configure script fails quietly when calling "wget http...". Worked when changing to "wget https..."

[pvo93]

This is an issue template made by the developers of ArchR. You MUST follow these instructions.

Questions related to how to use ArchR or requests for new features should be posted in the Discussions forum (https://github.com/GreenleafLab/ArchR/discussions).

Before you submit this Bug Report please update ArchR to the latest stable version and make sure that this issue has not already been fixed in the latest release. ArchR is still in active development and we will fix problems as they arise. To update ArchR:

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

If your issue persists, then please submit this bug report.

PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE.

Attach your log file
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Describe the bug
This is a personal GitHub account, but I work for the Mayo Clinic. I install and maintain the R packages in our high performance, shared Google Cloud Project research computing environment. Our GCP administrators will not whitelist http url's, only https. When I attempt to install ArchR, I get the following.

Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘ArchR/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md’
Warning: file 'ArchR/configure' did not have execute permissions: corrected
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/biotools/biotools/rpackages/R-4.5.1-2025-07-08’
(as ‘lib’ is unspecified)

• installing source package ‘ArchR’ ...
  ** this is package ‘ArchR’ version ‘1.0.3’
  ** using staged installation
  ERROR: configuration failed for package ‘ArchR’
• removing ‘/biotools/biotools/rpackages/R-4.5.1-2025-07-08/ArchR’
• restoring previous ‘/biotools/biotools/rpackages/R-4.5.1-2025-07-08/ArchR’
  Warning messages:
  1: install_github() was deprecated in devtools 2.5.0.
  ℹ Please use pak::pak("user/repo") instead.
  This warning is displayed once per session.
  Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.
  2: In i.p(...) :
  installation of package ‘/tmp/RtmpaHzqL0/file349331519840b/ArchR_1.0.3.tar.gz’ had non-zero exit status

To Reproduce
This is the output of running the ArchR configure script manually on our system.

[ext_wa02042_mayo_edu@hn2 ArchR-1.0.3-bak]$ grep http configure
IP=$(curl --silent https://ipinfo.io/ip)
curl --silent -X POST https://plausible.io/api/event
--data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}' > /dev/null
[ext_wa02042_mayo_edu@hn2 ArchR-1.0.3-bak]$ cd ..
[ext_wa02042_mayo_edu@hn2 src]$ cd ArchR
[ext_wa02042_mayo_edu@hn2 ArchR]$ ./confire
-bash: ./confire: No such file or directory
[ext_wa02042_mayo_edu@hn2 ArchR]$ ./configure

<title>WSS Policy Denied</title>

Access to this url is not allowed by Web Security Services. The url has been identified as an unauthorized category.

[ext_wa02042_mayo_edu@hn2 ArchR]$ [ext_wa02042_mayo_edu@hn2 ArchR]$ [ext_wa02042_mayo_edu@hn2 ArchR]$ [ext_wa02042_mayo_edu@hn2 ArchR]$ [ext_wa02042_mayo_edu@hn2 ArchR]$ [ext_wa02042_mayo_edu@hn2 ArchR]$ ./configure <title>WSS Policy Denied</title>

Access to this url is not allowed by Web Security Services. The url has been identified as an unauthorized category.

Expected behavior
I got around the problem by changing the following line of code:

This is the configure script.

IP=$(curl --silent https://ipinfo.io/ip)

IP=170.85.54.176

curl --silent -X POST https://plausible.io/api/event
-H "X-Forwarded-For: $IP"
-H 'Content-Type: application/json'
--data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}'

The problem is the hardcoded IP address on the second line. 170.85.54.176 points to a http domain, then script fails quietly without propagating any error message back to the R session. I made the following change to the configure script and it works.

IP=$(curl --silent https://ipinfo.io/ip)

This is extremely difficult to track down and debug. Please revert the configure script to the version that doesn't hard the IP address.

ext_wa02042_mayo_edu@hn2 ArchR]$ diff configure ../ArchR-1.0.3-bak/configure
1,2c1
< # IP=$(curl --silent https://ipinfo.io/ip)
< IP=170.85.54.176

IP=$(curl --silent https://ipinfo.io/ip)
7,8c6
< --data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}'
<

---

--data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}' > /dev/null
[ext_wa02042_mayo_edu@hn2 ArchR]$ cat ../ArchR-1.0.3-bak/configure
IP=$(curl --silent https://ipinfo.io/ip)

curl --silent -X POST https://plausible.io/api/event
-H "X-Forwarded-For: $IP"
-H 'Content-Type: application/json'
--data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}' > /dev/null

Thank you for your prompt attention to this matter so we don't run into this problem again the next time we update ArchR

Thanks,
Patrick Votruba
Senior/Analyst Programmer
votruba.patrick@mayo.edu

[immanuelazn]

Hi @pvo93! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.

In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[pvo93]

I had to fix your configure script to get it to install. This is an issue where your "free" software wasted thousands of dollars in person hours at a major medical organization to debug and fix. To summarize. Here's the current configure script.

IP=$(curl --silent https://ipinfo.io/ip)

IP=170.85.54.176

curl --silent -X POST https://plausible.io/api/event
-H "X-Forwarded-For: $IP"
-H 'Content-Type: application/json'
--data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}'

I changed the first line BACK to IP=$(curl --silent https://ipinfo.io/ip)

Hardcoding the IP variable to 170.85.54.176 points to your http domain, not https. Then it fails silently.

I'm assuming this was done for debugging purposes and never changed back. Please go back to the version that works for secure https connections.

More headaches like this and I'm worried our security team will discontinue whitelisting github altogether.

Please feel free to reach via email if you have any questions about this use case.

Thank you and have a nice day,
Pat

[rcorces]

Hi @pvo93 - apologies if I'm being dense but I dont see the problematic line in our code base (IP=170.85.54.176)

https://github.com/GreenleafLab/ArchR/blob/master/configure

I dont see this in any of the git history for the configure file

[pvo93]

And I apologize for misspeaking. It's curl, not wget. I tried to install the master branch using devtools:: install again today and it was still failing.

I don't see a problem in the config file you linked. The problem was the tar.gz source I've been downloading has the first line commented out and then IP is assigned in the next line to 170.85.54.176

I see I made some copy/paste errors, but it basically looks like this:

# IP=$(curl --silent https://ipinfo.io/ip)
IP=170.85.54.176

curl --silent -X POST https://plausible.io/api/event \
  -H "X-Forwarded-For: $IP" \
  -H 'Content-Type: application/json' \
  --data '{"name":"pageview","url":"https://corceslab.com/archr-configure","domain":"corceslab.com"}' > /dev/null

I used the following R furnction call to do the install.

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

Thanks for following up.

Pat