* using log directory ‘/srv/hornik/tmp/CRAN/rliger.Rcheck’
* using R Under development (unstable) (2023-11-07 r85491)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (16)
    GNU Fortran (Debian 13.2.0-5) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘rliger/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rliger’ version ‘1.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/6s] NOTE
Maintainer: ‘Yichen Wang <wayichen@umich.edu>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Gao (6:200)
  Kozareva (6:130)
  Liu (6:193)
  Sodicoff (6:207)
  Welch (6:121)
  al (6:145, 6:222)
  et (6:142, 6:219)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-10-27 as requires archived package
    'riverplot'.

Found the following (possibly) invalid URLs:
  URL: https://portals.broadinstitute.org/single_cell/study/SCP466
    From: README.md
    Status: Error
    Message: server certificate verification failed. CAfile: none CRLfile: none
      	(Status without verification: OK)
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘rliger’ can be installed ... [50s/50s] OK
* used C++ compiler: ‘Debian clang version 16.0.6 (16)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/17s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ligerToSeurat
> ### Title: Create a Seurat object containing the data from a liger object
> ### Aliases: ligerToSeurat
> 
> ### ** Examples
> 
> if (requireNamespace("Seurat")) {
+   ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
+   ligerex <- normalize(ligerex)
+   ligerex <- selectGenes(ligerex)
+   ligerex <- scaleNotCenter(ligerex)
+   ligerex <- optimizeALS(ligerex, k = 5, max.iters = 1)
+   ligerex <- quantile_norm(ligerex)
+   ligerex <- runUMAP(ligerex, distance = "cosine", min_dist = .3)
+   srt <- ligerToSeurat(ligerex)
+ }
Loading required namespace: Seurat

  |                                                                            
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  |======================================================================| 100%
Finished in 1.351561 secs, 1 iterations.
Max iterations set: 1.
Final objective delta: 0.9973349.
Best results with seed 1.
Warning: No assay specified, setting assay as RNA by default.
Warning: No columnames present in cell embeddings, setting to 'iNMF_1:5'
Warning: No assay specified, setting assay as RNA by default.
Warning: No columnames present in cell embeddings, setting to 'tSNE_1:2'
Error in validObject(.Object) : 
  invalid class “LogMap” object: superclass "mMatrix" not defined in the environment of the object's class
Calls: ligerToSeurat ... initialize -> initialize -> initMatrix -> validObject
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [25s/25s] OK
  Running ‘testthat.R’ [24s/24s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE