Issues setting up allbase for local development
abondrn opened this issue · 0 comments
abondrn commented
Apologies for poor formatting, I couldn't find an issue template (happy to open up a PR for that).
Issue Description
I was running the suggested setup command given in the README: git clone https://github.com/TimothyStiles/allbase && cd allbase && go test -v ./...
After download and installation of dependencies, the output of go test
was as follows:
? github.com/TimothyStiles/allbase [no test files]
? github.com/TimothyStiles/allbase/app [no test files]
? github.com/TimothyStiles/allbase/client [no test files]
# github.com/TimothyStiles/allbase/pkg/pathways.test
ld: warning: -no_pie is deprecated when targeting new OS versions
# github.com/TimothyStiles/allbase/pkg/rhea.test
ld: warning: -no_pie is deprecated when targeting new OS versions
# github.com/TimothyStiles/allbase/db/cmd.test
ld: warning: -no_pie is deprecated when targeting new OS versions
testing: warning: no tests to run
PASS
ok github.com/TimothyStiles/allbase/db/cmd 0.209s [no tests to run]
? github.com/TimothyStiles/allbase/pkg/config [no test files]
? github.com/TimothyStiles/allbase/pkg/db [no test files]
=== RUN TestFile
--- PASS: TestFile (6.27s)
=== RUN TestGetPageLinks
--- PASS: TestGetPageLinks (0.06s)
=== RUN TestTarball
--- PASS: TestTarball (0.88s)
PASS
ok github.com/TimothyStiles/allbase/pkg/download 7.525s
? github.com/TimothyStiles/allbase/pkg/env [no test files]
=== RUN TestGenbank
genbank_test.go:17: error creating test database: dial tcp [::1]:8000: connect: connection refused
=== RUN TestGenbank/TestGenbank
--- FAIL: TestGenbank (0.00s)
--- FAIL: TestGenbank/TestGenbank (0.00s)
panic: runtime error: invalid memory address or nil pointer dereference [recovered]
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x1268177]
goroutine 26 [running]:
testing.tRunner.func1.2({0x12aa6c0, 0x14fbe30})
/usr/local/Cellar/go/1.18.3/libexec/src/testing/testing.go:1389 +0x24e
testing.tRunner.func1()
/usr/local/Cellar/go/1.18.3/libexec/src/testing/testing.go:1392 +0x39f
panic({0x12aa6c0, 0x14fbe30})
/usr/local/Cellar/go/1.18.3/libexec/src/runtime/panic.go:838 +0x207
github.com/TimothyStiles/surrealdb%2ego.(*DB).send(0x0, {0x12eee47, 0x3}, {0xc0000feca0, 0x2, 0x2})
/Users/alex/go/pkg/mod/github.com/!timothy!stiles/surrealdb.go@v0.0.0-20220905012407-571308281d15/db.go:141 +0x77
github.com/TimothyStiles/surrealdb%2ego.(*DB).Use(...)
/Users/alex/go/pkg/mod/github.com/!timothy!stiles/surrealdb.go@v0.0.0-20220905012407-571308281d15/db.go:58
github.com/TimothyStiles/allbase/pkg/init.Genbank({0x136ede8?, _}, _, {0x0, {0xc0000c2540, 0x29}, {0xc0000a0280, 0x32}, {0x12f649b, 0x17}, ...})
/Users/alex/Documents/prog/e2ebio/allbase/pkg/init/genbank.go:49 +0x305
github.com/TimothyStiles/allbase/pkg/init.TestGenbank.func1(0xc00013e4e0)
/Users/alex/Documents/prog/e2ebio/allbase/pkg/init/genbank_test.go:44 +0x7b
testing.tRunner(0xc00013e4e0, 0xc000099110)
/usr/local/Cellar/go/1.18.3/libexec/src/testing/testing.go:1439 +0x102
created by testing.(*T).Run
/usr/local/Cellar/go/1.18.3/libexec/src/testing/testing.go:1486 +0x35f
FAIL github.com/TimothyStiles/allbase/pkg/init 0.192s
testing: warning: no tests to run
PASS
ok github.com/TimothyStiles/allbase/pkg/pathways 0.169s [no tests to run]
=== RUN TestReadRheaToUniprot
--- PASS: TestReadRheaToUniprot (0.00s)
PASS
ok github.com/TimothyStiles/allbase/pkg/rhea 0.314s
FAIL
System Environment
I am using go version go1.18.3 darwin/amd64
, and the above commands were executed under the default (dev
) branch.
Running system_profiler SPSoftwareDataType SPHardwareDataType
gives the following system details:
Software:
System Software Overview:
System Version: macOS 12.6.3 (21G419)
Kernel Version: Darwin 21.6.0
Boot Volume: Macintosh HD
Boot Mode: Normal
Secure Virtual Memory: Enabled
System Integrity Protection: Enabled
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i9
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 540.120.3~22
Next Steps
Here is what I will try to get up and running
- I notice there are some DB download commands under
db/cmd/root.go
, I have no idea how to run them but perhaps some tests depends on this. - If some tests depend on the service to be running, I would like to make it explicit that this is the case and either add helpful failure messages, or allow them to be disabled via environment variable.
- Once I figure out how to resolve this, update the README.