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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deconvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deconvR_1.4.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/deconvR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deconvR/DESCRIPTION’ ... OK
* this is package ‘deconvR’ version ‘1.4.5’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘deconvR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character � (U+FFFD)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character � (U+FFFD)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character � (U+FFFD)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character � (U+FFFD)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/deconvR.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL deconvR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘deconvR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (deconvR)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(deconvR)
Loading required package: data.table
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("deconvR")
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
Received list of locations.
Reading file.
Reading file.
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS : 
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR : 
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP : 
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
DECONVOLUTION WITH RLM

DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM : 
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH RLM
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH RLM
DECONVOLUTION WITH RLM
CELL TYPES IN EXTENDED ATLAS: 
example_cell_type 
CELL TYPES IN EXTENDED ATLAS: 
else 
that 
this 
CELL TYPES IN EXTENDED ATLAS: 
else 
that 
this 
CELL TYPES IN EXTENDED ATLAS: 
else_v2 
that_v2 
this_v2 
else 
that 
Monocytes_EPIC 
this 
CELL TYPES IN EXTENDED ATLAS: 
example_cell_type 
Monocytes_EPIC 
B.cells_EPIC 
CD4T.cells_EPIC 
NK.cells_EPIC 
CD8T.cells_EPIC 
Neutrophils_EPIC 
Erythrocyte_progenitors 
Adipocytes 
Cortical_neurons 
Hepatocytes 
Lung_cells 
Pancreatic_beta_cells 
Pancreatic_acinar_cells 
Pancreatic_duct_cells 
Vascular_endothelial_cells 
Colon_epithelial_cells 
Left_atrium 
Bladder 
Breast 
Head_and_neck_larynx 
Kidney 
Prostate 
Thyroid 
Upper_GI 
Uterus_cervix 
Unique used IDs: 0
example_cell_type

Unique used IDs: 200
Monocytes_EPIC

Unique used IDs: 400
B.cells_EPIC

Unique used IDs: 600
CD4T.cells_EPIC

Unique used IDs: 800
NK.cells_EPIC

Unique used IDs: 1000
CD8T.cells_EPIC

Unique used IDs: 1200
Neutrophils_EPIC

Unique used IDs: 1400
Erythrocyte_progenitors

Unique used IDs: 1600
Adipocytes

Unique used IDs: 1800
Cortical_neurons

Unique used IDs: 2000
Hepatocytes

Unique used IDs: 2200
Lung_cells

Unique used IDs: 2400
Pancreatic_beta_cells

Unique used IDs: 2600
Pancreatic_acinar_cells

Unique used IDs: 2800
Pancreatic_duct_cells

Unique used IDs: 3000
Vascular_endothelial_cells

Unique used IDs: 3200
Colon_epithelial_cells

Unique used IDs: 3400
Left_atrium

Unique used IDs: 3600
Bladder

Unique used IDs: 3800
Breast

Unique used IDs: 4000
Head_and_neck_larynx

Unique used IDs: 4200
Kidney

Unique used IDs: 4400
Prostate

Unique used IDs: 4600
Thyroid

Unique used IDs: 4800
Upper_GI

Unique used IDs: 5000
Uterus_cervix

CELL TYPES IN EXTENDED ATLAS: 
example_cell_type 
Monocytes_EPIC 
B.cells_EPIC 
CD4T.cells_EPIC 
NK.cells_EPIC 
CD8T.cells_EPIC 
Neutrophils_EPIC 
Erythrocyte_progenitors 
Adipocytes 
Cortical_neurons 
Hepatocytes 
Lung_cells 
Pancreatic_beta_cells 
Pancreatic_acinar_cells 
Pancreatic_duct_cells 
Vascular_endothelial_cells 
Colon_epithelial_cells 
Left_atrium 
Bladder 
Breast 
Head_and_neck_larynx 
Kidney 
Prostate 
Thyroid 
Upper_GI 
Uterus_cervix 
Extracting DMPs for example_sample
DMPs hyper: 0

Extracting DMPs for Monocytes_EPIC
DMPs hyper: 80

Extracting DMPs for B.cells_EPIC
DMPs hyper: 152

Extracting DMPs for CD4T.cells_EPIC
DMPs hyper: 90

Extracting DMPs for NK.cells_EPIC
DMPs hyper: 156

Extracting DMPs for CD8T.cells_EPIC
DMPs hyper: 60

Extracting DMPs for Neutrophils_EPIC
DMPs hyper: 147

Extracting DMPs for Erythrocyte_progenitors
DMPs hyper: 130

Extracting DMPs for Adipocytes
DMPs hyper: 53

Extracting DMPs for Cortical_neurons
DMPs hyper: 362

Extracting DMPs for Hepatocytes
DMPs hyper: 280

Extracting DMPs for Lung_cells
DMPs hyper: 143

Extracting DMPs for Pancreatic_beta_cells
DMPs hyper: 138

Extracting DMPs for Pancreatic_acinar_cells
DMPs hyper: 0

Extracting DMPs for Pancreatic_duct_cells
DMPs hyper: 91

Extracting DMPs for Vascular_endothelial_cells
DMPs hyper: 42

Extracting DMPs for Colon_epithelial_cells
DMPs hyper: 370

Extracting DMPs for Left_atrium
DMPs hyper: 37

Extracting DMPs for Bladder
DMPs hyper: 69

Extracting DMPs for Breast
DMPs hyper: 79

Extracting DMPs for Head_and_neck_larynx
DMPs hyper: 71

Extracting DMPs for Kidney
DMPs hyper: 133

Extracting DMPs for Prostate
DMPs hyper: 53

Extracting DMPs for Thyroid
DMPs hyper: 145

Extracting DMPs for Upper_GI
DMPs hyper: 53

Extracting DMPs for Uterus_cervix
DMPs hyper: 16

[ FAIL 0 | WARN 188 | SKIP 0 | PASS 154 ]

[ FAIL 0 | WARN 188 | SKIP 0 | PASS 154 ]
> 
> proc.time()
   user  system elapsed 
475.921  12.668 499.868