##############################################################################
##############################################################################
###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix
###
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* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Methylation_Modeling.Rmd’ using rmarkdown
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 36996192 bytes (35.3 MB)
==================================================
downloaded 35.3 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 2663096 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

2025-12-18 16:18:56.612 R[92074:445717808] XType: Using static font registry.

Quitting from Methylation_Modeling.Rmd:498-519 [unnamed-chunk-33]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'clusterProfiler':
 object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
---
Backtrace:
    ▆
 1. └─base::library(clusterProfiler)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Methylation_Modeling.Rmd' failed with diagnostics:
package or namespace load failed for 'clusterProfiler':
 object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
--- failed re-building ‘Methylation_Modeling.Rmd’

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

Error: Vignette re-building failed.
Execution halted