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sestaton / tephra

A tool for discovering transposable elements and describing patterns of genome evolution
MIT License
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Makefile.PL error #39

Open dejonggr opened 5 years ago

dejonggr commented 5 years ago

Hi there,

I'm trying to install Tephra on a RHEL-based OS. I've downloaded the lastest version as per your Github instructions and I've installed all the core/per dependencies (I'm using perl v5.16.0 via perlbrew). However, I've run into this error when initiating the Makefile:

$ perl Makefile.PL
Generating a Unix-style Makefile
Writing Makefile for Tephra
Writing MYMETA.yml and MYMETA.json
=====> Configuring Tephra, this may take some time...
[ERROR]: move failed: Is a directory

It seems like it's happening shortly after the directory gt-1.5.10-Linux_x86_64-64bit-barebone (genome tools?) is unzipped but I can't find any reference to this in your makefiles.

Do you have any idea what might be causing this?

Thanks, Grant

sestaton commented 5 years ago

Can you show me the output of the commands you ran before this? Specifically, the install commands listed in the INSTALL file. I believe that will explain the issue.

Thanks, Evan

dejonggr commented 5 years ago

sudo yum groupinstall -y "Development Tools"

This resulted in a number of problems. I ended up opting to use: $ sudo yum --skip-broken groupinstall "Development tools" --setopt=group_package_types=mandatory,default,optional

Updated: mercurial.x86_64 0:1.4-5.el6_9

Skipped (dependency problems): createrepo_c.x86_64 0:0.10.0-2.el6 createrepo_c-libs.x86_64 0:0.10.0-2.el6 distribution-gpg-keys.noarch 0:1.31-1.el6 mock.noarch 0:1.3.5-1.el6 pyliblzma.x86_64 0:0.5.3-3.el6 python-requests.noarch 0:2.6.0-4.el6
python-six.noarch 0:1.9.0-2.el6 python2-distro.noarch 0:1.0.3-1.el6

Complete!

That was followed by the following: $ sudo yum install -y perl-App-cpanminus ncurses ncurses-devel gd-devel libdb-devel expat expat-devel zlib-devel java-1.7.0-openjdk

Loaded plugins: priorities, refresh-packagekit, security 157 packages excluded due to repository priority protections Setting up Install Process No package perl-App-cpanminus available. <-- (I found a workaround) Package ncurses-5.7-3.20090208.el6.x86_64 already installed and latest version Package ncurses-devel-5.7-3.20090208.el6.x86_64 already installed and latest version Package gd-devel-2.0.35-10.el6.x86_64 already installed and latest version No package libdb-devel available. <-- (Apparently db4 is the equivalent for my version of RHEL) Package expat-2.0.1-13.el6_8.x86_64 already installed and latest version Package expat-devel-2.0.1-13.el6_8.x86_64 already installed and latest version Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version Package 1:java-1.7.0-openjdk-1.7.0.221-2.6.18.0.el6_10.x86_64 already installed and latest version Nothing to do

I used perlbrew for everything else.

I've already installed BioPerl using: $ cpanm Bio::Perl

I tried this option anyway: $ echo "n" | cpanm -n Data::Stag DB_File Bio::Root::Version Bio::SearchIO::blastxml Bio::SearchIO::hmmer

but apparently some dependencies of the version in your command throw errors:

cpanm Bio::Perlecho "n" | cpanm -n Data::Stag DB_File Bio::Root::Version Bio::SearchIO::blastxml Bio::SearchIO::hmmer Data::Stag is up to date. (0.14) DB_File is up to date. (1.852) --> Working on Bio::Root::Version Fetching http://www.cpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.5.tar.gz ... OK Configuring BioPerl-1.7.5 ... OK ! Finding Bio::Perlecho on cpanmetadb failed. ==> Found dependencies: XML::LibXML, XML::LibXML::Reader --> Working on XML::LibXML Fetching http://www.cpan.org/authors/id/S/SH/SHLOMIF/XML-LibXML-2.0201.tar.gz ... OK ==> Found dependencies: Alien::Libxml2 --> Working on Alien::Libxml2 Fetching http://www.cpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.09.tar.gz ... OK Configuring Alien-Libxml2-0.09 ... ! Finding Bio::Perlecho () on mirror http://www.cpan.org failed. ! Couldn't find module or a distribution Bio::Perlecho ! Finding n on cpanmetadb failed. OK ! Finding n () on mirror http://www.cpan.org failed. ! Couldn't find module or a distribution n Building Alien-Libxml2-0.09 ... FAIL ! Installing Alien::Libxml2 failed. See /root/.cpanm/work/1561666793.11445/build.log for details. Retry with --force to force install it. ! Installing the dependencies failed: Module 'Alien::Libxml2' is not installed ! Bailing out the installation for XML-LibXML-2.0201. ! Installing the dependencies failed: Module 'XML::LibXML' is not installed, Module 'XML::LibXML::Reader' is not installed ! Bailing out the installation for BioPerl-1.7.5. Bio::SearchIO::blastxml is up to date. (1.70) --> Working on Bio::SearchIO::hmmer Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-SearchIO-hmmer-1.7.3.tar.gz ... OK Configuring Bio-SearchIO-hmmer-1.7.3 ... OK Building Bio-SearchIO-hmmer-1.7.3 ... OK Successfully installed Bio-SearchIO-hmmer-1.7.3 1 distribution installed

I haven't been able to get these modules installed. I didn't think they would be a problem considering I already have BioPerl installed but perhaps they're the culprit?

Looking at the log files it seems to be related to this error:

undefined reference to `gzopen64'

which is related to zlib and to be frank I have no idea how to go about fixing that.

sestaton commented 5 years ago

I think the command was issued with a typo. That is one issue. Try this:

echo "n" | cpanm -n  Data::Stag DB_File Bio::Root::Version Bio::SearchIO::blastxml Bio::SearchIO::hmmer
dejonggr commented 5 years ago

The result was the same unfortunately:

! Installing the dependencies failed: Module 'Alien::Libxml2' is not installed ! Bailing out the installation for XML-LibXML-2.0201. ! Installing the dependencies failed: Module 'XML::LibXML' is not installed, Module 'XML::LibXML::Reader' is not installed ! Bailing out the installation for BioPerl-1.7.5.

The build.log:

./.libs/libxml2.a(xmlIO.o): In function xmlGzfileOpenW': /root/.cpanm/work/1561669891.26214/Alien-Libxml2-0.09/_alien/extract_v_pA/libxml2-2.9.9/xmlIO.c:1184: undefined reference togzopen64' ./.libs/libxml2.a(xmlIO.o): In function xmlGzfileOpen_real': /root/.cpanm/work/1561669891.26214/Alien-Libxml2-0.09/_alien/extract_v_pA/libxml2-2.9.9/xmlIO.c:1107: undefined reference togzopen64' collect2: ld returned 1 exit status

dejonggr commented 5 years ago

I updated libxml2-devel and the cpanm/BioPerl command finished successfully.

The makefile.PL error is still present though:

perl Makefile.PL

Generating a Unix-style Makefile Writing Makefile for Tephra Writing MYMETA.yml and MYMETA.json =====> Configuring Tephra, this may take some time... [ERROR]: move failed: Is a directory

sestaton commented 5 years ago

Thanks for the update. Can you tell me which OS version and Perl version you are using?

perl -v

and

cat /etc/redhat-release
dejonggr commented 5 years ago

I'm using Scientific Linux release 6.2 (Carbon) and perl v5.16

sestaton commented 5 years ago

Hi, I've been looking at how to recreate this issue but this is not a common Linux variant, and so it is not available from any common cloud providers.

Let's try to start from scratch and see if you get the same error. From the Tephra directory, try these commands:

rm -rf ~/.tephra
make clean
perl Makefile.PL

And let me know what you get.

Thanks.

dejonggr commented 5 years ago

I get the same error as before.

Which line might be throwing the error?

I get the follow code from grepping MV from the Makefile:

`MV = mv

It seems like the first three lines run successfully based on the directory but maybe the last one isn't working?

This is what the directory looks like after the error:

Screen Shot 2019-07-02 at 3 23 45 PM