* using log directory ‘/srv/hornik/tmp/CRAN_pretest/seam.Rcheck’
* using R Under development (unstable) (2026-04-11 r89869)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (3+b1)
    Debian flang version 21.1.8 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-04-12 19:12:06 UTC
* checking for file ‘seam/DESCRIPTION’ ... OK
* this is package ‘seam’ version ‘0.0.0.9000’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [2s/2s] NOTE
Maintainer: ‘Marketa Barac Makarova <marketa.makarova@mail.muni.cz>’

New submission

Version contains large components (0.0.0.9000)

Possibly misspelled words in DESCRIPTION:
  Eigengene (2:15)
  WGCNA (10:26)
  eigengene (8:18)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Marketa", "Barac"),
                      family = "Makarova",
                      role = c("aut", "cre"),
                      email = "marketa.makarova@mail.muni.cz"),
               person(given = "Jan",
                      family = "Kolacek",
                      role = "ctb"))
as necessary.

The build time stamp is missing.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘compute_activity.Rd’:
    \keyword{SPCA,}
  File ‘compute_module_trait_correlations.Rd’:
    \keyword{SPCA,}
    \keyword{classic,}
    \keyword{correlation,}
  File ‘compute_variable_trait_correlations.Rd’:
    \keyword{SPCA,}
    \keyword{classic,}
    \keyword{correlation,}
  File ‘insight_correlations_all.Rd’:
    \keyword{SPCA,}
    \keyword{association,}
    \keyword{diagnostics,}
    \keyword{visualization,}
  File ‘insight_correlations_lollipop.Rd’:
    \keyword{SPCA,}
    \keyword{correlation,}
    \keyword{plot,}
  File ‘insight_correlations_reconstruct.Rd’:
    \keyword{SPCA,}
    \keyword{plot,}
    \keyword{reconstruction,}
  File ‘insight_correlations_sign_changes.Rd’:
    \keyword{SPCA,}
    \keyword{plot,}
  File ‘plot_activity_bar.Rd’:
    \keyword{SPCA,}
    \keyword{activity,}
  File ‘plot_activity_bubble.Rd’:
    \keyword{SPCA,}
    \keyword{activity,}
  File ‘plot_explained_variance.Rd’:
    \keyword{SPCA,}
    \keyword{plot,}
  File ‘plot_sparsity.Rd’:
    \keyword{SPCA,}
    \keyword{plot,}
* 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 ... NOTE
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack knows about all of these
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... ERROR
Found the following files with insufficient permissions:
  .
  R
  man
  tests
  tests/testthat
Permissions should be at least 700 for directories and 400 for files.
Please fix permissions and try again.
 OK
* checking whether package ‘seam’ can be installed ... [7s/7s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘LICENSE.md’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... [10s/10s] 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 examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/4s] ERROR
  Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(seam)
  > 
  > test_check("seam")
  Saving _problems/test-plot_activity_bar-62.R
  Saving _problems/test-plot_activity_bubble-58.R
  Saving _problems/test-plot_module_heatmaps-66.R
  [ FAIL 19 | WARN 0 | SKIP 0 | PASS 90 ]
  
  Error in gzfile(file, mode) : cannot open the connection
  Calls: test_check ... o_apply -> lapply -> FUN -> <Anonymous> -> saveRDS -> gzfile
  In addition: Warning message:
  In gzfile(file, mode) :
    cannot open compressed file 'testthat-problems.rds', probable reason 'Permission denied'
  Execution halted
* 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: 2 ERRORs, 4 NOTEs