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hms-dbmi / spp

SPP - R package for analysis of ChIP-seq and other functional sequencing data
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version info on bioconda inconsistent with help text #45

Open cmatKhan opened 11 months ago

cmatKhan commented 11 months ago

I am confused about what version of spp I have installed through bioconda.

The bioconda release page lists versions through 1.16. When I install the latest, I get the following in the sessionInfo();

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS/LAPACK: /home/oguzkhan/miniconda3/lib/libopenblasp-r0.3.25.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Chicago
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] spp_1.16.0  Rcpp_1.0.11

loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1    parallel_4.3.1 caTools_1.18.2 bitops_1.0-7

But when I look at ?spp, I get this:

...
Details:

       Package:   spp                       
       Type:      Package                   
       Version:   1.11                      
       Date:      2012-06-20                
       License:   What license is it under? 
       LazyLoad:  yes                       

     See example below for typical processing sequence.y
...

The github repo doesn't have any releases past 1.15.2, and CRAN seems to think that spp was removed from the repo:

Package ‘spp’ was removed from the CRAN repository.

Formerly available versions can be obtained from the archive.

Archived on 2022-11-20 as issues were not corrected despite reminders.

A summary of the most recent check results can be obtained from the check results archive.

Please use the canonical form https://cran.r-project.org/package=spp to link to this page.

the archive does list version 1.16, with warnings on a build on some OS, which implies that there is a version 1.16 repo somewhere -- possibly this isn't the repository of record anymore?