Issues installing current master branch

[christianhuth]

As it was not possible to install the 19.0 release with the official release files, i tried to install from the current master branch.

While compiling the R packages i receive the following error:
cannot open URL 'http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.26.0.tar.gz': HTTP status was '404 Not Found'

After some investigation i found out, that Bioconductor only hosts v1.28.0. So http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.28.0.tar.gz seems to work.

Should we use 1.28.0 or 1.26.0 from another location?

[christianhuth]

For people looking at this error in the future:

After changing the path to QDNAseq in transmart-data/R/other_pkg.R i was not able to continue with the installation script, because of the following error:

------------------------------------------------------------
|  Checking for required folders and files for the R install
------------------------------------------------------------
The R package at /home/transmart/transmart/transmart-data/R/root/lib/R/library/WGCNA
  is required and does not exist; this should have been created
  in the 'buildR' step of the install; repeat that step
The R package at /home/transmart/transmart/transmart-data/R/root/lib/R/library/CGHtest
  is required and does not exist; this should have been created
  in the 'buildR' step of the install; repeat that step
The R package at /home/transmart/transmart/transmart-data/R/root/lib/R/library/CGHtestpar
  is required and does not exist; this should have been created
  in the 'buildR' step of the install; repeat that step
There are 3 R/BioConductor packages missing

i was able to solve this by running:

cd ~/transmart/transmart-data
cp vars.sample vars
. ./vars
make -C R install_packages

after this i was able to run ./Scripts/install-ubuntu20/InstallTransmart.sh 2>&1 | tee ~/install.log again

[christianhuth]

Next error:

++++++++++++++++++++++++++++++++++++++++++++++++++++
+  Set up basic PostgreSQL; supports transmart login
++++++++++++++++++++++++++++++++++++++++++++++++++++
DROP ROLE
CREATE ROLE
Setting up PostgreSQL database
make -C ddl/postgres/GLOBAL createdb
make[1]: Entering directory '/home/transmart/transmart/transmart-data/ddl/postgres/GLOBAL'
test `/usr/bin/psql -v ON_ERROR_STOP=1 --single-transaction -X -d template1 -c "select exists (select datname from pg_database where datname = 'transmart')" -tA` \
                = 'f' || (echo -e "\e[31mERROR\e[m: Database transmart already exists or connection error"; false)
/usr/bin/psql -v ON_ERROR_STOP=1 -X -d template1 -c "CREATE DATABASE transmart TEMPLATE template0 \
                ENCODING='UTF-8' LC_COLLATE='en_US.UTF-8'"
ERROR:  invalid locale name: "en_US.UTF-8"
make[1]: *** [Makefile:49: createdb] Error 1
make[1]: Leaving directory '/home/transmart/transmart/transmart-data/ddl/postgres/GLOBAL'
make: *** [Makefile:4: postgres] Error 2

[christianhuth]

Solution for the last error:

sudo locale-gen en_US.UTF-8
sudo systemctl restart postgresql

[christianhuth]

Next error:

make[3]: Entering directory '/home/transmart/transmart/transmart-data/data/common'
php gen_makefile.php searchapp > searchapp/makefile.inc
../../common/i2b2hive/makefile.inc:2: /home/pmr/git-master/transmart/transmart-data/data/common/makefile_schemas.inc: No such file or directory
make[3]: *** No rule to make target '/home/pmr/git-master/transmart/transmart-data/data/common/makefile_schemas.inc'.  Stop.
make[3]: Leaving directory '/home/transmart/transmart/transmart-data/data/postgres/i2b2hive'
make[2]: *** [../common/makefile.inc:37: load_schema_i2b2hive] Error 2
make[3]: Leaving directory '/home/transmart/transmart/transmart-data/data/common'
make[3]: Leaving directory '/home/transmart/transmart/transmart-data/data/common'
make[2]: Leaving directory '/home/transmart/transmart/transmart-data/data/postgres'
make[1]: *** [Makefile:9: postgres_load] Error 2
make[1]: Leaving directory '/home/transmart/transmart/transmart-data'
make: *** [Makefile:5: postgres] Error 2

[christianhuth]

I found out that these files need to be changed:

wrong

data/oracle/biomart_user/Makefile:COMMON_DIR := /home/pmr/git-master/transmart/transmart-data/data/common
data/oracle/i2b2hive/Makefile:COMMON_DIR := /home/pmr/git-master/transmart/transmart-data/data/common
data/postgres/biomart_user/Makefile:COMMON_DIR := /home/pmr/git-master/transmart/transmart-data/data/common
data/postgres/i2b2hive/Makefile:COMMON_DIR := /home/pmr/git-master/transmart/transmart-data/data/common

correct

data/oracle/biomart_user/Makefile:COMMON_DIR := /home/transmart/transmart/transmart-data/data/common
data/oracle/i2b2hive/Makefile:COMMON_DIR := /home/transmart/transmart/transmart-data/data/common
data/postgres/biomart_user/Makefile:COMMON_DIR := /home/transmart/transmart/transmart-data/data/common
data/postgres/i2b2hive/Makefile:COMMON_DIR := /home/transmart/transmart/transmart-data/data/common

to continue with the installation progress you have to delete the already created transmart database and roles. The easiest way for me was to completely uninstall postgresql and remove the postgres data directories from the host:

sudo apt-get purge -y postgresql*
sudo rm -rf /var/lib/postgresql

[christianhuth]

Here goes the next error:

Caught: java.sql.SQLException: No suitable driver found for jdbc:postgresql://localhost:5432/transmart
java.sql.SQLException: No suitable driver found for jdbc:postgresql://localhost:5432/transmart
        at java_sql_DriverManager$getConnection.call(Unknown Source)
        at read_cms_file.run(read_cms_file.groovy:28)
make[3]: *** [Makefile:8: read_cms_file] Error 1

[christianhuth]

i "solved" this problem by removing the execution of the make receipt read_cms_file

commented in transmart-data/data/postgres/biomart_user/Makefile:

#read_cms_file:
#               groovy -cp '$(CP_PSQL)' read_cms_file.groovy

removed in transmart-data/data/common/biomart_user/makefile.inc:

load: load_cms_file load_cms_section read_cms_file

load: load_cms_file load_cms_section

[christianhuth]

Next error:

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/home/transmart/transmart/transmart-data/samples/studies/build_datasets_index.groovy: 84: Error during @TupleConstructor processing: 'excludes' property 'URL' does not exist.
 @ line 84, column 1.
   @Canonical(excludes = 'URL')
   ^

/home/transmart/transmart/transmart-data/samples/studies/build_datasets_index.groovy: 84: Error during @EqualsAndHashCode processing: 'excludes' property 'URL' does not exist.
 @ line 84, column 1.
   @Canonical(excludes = 'URL')
   ^

2 errors

make[2]: *** [Makefile:5: datasets] Error 1

[christianhuth]

i "solved" this problem by commenting line 84 in transmart-data/samples/studies/build_datasets_index.groovy

//@Canonical(excludes = 'URL')

[christianhuth]

Next error:

ERROR: Error fetching data sets for feed HttpIndexFeed(http://localhost/datasets/OSPF/ospf_index): http://localhost/datasets/OSPF/ospf_index
make[2]: *** [Makefile:5: datasets] Error 1

[christianhuth]

I edited transmart-data/samples/studies/public-feeds and removed line 8:

http-index      http://localhost/datasets/OSPF/ospf_index

[christianhuth]

The installation now stops with

PostgreSQL does not appear to be running; start it
  with the command: sudo /etc/init.d/postgresql restart

[christianhuth]

I gave the solution already in another issue. Check it out here: #22 (comment)

[christianhuth]

But there is already the next problem...

-------------------------------------------------------------
|  Checking for required transmart/grails configuration files
-------------------------------------------------------------
The file at /var/lib/tomcat9/.grails/transmartConfig/Config.groovy
  is required and does not exist; this should have been created
  in the 'buildConfig' step of the install; repeat that step
The file at /var/lib/tomcat9/.grails/transmartConfig/DataSource.groovy
  is required and does not exist; this should have been created
  in the 'buildConfig' step of the install; repeat that step