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aaronpeikert / workflow-showcase

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Running workflow-showcase: fails when downloading the CFCS.zip file #4

Open rjlopez2 opened 2 years ago

rjlopez2 commented 2 years ago

Hello, newbie here :)

I am trying to run the show-case exercise and reproduce your analysis as described in your workflow here.

Unfortunately, I encounter with an issue when building or re-building the makefile after cloning the repo and building the docker image. By the message, I assume is related to the download of the dataset. If you can please help me to find out what could be wrong, I appreciate it.

The issue start when running this command:

make all DOCKER=TRUE

docker run --rm --user 501 -v /Users/rubencito/r_experimental/workflow-showcase:/home/rstudio workflow-showcase Rscript -e 'source("/home/rstudio/R/prepare_data.R")'
here() starts at /home/rstudio
trying URL 'http://openpsychometrics.org/_rawdata/CFCS.zip'
Error in download.file("http://openpsychometrics.org/_rawdata/CFCS.zip",  :
  cannot open URL 'http://openpsychometrics.org/_rawdata/CFCS.zip'
Calls: source -> withVisible -> eval -> eval -> download.file
In addition: Warning message:
In download.file("http://openpsychometrics.org/_rawdata/CFCS.zip",  :
  URL 'https://openpsychometrics.org/_rawdata/CFCS.zip': status was 'Peer certificate cannot be authenticated with given CA certificates'
Execution halted
make: *** [data/CFCS.csv] Error 1

Rebuilding the image using the instructions given give me the following output:

git pull && make rebuild && make -B DOCKER=TRUE

Already up to date.
docker build --no-cache -t workflow-showcase .
[+] Building 40.3s (8/8) FINISHED
 => [internal] load build definition from Dockerfile                                                                                                0.0s
 => => transferring dockerfile: 36B                                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                                   0.0s
 => => transferring context: 2B                                                                                                                     0.0s
 => [internal] load metadata for docker.io/rocker/verse:3.6.1                                                                                       1.7s
 => [auth] rocker/verse:pull token for registry-1.docker.io                                                                                         0.0s
 => CACHED [1/3] FROM docker.io/rocker/verse:3.6.1@sha256:c24df89866ec7444190c7d0929d3f050573c25449f37235f21b3d8bb8bf226c6                          0.0s
 => [2/3] RUN install2.r --error --skipinstalled  here lavaan                                                                                      38.5s
 => [3/3] WORKDIR /home/rstudio                                                                                                                     0.0s
 => exporting to image                                                                                                                              0.1s
 => => exporting layers                                                                                                                             0.1s
 => => writing image sha256:5412044640431f07051f46a79cb8eb14cc8948721a2f3006ade613df90d06286                                                        0.0s
 => => naming to docker.io/library/workflow-showcase                                                                                                0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
docker run --rm --user 501 -v /Users/rubencito/r_experimental/workflow-showcase:/home/rstudio workflow-showcase Rscript -e 'source("/home/rstudio/R/prepare_data.R")'
here() starts at /home/rstudio
trying URL 'http://openpsychometrics.org/_rawdata/CFCS.zip'
Error in download.file("http://openpsychometrics.org/_rawdata/CFCS.zip",  :
  cannot open URL 'http://openpsychometrics.org/_rawdata/CFCS.zip'
Calls: source -> withVisible -> eval -> eval -> download.file
In addition: Warning message:
In download.file("http://openpsychometrics.org/_rawdata/CFCS.zip",  :
  URL 'https://openpsychometrics.org/_rawdata/CFCS.zip': status was 'Peer certificate cannot be authenticated with given CA certificates'
Execution halted
make: *** [data/CFCS.csv] Error 1

Details of my system:

MacOS Monterrey version 12.3.

GNU Make version 3.81

Docker version

Client: Cloud integration: v1.0.22 Version: 20.10.13 API version: 1.41 Go version: go1.16.15 Git commit: a224086 Built: Thu Mar 10 14:08:44 2022 OS/Arch: darwin/amd64 Context: default Experimental: true

Server: Docker Desktop 4.6.1 (76265) Engine: Version: 20.10.13 API version: 1.41 (minimum version 1.12) Go version: go1.16.15 Git commit: 906f57f Built: Thu Mar 10 14:06:05 2022 OS/Arch: linux/amd64 Experimental: false containerd: Version: 1.5.10 GitCommit: 2a1d4dbdb2a1030dc5b01e96fb110a9d9f150ecc runc: Version: 1.0.3 GitCommit: v1.0.3-0-gf46b6ba docker-init: Version: 0.19.0 GitCommit: de40ad0

Thanks a lot in advance

Ruben

aaronpeikert commented 2 years ago

Hi Ruben, for a newbie this is a very thorough and well done error report! I‘ll take a look tomorrow. Best Aaron

Am 30.03.2022 um 21:38 schrieb Ruben Lopez @.***>:

 Hello, newbie here :)

I am trying to run the show-case exercise and reproduce your analysis as described in your workflow here.

Unfortunately I am encounter with an issue when building or re-building the makefile after cloning the repo and building the docker image. By the message, I assume is related to the download of the dataset. If you can please help me to find out what could be wrong, I appreciate it.

The issue start when running this command:

make all DOCKER=TRUE

docker run --rm --user 501 -v /Users/rubencito/r_experimental/workflow-showcase:/home/rstudio workflow-showcase Rscript -e 'source("/home/rstudio/R/prepare_data.R")' here() starts at /home/rstudio trying URL 'http://openpsychometrics.org/_rawdata/CFCS.zip' Error in download.file("http://openpsychometrics.org/_rawdata/CFCS.zip", : cannot open URL 'http://openpsychometrics.org/_rawdata/CFCS.zip' Calls: source -> withVisible -> eval -> eval -> download.file In addition: Warning message: In download.file("http://openpsychometrics.org/_rawdata/CFCS.zip", : URL 'https://openpsychometrics.org/_rawdata/CFCS.zip': status was 'Peer certificate cannot be authenticated with given CA certificates' Execution halted make: *** [data/CFCS.csv] Error 1

Rebuilding the image using the instructions given give me the following output:

git pull && make rebuild && make -B DOCKER=TRUE

Already up to date. docker build --no-cache -t workflow-showcase . [+] Building 40.3s (8/8) FINISHED => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 36B 0.0s => [internal] load .dockerignore 0.0s => => transferring context: 2B 0.0s => [internal] load metadata for docker.io/rocker/verse:3.6.1 1.7s => [auth] rocker/verse:pull token for registry-1.docker.io 0.0s => CACHED [1/3] FROM @.***:c24df89866ec7444190c7d0929d3f050573c25449f37235f21b3d8bb8bf226c6 0.0s => [2/3] RUN install2.r --error --skipinstalled here lavaan 38.5s => [3/3] WORKDIR /home/rstudio 0.0s => exporting to image 0.1s => => exporting layers 0.1s => => writing image sha256:5412044640431f07051f46a79cb8eb14cc8948721a2f3006ade613df90d06286 0.0s => => naming to docker.io/library/workflow-showcase 0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them docker run --rm --user 501 -v /Users/rubencito/r_experimental/workflow-showcase:/home/rstudio workflow-showcase Rscript -e 'source("/home/rstudio/R/prepare_data.R")' here() starts at /home/rstudio trying URL 'http://openpsychometrics.org/_rawdata/CFCS.zip' Error in download.file("http://openpsychometrics.org/_rawdata/CFCS.zip", : cannot open URL 'http://openpsychometrics.org/_rawdata/CFCS.zip' Calls: source -> withVisible -> eval -> eval -> download.file In addition: Warning message: In download.file("http://openpsychometrics.org/_rawdata/CFCS.zip", : URL 'https://openpsychometrics.org/_rawdata/CFCS.zip': status was 'Peer certificate cannot be authenticated with given CA certificates' Execution halted make: *** [data/CFCS.csv] Error 1 Details of my system:

MacOS Monterrey version 12.3.

GNU Make version 3.81

Docker version

Client: Cloud integration: v1.0.22 Version: 20.10.13 API version: 1.41 Go version: go1.16.15 Git commit: a224086 Built: Thu Mar 10 14:08:44 2022 OS/Arch: darwin/amd64 Context: default Experimental: true

Server: Docker Desktop 4.6.1 (76265) Engine: Version: 20.10.13 API version: 1.41 (minimum version 1.12) Go version: go1.16.15 Git commit: 906f57f Built: Thu Mar 10 14:06:05 2022 OS/Arch: linux/amd64 Experimental: false containerd: Version: 1.5.10 GitCommit: 2a1d4dbdb2a1030dc5b01e96fb110a9d9f150ecc runc: Version: 1.0.3 GitCommit: v1.0.3-0-gf46b6ba docker-init: Version: 0.19.0 GitCommit: de40ad0

Thanks a lot in advance

Ruben

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aaronpeikert commented 2 years ago

So the problem is that old SSL installations (like in this docker image) do not accept new SSL certificates. So this container cannot download anything. I will merge a PR that fixes this your problem shortly. We developed our thinking on this in the new paper on the topic:

https://github.com/aaronpeikert/repro-tutorial/blob/a8bb0d4df4afa4f7dbb5cd2344ae16043cb8a99d/manuscript.Rmd#L1392-L1394

This is still not perfect but we have some ideas to get true long term reproducibility. Just no idea when we have the time to write these down.

This PR then describes how even when things become outdated again you can "recover" more or less gracefilly.

rjlopez2 commented 2 years ago

Thanks a lot for your reply,

I will have a look at that work as well.

I look forward for the follow up on this :)

cheers