##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data celda
###
##############################################################################
##############################################################################
* checking for file ‘celda/DESCRIPTION’ ... OK
* preparing ‘celda’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DecontX-analysis.Rmd’ using rmarkdown
Quitting from lines 75-76 (DecontX-analysis.Rmd)
Error: processing vignette 'DecontX-analysis.Rmd' failed with diagnostics:
unused argument (counts = c(1, 0, 1, 16, 8, 7, 1, 1, 2, 2, 2, 6, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 3, 5, 7, 3, 1, 2, 4, 1, 6, 2, 3, 0, 0, 3, 2, 4, 0, 0, 0, 0, 3, 0, 1, 1, 5, 1, 10, 3, 2, 0, 11, 4, 12, 0, 3, 1, 8, 1, 0, 7, 5, 11, 1, 2, 1, 12, 12, 2, 0, 0, 0, 1, 8, 0, 0, 4, 2, 2, 3, 2, 1, 1, 0, 4, 0, 0, 0, 1, 0, 0, 0, 4, 0, 1, 0, 5, 0, 3, 0, 21, 0, 1, 0, 2, 1, 0, 0, 3, 2, 8, 8, 1, 2, 9, 1, 1, 4, 0, 10, 1, 1, 0, 0, 6, 0, 0, 1, 5, 0, 0, 3, 1, 5, 2, 1, 5, 0, 1, 0, 1, 2, 0, 3, 1, 1, 3, 4, 4, 1, 4, 0, 4, 0, 1, 1,
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0, 0, 0, 0, 3, 6, 2, 0, 5, 0, 1, 5, 4, 1, 1, 2, 4, 1, 1, 4, 1, 3, 0, 1, 2, 1, 0, 0, 4, 0, 2, 1, 18, 1, 1, 0, 1, 4, 1, 0, 2, 0, 8, 11, 1, 0, 9, 1, 0, 5, 0, 7, 4, 4, 3, 0, 6, 3, 1, 1, 2, 2, 0, 5, 1, 7, 1, 1, 6, 1, 3, 1, 2, 3, 1, 2, 0, 0, 6, 8, 4, 4, 2, 0, 5, 0, 0, 4, 2, 0, 2, 1, 1, 1, 0, 3, 4, 0, 1, 0, 0, 1, 2, 2, 16, 3, 0, 3, 4, 2, 2, 6, 6, 1, 0, 2, 2, 0, 5, 0, 0, 0, 2, 4, 1, 5, 2, 1, 1, 2, 11, 1, 2, 5, 0, 0, 2, 3, 2, 0, 0, 1, 3, 0, 1, 2, 4, 7, 1, 1, 1, 2, 2, 0, 1, 7, 6, 0, 5, 2, 2, 0, 1, 1, 0, 2,
0, 5, 4, 1, 2, 1, 7, 0, 1, 7, 3, 1, 2, 8, 2, 17, 4, 2, 0, 3, 2, 5, 0, 2, 1, 1, 0, 1, 1, 2, 2, 3, 5, 2, 1, 1, 12, 3, 0, 1, 6,
--- failed re-building ‘DecontX-analysis.Rmd’
--- re-building ‘FindMarkers-analysis.Rmd’ using rmarkdown
Building tree...
Computing performance metrics...
Warning in has_utility("convert", "ImageMagick") :
ImageMagick not installed or not in PATH
Building tree for all cell types...
Building tree for cell type metaLabel
Computing performance statistics...
--- finished re-building ‘FindMarkers-analysis.Rmd’
--- re-building ‘celda-analysis.Rmd’ using rmarkdown
Warning in has_utility("convert", "ImageMagick") :
ImageMagick not installed or not in PATH
Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
Done!
Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
Done!
==================================================
Starting recursive module splitting.
==================================================
Thu Jan 16 00:48:28 2020 .. Collapsing to 100 temporary cell populations
Thu Jan 16 00:48:33 2020 .. Initializing with 2 modules
Thu Jan 16 00:48:34 2020 .. Created module 3 | logLik: -678732.551189294
Thu Jan 16 00:48:34 2020 .. Created module 4 | logLik: -671199.811010666
Thu Jan 16 00:48:35 2020 .. Created module 5 | logLik: -665021.359168605
Thu Jan 16 00:48:35 2020 .. Created module 6 | logLik: -662390.69018795
Thu Jan 16 00:48:35 2020 .. Created module 7 | logLik: -658844.323573955
Thu Jan 16 00:48:36 2020 .. Created module 8 | logLik: -656299.865426257
Thu Jan 16 00:48:36 2020 .. Created module 9 | logLik: -655705.42933633
Thu Jan 16 00:48:37 2020 .. Created module 10 | logLik: -655484.348670972
Thu Jan 16 00:48:37 2020 .. Created module 11 | logLik: -655783.727789893
Thu Jan 16 00:48:38 2020 .. Created module 12 | logLik: -656075.374736308
Thu Jan 16 00:48:38 2020 .. Created module 13 | logLik: -656366.383186038
Thu Jan 16 00:48:39 2020 .. Created module 14 | logLik: -656645.051488647
Thu Jan 16 00:48:39 2020 .. Created module 15 | logLik: -656927.154756458
Thu Jan 16 00:48:39 2020 .. Calculating perplexity
==================================================
Completed recursive module splitting. Total time: 11.61155 secs
==================================================
==================================================
Starting recursive cell population splitting.
==================================================
Thu Jan 16 00:48:41 2020 .. Collapsing to 10 modules
Thu Jan 16 00:48:41 2020 .. Initializing with 3 populations
Thu Jan 16 00:48:43 2020 .. Current cell population 4 | logLik: -660513.364626795
Thu Jan 16 00:48:43 2020 .. Current cell population 5 | logLik: -652211.87271298
Thu Jan 16 00:48:43 2020 .. Current cell population 6 | logLik: -652238.922577439
Thu Jan 16 00:48:43 2020 .. Current cell population 7 | logLik: -652265.917589273
Thu Jan 16 00:48:44 2020 .. Current cell population 8 | logLik: -652294.545176752
Thu Jan 16 00:48:44 2020 .. Current cell population 9 | logLik: -652317.876861829
Thu Jan 16 00:48:44 2020 .. Current cell population 10 | logLik: -652344.681907275
Thu Jan 16 00:48:46 2020 .. Current cell population 11 | logLik: -652358.027508618
Thu Jan 16 00:48:46 2020 .. Current cell population 12 | logLik: -652380.259513891
Thu Jan 16 00:48:46 2020 .. Calculating perplexity
==================================================
Completed recursive cell population splitting. Total time: 6.484704 secs
==================================================
--------------------------------------------------
Starting celdaGridSearch with celda_CG
Number of cores: 4
--------------------------------------------------
Thu Jan 16 00:49:47 2020 .. Calculating perplexity
--------------------------------------------------
Completed celdaGridSearch. Total time: 59.16489 secs
--------------------------------------------------
--------------------------------------------------
Starting celdaGridSearch with celda_CG
Number of cores: 4
--------------------------------------------------
Thu Jan 16 00:50:50 2020 .. Calculating perplexity
--------------------------------------------------
Completed celdaGridSearch. Total time: 1.019961 mins
--------------------------------------------------
--- finished re-building ‘celda-analysis.Rmd’
SUMMARY: processing the following file failed:
‘DecontX-analysis.Rmd’
Error: Vignette re-building failed.
Execution halted