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Kurtwheeler/increase cran timeout #759

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Oct 30, 2018
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Kurtwheeler/increase cran timeout #759

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97e34ee
Increase CURL timeout for checking CRAN packages to 1 minute.
kurtwheeler Oct 29, 2018
65ae920
Bump up version of requests to avoid security vulnerability that Gith…
kurtwheeler Oct 29, 2018
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2 changes: 1 addition & 1 deletion api/requirements.in
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ coverage
django
psycopg2-binary
boto3
requests
requests>=2.20.0
python-nomad
djangorestframework
djangorestframework-hstore
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2 changes: 1 addition & 1 deletion api/requirements.txt
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Expand Up @@ -28,7 +28,7 @@ psycopg2==2.7.5 # via djangorestframework-hstore
python-dateutil==2.7.3 # via botocore
python-nomad==0.9.0
pytz==2018.5 # via django
requests==2.19.1
requests==2.20.0
s3transfer==0.1.13 # via boto3
six==1.11.0 # via python-dateutil
uritemplate==3.0.0 # via coreapi
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5 changes: 3 additions & 2 deletions common/install_devtools.R
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Expand Up @@ -29,12 +29,13 @@ install_package_version <- function(package_name, version) {
package_tarball <- paste0(package_name, "_", version, ".tar.gz")
package_url <- paste0("https://cran.r-project.org/src/contrib/", package_tarball)

curl_result <- system(paste0("curl --head ", package_url), intern=TRUE)
# Give CRAN a full minute to timeout since it's not always the most reliable.
curl_result <- system(paste0("curl --head --connect-timeout 60 ", package_url), intern=TRUE)
if (grepl("404", curl_result[1])) {
package_url <- paste0("https://cran.r-project.org/src/contrib/Archive/", package_name, "/", package_tarball)

# Make sure the package actually exists in the archive!
curl_result <- system(paste0("curl --head ", package_url), intern=TRUE)
curl_result <- system(paste0("curl --head --connect-timeout 60 ", package_url), intern=TRUE)
if (grepl("404", curl_result[1])) {
stop(paste("Package", package_name, "version", version, "does not exist!"))
}
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2 changes: 1 addition & 1 deletion common/requirements.in
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ coverage
django
psycopg2-binary
boto3
requests
requests>=2.20.0
retrying
daiquiri
python-nomad
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2 changes: 1 addition & 1 deletion common/requirements.txt
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Expand Up @@ -19,7 +19,7 @@ python-dateutil==2.7.3 # via botocore
python-nomad==0.9.0
pytz==2018.5 # via django
raven==6.9.0
requests==2.19.1
requests==2.20.0
retrying==1.3.3
s3transfer==0.1.13 # via boto3
six==1.11.0 # via python-dateutil, retrying
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2 changes: 1 addition & 1 deletion foreman/requirements.in
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
django
psycopg2-binary
requests
requests>=2.20.0
retrying
python-nomad
coverage
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2 changes: 1 addition & 1 deletion foreman/requirements.txt
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Expand Up @@ -18,7 +18,7 @@ python-dateutil==2.7.3
python-nomad==0.9.0
pytz==2018.5 # via django, pandas
raven==6.9.0
requests==2.19.1
requests==2.20.0
retrying==1.3.3
six==1.11.0 # via python-dateutil, retrying
urllib3==1.23 # via requests
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2 changes: 1 addition & 1 deletion workers/data_refinery_workers/downloaders/requirements.in
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
django
requests
requests>=2.20.0
psycopg2-binary
retrying
python-nomad
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2 changes: 1 addition & 1 deletion workers/data_refinery_workers/downloaders/requirements.txt
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Expand Up @@ -14,7 +14,7 @@ idna==2.7 # via requests
psycopg2-binary==2.7.5
python-nomad==0.9.0
pytz==2018.5 # via django
requests==2.19.1
requests==2.20.0
retrying==1.3.3
six==1.11.0 # via retrying
urllib3==1.23 # via requests
2 changes: 1 addition & 1 deletion workers/data_refinery_workers/processors/requirements.in
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
django
requests
requests>=2.20.0
psycopg2-binary
boto3
retrying
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2 changes: 1 addition & 1 deletion workers/data_refinery_workers/processors/requirements.txt
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Expand Up @@ -37,7 +37,7 @@ python-dateutil==2.7.3 # via botocore, matplotlib, pandas
python-nomad==0.9.0
pytz==2018.5 # via django, pandas
pyyaml==3.13 # via multiqc
requests==2.19.1
requests==2.20.0
retrying==1.3.3
s3transfer==0.1.13 # via boto3
scikit-learn==0.20.0
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