ERROR: relation "cov_m_below" does not exist about cohortmethod

[msuchard]

@ChristopheLambert can you provide the file /tmp/errorReport.txt?

[ChristopheLambert]

Here you go:

DBMS:
postgresql

Error:
execute JDBC update query failed in dbSendUpdate (ERROR: relation "cov_m_below" does not exist
  Position: 829)

SQL:
CREATE TEMP TABLE cov_all

AS
SELECT
 row_id, covariate_id, covariate_value

FROM

(

SELECT row_id, covariate_id, covariate_value FROM dummy




UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_gender




UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_race




UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_ethnicity






UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_year










UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_co_365d














UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_cg











UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dera_365d


















UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_po_365d














UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_m_below






UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_m_above








UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_m_365d







UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_m_count365d







UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_cond

UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_drug

UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_proc

UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_obs

UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_visit_all

UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_visit_inpt

UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_visit_er


UNION

SELECT row_id, covariate_id, covariate_value
FROM cov_dd_meas






) all_covariates


R version:
R version 3.2.3 (2015-12-10)

Platform:
x86_64-redhat-linux-gnu

Attached base packages:
- stats
- graphics
- grDevices
- utils
- datasets
- methods
- base

Other attached packages:
- CohortMethod (2.0.6)
- FeatureExtraction (1.0.1)
- Cyclops (1.2.2)
- DatabaseConnector (1.3.0)
- RJDBC (0.2-5)
- rJava (0.9-8)
- DBI (0.3.1)
- SqlRender (1.1.7)

[schuemie]

Hi @ChristopheLambert ,

I'm sorry about that! It seems I made a typo in the code for constructing covariates. Could you try again using the latest version of the FeatureExtraction package. Close all instances of R, open only one, and type this code to get the latest version:

install.packages("devtools")
devtools::install_github("ohdsi/StudyProtocols/FeatureExtraction")

Let me know if this resolves this problem.

Cheers,
Martijn

[ChristopheLambert]

I get this error:

> devtools::install_github("ohdsi/StudyProtocols/FeatureExtraction")
Downloading GitHub repo ohdsi/StudyProtocols@master
from URL https://api.github.com/repos/ohdsi/StudyProtocols/zipball/master
Error: Does not appear to be an R package (no DESCRIPTION)

[msuchard]

Use

devtools::install_github("OHDSI/FeatureExtraction")

Note: no StudyProtocols

[ChristopheLambert]

I was able to run through a study successfully now with the new version of CohortMethod.
Thanks for the quick response!