ensembl-gh-mirror issueshttps://gitlab.ebi.ac.uk/groups/ensembl-gh-mirror/-/issues2018-03-21T12:18:10Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/70VCF/BCF returning the raw header2018-03-21T12:18:10ZMarek SzubaVCF/BCF returning the raw header*Created by: avullo*
This is a request coming from the Ensembl variation team, which would allow them to start supporting BCF reading via htslib in the ensembl-io framework.*Created by: avullo*
This is a request coming from the Ensembl variation team, which would allow them to start supporting BCF reading via htslib in the ensembl-io framework.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/33Error while installing VEP2016-08-16T08:07:36ZMarek SzubaError while installing VEP*Created by: raonyguimaraes*
Hi I just received this error while installing VEP from ensembl-tools. What can be wrong?
```
** GET https://codeload.github.com/Ensembl/Bio-DB-HTS/zip/master ==> 200 OK (2s)
- unpacking ./Bio/tmp/biodbhts...*Created by: raonyguimaraes*
Hi I just received this error while installing VEP from ensembl-tools. What can be wrong?
```
** GET https://codeload.github.com/Ensembl/Bio-DB-HTS/zip/master ==> 200 OK (2s)
- unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/
./Bio/tmp/Bio-HTS-master - moving files to ./biodbhts
ERROR: Could not move directory
No such file or directory at INSTALL.pl line 563.
```
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/78Reduce Module::Build version dependency2018-07-11T13:40:53ZMarek SzubaReduce Module::Build version dependency*Created by: jmarshall*
CentOS 7.5 (released in May) provides Module::Build 0.40.05.
Bio-DB-HTS currently requires Module::Build 0.42, so is difficult to install on the current version of CentOS. You need to either install a bespoke ...*Created by: jmarshall*
CentOS 7.5 (released in May) provides Module::Build 0.40.05.
Bio-DB-HTS currently requires Module::Build 0.42, so is difficult to install on the current version of CentOS. You need to either install a bespoke Module::Build or downgrade Bio-DB-HTS's requirements before trying to build it.
M::B 0.42 is functionally identical to 0.40_11, and there doesn't appear to be too much of significance for people installing Bio-DB-HTS in M::B Changes between 0.40 and 0.40_11.
Is there a particular M::B feature that Bio-DB-HTS depends on? It looks a bit like the 0.42 dependency is there simply because relevant files were generated using 0.42xy which produced `configure_requires` entries accordingly (see 115fc165b1d2782c99673894daf3eab88be36878), and is not a strict Bio-DB-HTS requirement.
35cec2c00a40f47cb174315847b4b25226967b59 attempted to reduce the M::B requirement to 0.38, but was reverted in e9cdd6fe66ec7fe952b06ff46936efc3fef85fa5 as “the 0.38 seemed to be ignored on target machines anyway”. It was ignored because the corresponding lines in META.json and META.yml also needed to be changed for this to be effective.
Would you consider reducing the Module::Build version requirement so that Bio-DB-HTS builds out of the box on CentOS 7? I would recommend one of 0.38 (per @rishidev), 0.40, or something in between if there are other common distributions that can be accommodated too. (CentOS 6 provided M::B 0.35.)
This can be done by changing one line in each of Build.PL, META.json, and META.yml — grep for `Module::Build.*42[^0-9]`.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/75Illegal versioning scheme2019-04-26T12:29:28ZMarek SzubaIllegal versioning scheme*Created by: mkszuba*
The current Bio-DB-HTS versioning scheme is, sadly, incompatible with what Perl expects, and according to a Perl-veteran colleague of mine it is in fact illegal on CPAN, where this module has been present since ver...*Created by: mkszuba*
The current Bio-DB-HTS versioning scheme is, sadly, incompatible with what Perl expects, and according to a Perl-veteran colleague of mine it is in fact illegal on CPAN, where this module has been present since version 2.10. Specifically, Perl runtime expects version numbers in the form of x.yy to be floating-point numbers - meaning that from the runtime's point of view, 2.10 == 2.1 < 2.9.
Demonstration:
1. Install Bio-DB-HTS version 2.10
2. perl -e 'use Bio::DB::HTS 2.5'
Expected result: in the current versioning scheme 2.10 > 2.5 so it should work.
Actual result: "Bio::DB::HTS version 2.5 required--this is only version 2.10".
At least as far as CPAN is concerned there is no actual violation yet (2.10 < 2.11), however there might be trouble once the module has reached version 2.20 according to the current scheme.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/67Multiple, conflicting, index memory release attempts may lead to segfault2018-03-20T14:29:21ZMarek SzubaMultiple, conflicting, index memory release attempts may lead to segfault*Created by: avullo*
Some glitches in the way index memory is released.
From @jmarshall:
--
"Running the t/03cram.t tests under valgrind shows a double-free bug (the cram index is freed via both hts_close and hts_idx_destroy), pres...*Created by: avullo*
Some glitches in the way index memory is released.
From @jmarshall:
--
"Running the t/03cram.t tests under valgrind shows a double-free bug (the cram index is freed via both hts_close and hts_idx_destroy), present also on the master branch and with any version of HTSlib, that occasionally leads to a segfault (only once in my attempts to reproduce this). I suspect it is this that caused the failed travis run, which ran the t/03cram.t tests twice: once successfully (via ./Build test) and once with a segfault (via travisci/harness.sh)."https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/76Bus error/segfault on freebsd2019-02-22T10:36:07ZMarek SzubaBus error/segfault on freebsd*Created by: avullo*
From CPAN testers report, the latest changes on the VCF interface have trouble with some freebsd systems. Compilation works, but the test suite fails on system 10 and 11:
..
t/05vcf.t ........
Failed 130/177 su...*Created by: avullo*
From CPAN testers report, the latest changes on the VCF interface have trouble with some freebsd systems. Compilation works, but the test suite fails on system 10 and 11:
..
t/05vcf.t ........
Failed 130/177 subtests
..
t/10leak.t .......
Failed 1/6 subtests
Test Summary Report
-------------------
t/05vcf.t (Wstat: 10 Tests: 47 Failed: 0)
Non-zero wait status: 10
Parse errors: Bad plan. You planned 177 tests but ran 47.
t/10leak.t (Wstat: 10 Tests: 5 Failed: 0)
Non-zero wait status: 10
Parse errors: Bad plan. You planned 6 tests but ran 5.
..
Status 10 means bus error. Depending on the system it could also be a segmentation fault here.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/54'missing SAM header' when opening SAM files2018-03-13T14:15:45ZMarek Szuba'missing SAM header' when opening SAM files*Created by: AlexanderDilthey*
Hi,
There seems to be an issue with iterating over alignments in a SAM file. I get the errors
````
[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 4
````
although there are ...*Created by: AlexanderDilthey*
Hi,
There seems to be an issue with iterating over alignments in a SAM file. I get the errors
````
[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 4
````
although there are headers.
Code for reproducing the problem:
````
use Bio::DB::HTS;
my $sam = Bio::DB::HTS->new(-bam => 'test.sam');
my $alignment_iterator = $sam->features(-iterator => 1);
$alignment_iterator->next_seq;
````
and test.sam:
````
@HD VN:1.5 SO:coordinate
@SQ SN:ref LN:100
r001 99 ref 1 30 1M3D2M = 37 3 TAT *
r002 99 ref 1 30 1M2D2M = 37 3 TAT *
````
samtools can view the SAM without problems.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/72Bio__DB__HTS__VCFfile now defined twice2018-05-01T06:42:33ZMarek SzubaBio__DB__HTS__VCFfile now defined twice*Created by: jgrigonis*
lib/Bio/DB/HTS.xs:80: error: redefinition of typedef ‘Bio__DB__HTS__VCFfile’
lib/Bio/DB/HTS.xs:72: note: previous declaration of ‘Bio__DB__HTS__VCFfile’ was here
Offensive code:
typedef htsFile* ...*Created by: jgrigonis*
lib/Bio/DB/HTS.xs:80: error: redefinition of typedef ‘Bio__DB__HTS__VCFfile’
lib/Bio/DB/HTS.xs:72: note: previous declaration of ‘Bio__DB__HTS__VCFfile’ was here
Offensive code:
typedef htsFile* Bio__DB__HTS__VCFfile;
typedef vcfFile* Bio__DB__HTS__VCFfile;
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/77Trouble installing under Ubuntu and Windows2019-04-26T12:31:00ZMarek SzubaTrouble installing under Ubuntu and Windows*Created by: prishly*
Hi,
I'm having trouble installing Bio::DB::HTS under Ubuntu and Windows 10.
Last part of the output is:
"Warning: No success on command[C:\Strawberry\perl\bin\perl.exe Build.PL]
AVULLO/Bio-DB-HTS-2.11.tar.gz
...*Created by: prishly*
Hi,
I'm having trouble installing Bio::DB::HTS under Ubuntu and Windows 10.
Last part of the output is:
"Warning: No success on command[C:\Strawberry\perl\bin\perl.exe Build.PL]
AVULLO/Bio-DB-HTS-2.11.tar.gz
C:\Strawberry\perl\bin\perl.exe Build.PL -- NOT OK
Stopping: 'install' failed for 'Bio::DB::HTS'.
Failed during this command:
AVULLO/Bio-DB-HTS-2.11.tar.gz : writemakefile NO 'C:\Strawberry\perl\bin\perl.exe Build.PL' returned status 512"
On Ubuntu it's the same message except that the line "C:\Strawberry\perl\bin\perl.exe Build.PL -- NOT OK" is replaced with "/usr/bin/perl Build.PL -- NOT OK"https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/85INSTALL.pl from cloned repository failing on Ubuntu/perl5.22.12019-03-07T14:32:29ZMarek SzubaINSTALL.pl from cloned repository failing on Ubuntu/perl5.22.1*Created by: pmcarlton*
I'm trying to install Bio-DB-HTS as a prerequisite of [BRASS](https://github.com/cancerit/BRASS). I'm using Ubuntu 16.04, perl 5.22.1 (details in Gist at https://gist.github.com/pmcarlton/19dd97bf075160e672938625...*Created by: pmcarlton*
I'm trying to install Bio-DB-HTS as a prerequisite of [BRASS](https://github.com/cancerit/BRASS). I'm using Ubuntu 16.04, perl 5.22.1 (details in Gist at https://gist.github.com/pmcarlton/19dd97bf075160e672938625b700b77d)
I've cloned the git repo and tried to install from within the cloned directory.
`perl INSTALL.pl` is failing with: (see gist for complete log)
```
...
[fai_load] build FASTA index.
panic: sv_setpvn called with negative strlen -1 at t/07cramwrite.t line 117.
panic: sv_setpvn called with negative strlen -1 at t/08bamwrite.t line 117.
Failed 4/11 test programs. 0/397 subtests failed.
Build test failed. Not continuing at INSTALL.pl line 198.
cannot remove path when cwd is /tmp/DaEfuzO1DW/Bio-DB-HTS for /tmp/DaEfuzO1DW: at /usr/share/perl/5.22/File/Temp.pm line 778.
```
I'm not sure how to go about fixing it, so any advice would be appreciated. Thanks
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/81INSTALL.pl assumes sudo is installed but fails to install anything2019-03-08T10:54:09ZMarek SzubaINSTALL.pl assumes sudo is installed but fails to install anything*Created by: eburgueno*
The `INSTALL.pl` script assumes `sudo` is installed in the system, and warns "If this step fails... run this script again as superuser". If `sudo` is not installed, the script does not install anything, and print...*Created by: eburgueno*
The `INSTALL.pl` script assumes `sudo` is installed in the system, and warns "If this step fails... run this script again as superuser". If `sudo` is not installed, the script does not install anything, and prints the success message. Running the script as `root` does not actually do anything.
From a Docker container running `ubuntu:bionic` (ie: `docker run -ti --rm ubuntu:bionic bash`):
```
# apt-get update && apt-get -y install bioperl gcc git libbz2-dev liblzma-dev libmodule-build-perl make wget zlib1g-dev
# id
uid=0(root) gid=0(root) groups=0(root)
# cat /etc/issue
Ubuntu 18.04.1 LTS \n \l
# cd /opt ; wget https://github.com/Ensembl/Bio-DB-HTS/archive/2.11.tar.gz ; tar -xzf 2.11.tar.gz ; cd Bio-DB-HTS-2.11; ./INSTALL.pl
/opt/Bio-DB-HTS-2.11
*** Performing build in /tmp/FyEvcsvHL7 ***
(...)
*** Installing Bio::DB::HTS using sudo. You will be asked for your password. ***
*** If this step fails because sudo isn't installed, go back and run this script again as superuser. ***
*** Bio::DB::HTS v2.11 is now installed. ***
# ls /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/
ls: cannot access '/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/': No such file or directory
```
Behaviour when `sudo` is installed. Note that I am still `root`, so using `sudo` here is redundant.
```
# apt-get -y install sudo
# ./INSTALL.pl
/opt/Bio-DB-HTS-2.11
*** Performing build in /tmp/AoqhX1iJBN ***
(...)
*** Installing Bio::DB::HTS using sudo. You will be asked for your password. ***
*** If this step fails because sudo isn't installed, go back and run this script again as superuser. ***
Building Bio-DB-HTS
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/auto/Bio/DB/HTS/HTS.so
(...)
*** Bio::DB::HTS v2.11 is now installed. ***
```
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/82Problems when installing Bio::DB::HTS, possibly due to memory leak2019-02-22T13:00:12ZMarek SzubaProblems when installing Bio::DB::HTS, possibly due to memory leak*Created by: AndreVidas*
Hi Ensembl team.
I'm trying to install Bio::DB::HTS, but I get the following error during the installation:
sudo cpanm Bio::DB::HTS
Password:
--> Working on Bio::DB::HTS
Fetching http://www.cpan.org...*Created by: AndreVidas*
Hi Ensembl team.
I'm trying to install Bio::DB::HTS, but I get the following error during the installation:
sudo cpanm Bio::DB::HTS
Password:
--> Working on Bio::DB::HTS
Fetching http://www.cpan.org/authors/id/A/AV/AVULLO/Bio-DB-HTS-2.11.tar.gz ... OK
Configuring Bio-DB-HTS-2.11 ... OK
Broadcast Message from _distnote@SUND33194
(no tty) at 15:41 CET...
perl(90621,0x11b35c5c0) malloc: *** error for object 0x7fe849915dd0: pointer be
ing realloc'd was not allocated
FAIL
! Installing Bio::DB::HTS failed. See /Users/gdn417/.cpanm/work/1550673676.90567/build.log for details. Retry with --force to force install it.
Broadcast Message from _distnote@SUND33194
(no tty) at 15:41 CET...
perl(90627,0x1103895c0) malloc: *** error for object 0x7fca65d00840: pointer be
ing realloc'd was not allocated
SUND33194:bin gdn417$ cpan -D Bio
Reading '/Users/gdn417/.cpan/Metadata'
Database was generated on Tue, 19 Feb 2019 23:17:03 GMT
Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146.
SUND33194:bin gdn417$ cpan -D Bio/DB/HTS
Reading '/Users/gdn417/.cpan/Metadata'
Database was generated on Tue, 19 Feb 2019 23:17:03 GMT
Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146.
SUND33194:bin gdn417$ cpan -D Bio/DB/HTS.pm
Reading '/Users/gdn417/.cpan/Metadata'
Database was generated on Tue, 19 Feb 2019 23:17:03 GMT
Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146.
SUND33194:bin gdn417$ cpan -D HEJ
Reading '/Users/gdn417/.cpan/Metadata'
Database was generated on Tue, 19 Feb 2019 23:17:03 GMT
Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146.
[installedModules.txt](https://github.com/Ensembl/Bio-DB-HTS/files/2885246/installedModules.txt)
Do you have any idea of why this is happening? From what I could read from other posts on stackoverflow etc. this might have something to do with memory leak in C.
I have attached a list of my installed modules.
Best,
Andréhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/86Install fails with "cannot remove path when cwd is /tmp/SokefcfsUv/Bio-DB-HTS"2019-03-22T11:38:24ZMarek SzubaInstall fails with "cannot remove path when cwd is /tmp/SokefcfsUv/Bio-DB-HTS"*Created by: MurphyDavid*
On an ubuntu server I've been trying to install Bio-DB-HT
Running these commands
```
git clone https://github.com/Ensembl/Bio-DB-HT
cd Bio-DB-HTS/
sudo perl INSTALL.pl
```
It fails with this error....*Created by: MurphyDavid*
On an ubuntu server I've been trying to install Bio-DB-HT
Running these commands
```
git clone https://github.com/Ensembl/Bio-DB-HT
cd Bio-DB-HTS/
sudo perl INSTALL.pl
```
It fails with this error. it does not prompt for password as I was already running with sudo.
Running the same command without sudo gives a prompt but the same error
switching to root with sudo su root gives the same results.
```
*** Installing Bio::DB::HTS using sudo. You will be asked for your password. ***
*** If this step fails because sudo isn't installed, go back and run this script again as superuser. ***
Couldn't install system-wide: 0 at INSTALL.pl line 212.
cannot remove path when cwd is /tmp/SokefcfsUv/Bio-DB-HTS for /tmp/SokefcfsUv: at /usr/share/perl/5.22/File/Temp.pm line 778.
```https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/80Issues running in ubuntu2019-03-07T11:45:28ZMarek SzubaIssues running in ubuntu*Created by: juancrescente*
I installed using perl INSTALL.pl because using cpan I always got a problem with htslib. So now when running there's still an issue
machine@1 :~/tephra$ tephra all -c tephra_config.yml
Can't load '/usr/...*Created by: juancrescente*
I installed using perl INSTALL.pl because using cpan I always got a problem with htslib. So now when running there's still an issue
machine@1 :~/tephra$ tephra all -c tephra_config.yml
Can't load '/usr/local/lib/x86_64-linux-gnu/perl/5.22.1/auto/Bio/DB/HTS/HTS.so' for module Bio::DB::HTS: libhts.so.2: cannot open shared object file: No such file or directory at /usr/lib/x86_64-linux-gnu/perl/5.22/DynaLoader.pm line 187.
at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71.
BEGIN failed--compilation aborted at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/share/perl/5.22.1/Tephra/Stats/Age.pm line 17.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.22.1/Tephra/Stats/Age.pm line 17.
Compilation failed in require at /usr/local/share/perl/5.22.1/Tephra/Command/age.pm line 11.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.22.1/Tephra/Command/age.pm line 11.
Compilation failed in require at /usr/local/share/perl/5.22.1/App/Cmd.pm line 194.
App::Cmd::_command("Tephra", HASH(0x1336f30)) called at /usr/local/share/perl/5.22.1/App/Cmd.pm line 171
App::Cmd::new("Tephra", HASH(0x1336f30)) called at /usr/local/bin/tephra line 25
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/92htslib 1.10 compatibility (released Dec2019)2020-09-23T11:20:46ZMarek Szubahtslib 1.10 compatibility (released Dec2019)*Created by: keiranmraine*
Can you confirm that Bio::DB::HTS is fully compatible with htslib 1.10?*Created by: keiranmraine*
Can you confirm that Bio::DB::HTS is fully compatible with htslib 1.10?https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/94Tests fail with htslib 1.112020-09-23T11:21:57ZMarek SzubaTests fail with htslib 1.11*Created by: keiranmraine*
Worked okay with 1.10.2 but no longer installs with htslib 1.11:
```
c_tests/02_bam_access_tests.c:32:19: error: conflicting types for ‘kputsn’
32 | static inline int kputsn(const char *p, int l, kstri...*Created by: keiranmraine*
Worked okay with 1.10.2 but no longer installs with htslib 1.11:
```
c_tests/02_bam_access_tests.c:32:19: error: conflicting types for ‘kputsn’
32 | static inline int kputsn(const char *p, int l, kstring_t *s)
| ^~~~~~
In file included from /install_tmp/tmp_htslib/htslib/hts.h:37,
from /install_tmp/tmp_htslib/htslib/sam.h:31,
from ./bam_access.h:26,
from c_tests/02_bam_access_tests.c:22:
/install_tmp/tmp_htslib/htslib/kstring.h:224:19: note: previous definition of ‘kputsn’ was here
224 | static inline int kputsn(const char *p, size_t l, kstring_t *s)
| ^~~~~~
c_tests/02_bam_access_tests.c:46:19: error: redefinition of ‘kputs’
46 | static inline int kputs(const char *p, kstring_t *s)
| ^~~~~
In file included from /install_tmp/tmp_htslib/htslib/hts.h:37,
from /install_tmp/tmp_htslib/htslib/sam.h:31,
from ./bam_access.h:26,
from c_tests/02_bam_access_tests.c:22:
/install_tmp/tmp_htslib/htslib/kstring.h:235:19: note: previous definition of ‘kputs’ was here
235 | static inline int kputs(const char *p, kstring_t *s)
| ^~~~~
c_tests/02_bam_access_tests.c: In function ‘test_bam_access_parse_header’:
c_tests/02_bam_access_tests.c:103:16: warning: unused variable ‘grp_stats’ [-Wunused-variable]
103 | stats_rd_t*** grp_stats;
| ^~~~~~~~~
c_tests/02_bam_access_tests.c:102:6: warning: unused variable ‘grps_size’ [-Wunused-variable]
102 | int grps_size = 0;
| ^~~~~~~~~
make: *** [<builtin>: c_tests/02_bam_access_tests] Error 1
```