cyCONDOR Installation FAILS bc of destiny dep package smoother

[semmrich]

Hy,

1st off I rly luv ur work, this package is SLIC! Working with it since last yr oct or so, whatever...

Sad to see I cannot "spread" the install to our server anymore bc:

── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/Rtmpy3lsuP/remotes38594c34bc151/lorenzobonaguro-cyCONDOR-0b9cb7d/DESCRIPTION’ ...
─  preparing ‘cyCONDOR’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘cyCONDOR_0.3.1.tar.gz’
   
Installing package into ‘/home/StephanEmmrich/R/x86_64-redhat-linux-gnu-library/4.5’
(as ‘lib’ is unspecified)
ERROR: dependency ‘destiny’ is not available for package ‘cyCONDOR’
Perhaps try a variation of:
install.packages('destiny')
* removing ‘/home/StephanEmmrich/R/x86_64-redhat-linux-gnu-library/4.5/cyCONDOR’
Warning messages:
1: package ‘smoother’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In i.p(...) : installation of package ‘ragg’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘destiny’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘/tmp/Rtmpy3lsuP/file38594c429cfb4b/cyCONDOR_0.3.1.tar.gz’ had non-zero exit status

> install.packages("destiny")
Installing package into ‘/home/StephanEmmrich/R/x86_64-redhat-linux-gnu-library/4.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependency ‘smoother’ is not available
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/destiny_3.24.0.tar.gz'
Content type 'application/x-gzip' length 900683 bytes (879 KB)
==================================================
downloaded 879 KB

ERROR: dependency ‘smoother’ is not available for package ‘destiny’
Perhaps try a variation of:
install.packages('smoother')
* removing ‘/home/StephanEmmrich/R/x86_64-redhat-linux-gnu-library/4.5/destiny’

If you check CRAN, they removed that package.
https://cran.r-project.org/web/packages/smoother/index.html

Hope cyCONDOR will be installable soon!

Kepp it up guys :)

[SamGG]

Hi,
I can reproduce the error you encountered on a fresh Windows install.
You can install smoother from github before installing cyCONDOR. It worked for me.
Best.

devtools::install_github("cran/smoother")

[lorenzobonaguro]

Hi @semmrich and @SamGG ,

This is indeed annoying! Can you let me know which version of R you are currently using? Would like to see if this is only on the newest version of R or something has changed with the dependency.

Thanks @SamGG for the workaround!

[semmrich]

Hey,

Thanks so much @SamGG - smoother installs!

This hack got us cyCONDOR on the server - issue resolved?!

Here is my version info:

session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.2 (2025-10-31)
 os       CentOS Stream 9
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Berlin
 date     2026-02-06
 rstudio  2025.05.1+513 Mariposa Orchid (server)
 pandoc   2.14.0.3 @ /usr/bin/pandoc
 quarto   1.6.42 @ /usr/lib/rstudio-server/bin/quarto/bin/quarto

The link I posted above means they removed the destiny dep bc of CRAN rules pertaining to regular maintenance and package author contact response I presume, plz correct if I'm mistaken :)

[SamGG]

You are correct.
EmbedSOM was also moved to archive although there are only NOTE during the testing phase of December. I think the CRAN rules where too strict in that release.
Please, close the issue if cyCONDOR correctly installs.