINUXs still allocated at reset
SCREEN: 0 objects of 256 bytes = 0 total bytes 0 private allocs
DEVICE: 0 objects of 96 bytes = 0 total bytes 0 private allocs
CLIENT: 0 objects of 136 bytes = 0 total bytes 0 private allocs
WINDOW: 0 objects of 32 bytes = 0 total bytes 0 private allocs
PIXMAP: 1 objects of 16 bytes = 16 total bytes 0 private allocs
GC: 4 objects of 16 bytes = 64 total bytes 0 private allocs
CURSOR: 1 objects of 8 bytes = 8 total bytes 0 private allocs
TOTAL: 6 objects, 88 bytes, 0 allocs
1 PIXMAPs still allocated at reset
PIXMAP: 1 objects of 16 bytes = 16 total bytes 0 private allocs
GC: 4 objects of 16 bytes = 64 total bytes 0 private allocs
CURSOR: 1 objects of 8 bytes = 8 total bytes 0 private allocs
TOTAL: 6 objects, 88 bytes, 0 allocs
4 GCs still allocated at reset
GC: 4 objects of 16 bytes = 64 total bytes 0 private allocs
CURSOR: 1 objects of 8 bytes = 8 total bytes 0 private allocs
TOTAL: 5 objects, 72 bytes, 0 allocs
1 CURSORs still allocated at reset
CURSOR: 1 objects of 8 bytes = 8 total bytes 0 private allocs
TOTAL: 1 objects, 8 bytes, 0 allocs
1 CURSOR_BITSs still allocated at reset
TOTAL: 0 objects, 0 bytes, 0 allocs
But I do not see the output of the spec-e2e going to the firefox window.
Must use selenium/selenium-server-standalone-2.42.2.jar and not other versions.
Analyzing heap dump of tomcat app that based hibernate 4.3.1.final + `Spring 4'
shows that there is a leak on
org.hibernate.internal.SessionFactoryImpl it seems related to with MetaModel (maybe meta model with #embeddedId)
Does any one have experience that ?
Thanks ,
Alon
some info from dump :
Class Name | Shallow Heap| Retained Heap
org.hibernate.internal.SessionFactoryImpl # 0x7839de890
136 8,109,256
\factory org.hibernate.type.TypeFactory$TypeScopeImpl # 0x7839de880
16 16
.\typeScope org.hibernate.type.ComponentType # 0x783d8c760
56 616
..\hibernateType org.hibernate.jpa.internal.metamodel.EmbeddableTypeImpl # 0x783d8c3f8
48 1,216
...\attributeType org.hibernate.jpa.internal.metamodel.SingularAttributeImpl$Identifier # 0x783d8c338
40 40
....\id class org.jpp.domain.security.ProjectPermission_ # 0x784134cf8
8 8
.....\[3985] java.lang.Object[10240] # 0x784ecd118
40,976 1,087,264
......\elementData java.util.Vector # 0x7832e2680
32 1,087,296
.......\classes org.apache.catalina.loader.WebappClassLoader # 0x7832c76c0
184 1,454,824
........+<classloader> class com.mysql.jdbc.AbandonedConnectionCleanupThread # 0x783bbda40