Building vignettes fail ufter update

[bounlu]

After the last updates, building the vignettes fail as below:

> devtools::install_github(repo = "Danis102/seqpac",
+                          dependencies = TRUE,
+                          build_manual = TRUE,
+                          build_vignettes = TRUE)
Downloading GitHub repo Danis102/seqpac@HEAD
✔  checking for file ‘/private/var/folders/d4/89wwgrcn7j70w9m7n2pwxgr00000gp/T/Rtmpi2uo0P/remotesbdd6dc6b062/Danis102-seqpac-b53534e/DESCRIPTION’ ...
─  preparing ‘seqpac’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
E  creating vignettes (37.9s)
   --- re-building ‘seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd’ using rmarkdown
   Welcome to seqpac.
   Please, cite 'Skog et al. 2021, bioRxiv'
   
   Attaching package: 'seqpac'
   
   The following objects are masked from 'package:base':
   
       norm, summary
   
   
   Input type was set to untrimmed fastq.
   The following fastq files were found in the path:
   [1] "/var/folders/d4/89wwgrcn7j70w9m7n2pwxgr00000gp/T//RtmprXT01Q/seqpac_temp/fq1.fastq.gz"
   [2] "/var/folders/d4/89wwgrcn7j70w9m7n2pwxgr00000gp/T//RtmprXT01Q/seqpac_temp/fq2.fastq.gz"
   [3] "/var/folders/d4/89wwgrcn7j70w9m7n2pwxgr00000gp/T//RtmprXT01Q/seqpac_temp/fq3.fastq.gz"
   
   Seqpac trimming using the make_trim function was specified.
   --- Temporary trimmed fastq are stored in:  /var/folders/d4/89wwgrcn7j70w9m7n2pwxgr00000gp/T//RtmprXT01Q/seqpac/
   --- Unless moved, these will be removed when system restarts.
   --- Please run 'make_trim' separately for more storage options.
   
   Default trimming:   
   ----------------------------------------------
   adapt_3: 
   AGATCGGAAGAGCACACGTCTGAACTCCA 
        type       min  mismatch 
   "soft_rm"      "10"     "0.1" 
   ----------------------------------------------
   poly G: 
          type         min    mismatch 
   "hard_trim"        "20"       "0.1" 
   ----------------------------------------------
   size filter:
   min max 
    14  70 
   ----------------------------------------------
   quality filter:
   threshold   percent 
        20.0       0.8 
   ----------------------------------------------
   
   Now entering the parallel trimming loop (R may stop respond) ...
   (progress may be followed in: /var/folders/d4/89wwgrcn7j70w9m7n2pwxgr00000gp/T//RtmprXT01Q/seqpac/)
   Done trimming
   
   Identifying unique sequences in trimmed fastq files ...
   Compiling unique sequences ...
   Making a count table with sequences appearing in at least 2 independent samples ...
   Finalizing at  2022-08-10 15:03:35 
   Quitting from lines 278-284 (seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd) 
   Quitting from lines 278-284 (seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd) 
   Error: processing vignette 'seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd' failed with diagnostics:
   invalid connection
   --- failed re-building ‘seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd’
   
   SUMMARY: processing the following file failed:
     ‘seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd’
   
   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'seqpac' from GitHub:
  ! System command 'R' failed