* using log directory ‘/srv/hornik/tmp/CRAN/ssdGSA.Rcheck’
* using R Under development (unstable) (2024-07-02 r86867)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ssdGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ssdGSA’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Xingpeng Li <xingpeng.li@pfizer.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  GSVA (7:79)
  NL (7:192)
* 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 whether package ‘ssdGSA’ can be installed ... [25s/25s] OK
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [34s/34s] NOTE
avg_expression : cal.avg.logcpm: no visible binding for global variable
  ‘gene’
median_expression : cal.med.logcpm: no visible binding for global
  variable ‘gene’
median_expression : cal.med.logcpm: no visible binding for global
  variable ‘.’
ssdGSA: no visible binding for global variable ‘ES’
ssdGSA: no visible binding for global variable ‘gene’
ssdGSA: no visible binding for global variable ‘.’
ssdGSA: no visible binding for global variable ‘cal_ES’
ssdGSA_individual: no visible binding for global variable ‘ES’
ssdGSA_individual: no visible binding for global variable ‘gene’
ssdGSA_individual: no visible binding for global variable ‘GS_pov’
ssdGSA_individual: no visible binding for global variable ‘GS_neg’
ssdGSA_individual: no visible binding for global variable ‘.’
ssdGSA_individual: no visible binding for global variable ‘rowname’
ssdGSA_individual: no visible global function definition for ‘last_col’
transform_ensembl_2_entrez: no visible binding for global variable
  ‘gene’
Undefined global functions or variables:
  . ES GS_neg GS_pov cal_ES gene last_col rowname
* 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] ERROR
Running examples in ‘ssdGSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ssdGSA
> ### Title: Single Sample Directional Gene Set Analysis (ssdGSA)
> ### Aliases: ssdGSA
> ### Keywords: analysis gene set variation
> 
> ### ** Examples
> 
> 
> ssdGSA(Data = data_matrix_entrezID,
+        Gene_sets = gene_sets[c(1,2,4)],
+        Direction_matrix = direction_matrix,
+        GSA_weight = "group_weighted",
+        GSA_weighted_by = "sum.ES",
+        GSA_method = "gsva",
+        min.sz = 6,
+        max.sz = 2000,
+        mx.diff = TRUE
+        )
Warning messages: 
100% (3/3) of gene sets have information missing in the data matrix for at least one gene; 
0% (0/3) of gene sets have information missing in the direction matrix for at least one gene. 

TCELL.KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY: 
 6.48% of genes (7/108) in this gene set have information missing in the data matrix; 

TLR.KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY: 
 18.63% of genes (19/102) in this gene set have information missing in the data matrix; 

NEUROTROPHIN.KEGG_NEUROTROPHIN_SIGNALING_PATHWAY: 
 2.38% of genes (3/126) in this gene set have information missing in the data matrix; 

Note since more than 10 gene sets have missing information in the direction matrix, no detailed individual gene set missing information will be reported.
Note: Running GSA for 3 gene sets using 'gsva' method with 'group_weighted' weights.
Error in gsva(Data, Gene_sets_pov, method = GSA_method, min.sz = min.sz,  : 
  Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Calls: ssdGSA ... suppressMessages -> withCallingHandlers -> gsva -> gsva -> .Defunct
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [9s/9s] ERROR
  Running ‘testthat.R’ [9s/9s]
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(ssdGSA)
  
  
  > 
  > test_check("ssdGSA")
  Warning messages: 
  100% (10/10) of gene sets have information missing in the data matrix for at least one gene; 
  50% (5/10) of gene sets have information missing in the direction matrix for at least one gene. 
  
  Note since more than 10 gene sets have missing information in the data matrix, no detailed individual gene set missing information will be reported.
  MAPK.KEGG_MAPK_SIGNALING_PATHWAY: 
   0.75% of genes (2/267) in this gene set have information missing in the direction matrix; 
  
  CALCIUM.KEGG_CALCIUM_SIGNALING_PATHWAY: 
   0.56% of genes (1/178) in this gene set have information missing in the direction matrix; 
  
  CHEMOKINE.KEGG_CHEMOKINE_SIGNALING_PATHWAY: 
   1.05% of genes (2/190) in this gene set have information missing in the direction matrix; 
  
  GNRH.KEGG_GNRH_SIGNALING_PATHWAY: 
   0.99% of genes (1/101) in this gene set have information missing in the direction matrix; 
  
  VEGF.KEGG_VEGF_SIGNALING_PATHWAY: 
   1.32% of genes (1/76) in this gene set have information missing in the direction matrix; 
  
  Note: Running GSA for 10 gene sets using 'gsva' method with 'group_weighted' weights.
  Warning messages: 
  100% (10/10) of gene sets have information missing in the data matrix for at least one gene; 
  50% (5/10) of gene sets have information missing in the direction matrix for at least one gene. 
  
  Note since more than 10 gene sets have missing information in the data matrix, no detailed individual gene set missing information will be reported.
  MAPK.KEGG_MAPK_SIGNALING_PATHWAY: 
   0.75% of genes (2/267) in this gene set have information missing in the direction matrix; 
  
  CALCIUM.KEGG_CALCIUM_SIGNALING_PATHWAY: 
   0.56% of genes (1/178) in this gene set have information missing in the direction matrix; 
  
  CHEMOKINE.KEGG_CHEMOKINE_SIGNALING_PATHWAY: 
   1.05% of genes (2/190) in this gene set have information missing in the direction matrix; 
  
  GNRH.KEGG_GNRH_SIGNALING_PATHWAY: 
   0.99% of genes (1/101) in this gene set have information missing in the direction matrix; 
  
  VEGF.KEGG_VEGF_SIGNALING_PATHWAY: 
   1.32% of genes (1/76) in this gene set have information missing in the direction matrix; 
  
  Note: Running GSA for 10 gene sets using individual weights.
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-ssdGSA_individual.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ssdGSA.R:2:3'): ssdGSA works ───────────────────────────────────
  <defunctError/error/condition>
  Error in `gsva(Data, Gene_sets_pov, method = GSA_method, min.sz = min.sz, 
      max.sz = max.sz, mx.diff = mx.diff)`: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
  Backtrace:
      ▆
   1. └─ssdGSA::ssdGSA(...) at test-ssdGSA.R:2:3
   2.   ├─base::suppressMessages(...)
   3.   │ └─base::withCallingHandlers(...)
   4.   ├─GSVA::gsva(...)
   5.   └─GSVA::gsva(...)
   6.     └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [9s/9s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ssdGSA.Rmd’ using rmarkdown

Quitting from lines 96-106 [unnamed-chunk-7] (ssdGSA.Rmd)
Error: processing vignette 'ssdGSA.Rmd' failed with diagnostics:
Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
--- failed re-building ‘ssdGSA.Rmd’

SUMMARY: processing the following file failed:
  ‘ssdGSA.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs, 2 NOTEs