##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings projectR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/projectR.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 ‘projectR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘projectR’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘projectR’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
alluvialMat: no visible binding for global variable ‘celltype’
alluvialMat: no visible binding for global variable ‘variable’
alluvialMat: no visible binding for global variable ‘value’
alluvialMat: no visible binding for global variable ‘nCells’
alluvialMat: no visible binding for global variable ‘nCells_per_type’
alluvialMat: no visible binding for global variable
  ‘nCells_per_pattern’
alluvialMat: no visible binding for global variable ‘prop’
Undefined global functions or variables:
  celltype nCells nCells_per_pattern nCells_per_type prop value
  variable
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
projectR-methods 24.627  0.071   24.75
* 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 ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/projectR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL projectR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘projectR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (projectR)

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(projectR)
> 
> test_check("projectR")

This is CoGAPS version 3.18.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 37 
sparseOptimization   FALSE 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

Data Model: Dense, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
-- Equilibration Phase --
1000 of 50000, Atoms: 197(A), 145(P), ChiSq: 50997, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 244(A), 170(P), ChiSq: 39416, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 272(A), 190(P), ChiSq: 34718, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 285(A), 203(P), ChiSq: 33026, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 278(A), 214(P), ChiSq: 32634, Time: 00:00:00 / 00:00:00
6000 of 50000, Atoms: 300(A), 212(P), ChiSq: 32054, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 314(A), 214(P), ChiSq: 31599, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 310(A), 219(P), ChiSq: 31559, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 324(A), 215(P), ChiSq: 31108, Time: 00:00:01 / 00:00:14
10000 of 50000, Atoms: 320(A), 217(P), ChiSq: 31150, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 332(A), 240(P), ChiSq: 30933, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 346(A), 240(P), ChiSq: 30820, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 372(A), 224(P), ChiSq: 30676, Time: 00:00:02 / 00:00:19
14000 of 50000, Atoms: 360(A), 231(P), ChiSq: 30411, Time: 00:00:02 / 00:00:17
15000 of 50000, Atoms: 367(A), 229(P), ChiSq: 30382, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 370(A), 250(P), ChiSq: 30316, Time: 00:00:03 / 00:00:22
17000 of 50000, Atoms: 381(A), 246(P), ChiSq: 30325, Time: 00:00:03 / 00:00:21
18000 of 50000, Atoms: 375(A), 254(P), ChiSq: 30237, Time: 00:00:03 / 00:00:19
19000 of 50000, Atoms: 383(A), 256(P), ChiSq: 30192, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 383(A), 252(P), ChiSq: 30172, Time: 00:00:04 / 00:00:23
21000 of 50000, Atoms: 373(A), 247(P), ChiSq: 30139, Time: 00:00:04 / 00:00:22
22000 of 50000, Atoms: 391(A), 240(P), ChiSq: 30091, Time: 00:00:04 / 00:00:21
23000 of 50000, Atoms: 401(A), 260(P), ChiSq: 30081, Time: 00:00:04 / 00:00:20
24000 of 50000, Atoms: 399(A), 261(P), ChiSq: 29975, Time: 00:00:05 / 00:00:24
25000 of 50000, Atoms: 401(A), 254(P), ChiSq: 30031, Time: 00:00:05 / 00:00:23
26000 of 50000, Atoms: 394(A), 252(P), ChiSq: 29981, Time: 00:00:05 / 00:00:22
27000 of 50000, Atoms: 407(A), 265(P), ChiSq: 29948, Time: 00:00:05 / 00:00:21
28000 of 50000, Atoms: 405(A), 258(P), ChiSq: 29987, Time: 00:00:06 / 00:00:24
29000 of 50000, Atoms: 389(A), 263(P), ChiSq: 30007, Time: 00:00:06 / 00:00:23
30000 of 50000, Atoms: 410(A), 266(P), ChiSq: 29976, Time: 00:00:06 / 00:00:22
31000 of 50000, Atoms: 390(A), 269(P), ChiSq: 29994, Time: 00:00:06 / 00:00:21
32000 of 50000, Atoms: 407(A), 250(P), ChiSq: 29926, Time: 00:00:07 / 00:00:24
33000 of 50000, Atoms: 405(A), 258(P), ChiSq: 29970, Time: 00:00:07 / 00:00:23
34000 of 50000, Atoms: 412(A), 265(P), ChiSq: 29949, Time: 00:00:07 / 00:00:22
35000 of 50000, Atoms: 408(A), 252(P), ChiSq: 29952, Time: 00:00:07 / 00:00:22
36000 of 50000, Atoms: 403(A), 247(P), ChiSq: 29933, Time: 00:00:08 / 00:00:24
37000 of 50000, Atoms: 407(A), 249(P), ChiSq: 29971, Time: 00:00:08 / 00:00:23
38000 of 50000, Atoms: 408(A), 249(P), ChiSq: 29927, Time: 00:00:08 / 00:00:23
39000 of 50000, Atoms: 388(A), 256(P), ChiSq: 30057, Time: 00:00:08 / 00:00:22
40000 of 50000, Atoms: 398(A), 265(P), ChiSq: 29943, Time: 00:00:09 / 00:00:24
41000 of 50000, Atoms: 396(A), 255(P), ChiSq: 30032, Time: 00:00:09 / 00:00:23
42000 of 50000, Atoms: 409(A), 262(P), ChiSq: 29995, Time: 00:00:09 / 00:00:23
43000 of 50000, Atoms: 411(A), 264(P), ChiSq: 29948, Time: 00:00:09 / 00:00:22
44000 of 50000, Atoms: 421(A), 276(P), ChiSq: 29943, Time: 00:00:10 / 00:00:24
45000 of 50000, Atoms: 391(A), 254(P), ChiSq: 29980, Time: 00:00:10 / 00:00:24
46000 of 50000, Atoms: 410(A), 253(P), ChiSq: 29936, Time: 00:00:10 / 00:00:23
47000 of 50000, Atoms: 386(A), 255(P), ChiSq: 30089, Time: 00:00:10 / 00:00:22
48000 of 50000, Atoms: 405(A), 251(P), ChiSq: 30000, Time: 00:00:11 / 00:00:24
49000 of 50000, Atoms: 411(A), 267(P), ChiSq: 30022, Time: 00:00:11 / 00:00:24
50000 of 50000, Atoms: 416(A), 264(P), ChiSq: 30040, Time: 00:00:11 / 00:00:23
-- Sampling Phase --
1000 of 50000, Atoms: 415(A), 259(P), ChiSq: 29955, Time: 00:00:11 / 00:00:23
2000 of 50000, Atoms: 411(A), 256(P), ChiSq: 29899, Time: 00:00:12 / 00:00:24
3000 of 50000, Atoms: 405(A), 267(P), ChiSq: 29978, Time: 00:00:12 / 00:00:24
4000 of 50000, Atoms: 421(A), 249(P), ChiSq: 29951, Time: 00:00:12 / 00:00:23
5000 of 50000, Atoms: 406(A), 248(P), ChiSq: 29987, Time: 00:00:12 / 00:00:23
6000 of 50000, Atoms: 401(A), 260(P), ChiSq: 29978, Time: 00:00:13 / 00:00:24
7000 of 50000, Atoms: 392(A), 257(P), ChiSq: 29958, Time: 00:00:13 / 00:00:24
8000 of 50000, Atoms: 409(A), 265(P), ChiSq: 29969, Time: 00:00:13 / 00:00:23
9000 of 50000, Atoms: 404(A), 261(P), ChiSq: 29998, Time: 00:00:13 / 00:00:23
10000 of 50000, Atoms: 411(A), 264(P), ChiSq: 29975, Time: 00:00:14 / 00:00:24
11000 of 50000, Atoms: 404(A), 263(P), ChiSq: 29964, Time: 00:00:14 / 00:00:24
12000 of 50000, Atoms: 424(A), 265(P), ChiSq: 29958, Time: 00:00:14 / 00:00:23
13000 of 50000, Atoms: 392(A), 258(P), ChiSq: 29959, Time: 00:00:14 / 00:00:23
14000 of 50000, Atoms: 410(A), 261(P), ChiSq: 29977, Time: 00:00:15 / 00:00:24
15000 of 50000, Atoms: 419(A), 268(P), ChiSq: 29987, Time: 00:00:15 / 00:00:24
16000 of 50000, Atoms: 394(A), 264(P), ChiSq: 29948, Time: 00:00:15 / 00:00:23
17000 of 50000, Atoms: 400(A), 275(P), ChiSq: 30005, Time: 00:00:15 / 00:00:23
18000 of 50000, Atoms: 398(A), 243(P), ChiSq: 29938, Time: 00:00:16 / 00:00:24
19000 of 50000, Atoms: 394(A), 263(P), ChiSq: 30045, Time: 00:00:16 / 00:00:24
20000 of 50000, Atoms: 407(A), 250(P), ChiSq: 29942, Time: 00:00:16 / 00:00:23
21000 of 50000, Atoms: 415(A), 247(P), ChiSq: 29967, Time: 00:00:16 / 00:00:23
22000 of 50000, Atoms: 395(A), 239(P), ChiSq: 29995, Time: 00:00:17 / 00:00:24
23000 of 50000, Atoms: 408(A), 263(P), ChiSq: 29972, Time: 00:00:17 / 00:00:24
24000 of 50000, Atoms: 406(A), 266(P), ChiSq: 29973, Time: 00:00:17 / 00:00:23
25000 of 50000, Atoms: 392(A), 259(P), ChiSq: 30063, Time: 00:00:17 / 00:00:23
26000 of 50000, Atoms: 393(A), 269(P), ChiSq: 30060, Time: 00:00:18 / 00:00:24
27000 of 50000, Atoms: 402(A), 259(P), ChiSq: 29950, Time: 00:00:18 / 00:00:23
28000 of 50000, Atoms: 399(A), 253(P), ChiSq: 29935, Time: 00:00:18 / 00:00:23
29000 of 50000, Atoms: 409(A), 250(P), ChiSq: 29998, Time: 00:00:18 / 00:00:23
30000 of 50000, Atoms: 406(A), 252(P), ChiSq: 29999, Time: 00:00:19 / 00:00:24
31000 of 50000, Atoms: 395(A), 248(P), ChiSq: 29999, Time: 00:00:19 / 00:00:23
32000 of 50000, Atoms: 385(A), 273(P), ChiSq: 30002, Time: 00:00:19 / 00:00:23
33000 of 50000, Atoms: 406(A), 251(P), ChiSq: 29948, Time: 00:00:20 / 00:00:24
34000 of 50000, Atoms: 380(A), 265(P), ChiSq: 30019, Time: 00:00:20 / 00:00:24
35000 of 50000, Atoms: 405(A), 250(P), ChiSq: 29985, Time: 00:00:20 / 00:00:23
36000 of 50000, Atoms: 426(A), 258(P), ChiSq: 30020, Time: 00:00:20 / 00:00:23
37000 of 50000, Atoms: 404(A), 257(P), ChiSq: 30039, Time: 00:00:21 / 00:00:24
38000 of 50000, Atoms: 393(A), 266(P), ChiSq: 29977, Time: 00:00:21 / 00:00:24
39000 of 50000, Atoms: 414(A), 257(P), ChiSq: 30021, Time: 00:00:21 / 00:00:23
40000 of 50000, Atoms: 401(A), 269(P), ChiSq: 30074, Time: 00:00:21 / 00:00:23
41000 of 50000, Atoms: 405(A), 253(P), ChiSq: 30028, Time: 00:00:22 / 00:00:24
42000 of 50000, Atoms: 407(A), 274(P), ChiSq: 29933, Time: 00:00:22 / 00:00:24
43000 of 50000, Atoms: 402(A), 270(P), ChiSq: 29984, Time: 00:00:22 / 00:00:23
44000 of 50000, Atoms: 426(A), 260(P), ChiSq: 29956, Time: 00:00:22 / 00:00:23
45000 of 50000, Atoms: 414(A), 272(P), ChiSq: 29942, Time: 00:00:23 / 00:00:24
46000 of 50000, Atoms: 429(A), 246(P), ChiSq: 29966, Time: 00:00:23 / 00:00:24
47000 of 50000, Atoms: 399(A), 247(P), ChiSq: 29997, Time: 00:00:23 / 00:00:23
48000 of 50000, Atoms: 380(A), 272(P), ChiSq: 29972, Time: 00:00:24 / 00:00:24
49000 of 50000, Atoms: 403(A), 255(P), ChiSq: 30044, Time: 00:00:24 / 00:00:24
50000 of 50000, Atoms: 399(A), 265(P), ChiSq: 29978, Time: 00:00:24 / 00:00:24
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 24 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
 32.308   0.484  32.857