##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/projectR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.12.0’
* 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 42.988  0.114  43.149
* 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-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 3.16.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 240 
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: 206(A), 123(P), ChiSq: 52005, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 270(A), 160(P), ChiSq: 39391, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 307(A), 168(P), ChiSq: 35106, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 322(A), 165(P), ChiSq: 33808, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 348(A), 186(P), ChiSq: 32707, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 351(A), 174(P), ChiSq: 32052, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 417(A), 175(P), ChiSq: 30607, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 426(A), 189(P), ChiSq: 30327, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 392(A), 191(P), ChiSq: 29957, Time: 00:00:03 / 00:00:43
10000 of 50000, Atoms: 382(A), 202(P), ChiSq: 29799, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 413(A), 206(P), ChiSq: 29357, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 410(A), 196(P), ChiSq: 28909, Time: 00:00:04 / 00:00:41
13000 of 50000, Atoms: 436(A), 202(P), ChiSq: 28859, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 402(A), 209(P), ChiSq: 28850, Time: 00:00:05 / 00:00:43
15000 of 50000, Atoms: 432(A), 214(P), ChiSq: 28718, Time: 00:00:05 / 00:00:40
16000 of 50000, Atoms: 434(A), 224(P), ChiSq: 28627, Time: 00:00:06 / 00:00:45
17000 of 50000, Atoms: 429(A), 228(P), ChiSq: 28557, Time: 00:00:06 / 00:00:42
18000 of 50000, Atoms: 449(A), 218(P), ChiSq: 28426, Time: 00:00:06 / 00:00:39
19000 of 50000, Atoms: 439(A), 240(P), ChiSq: 28449, Time: 00:00:07 / 00:00:43
20000 of 50000, Atoms: 457(A), 232(P), ChiSq: 28449, Time: 00:00:07 / 00:00:41
21000 of 50000, Atoms: 447(A), 219(P), ChiSq: 28426, Time: 00:00:08 / 00:00:44
22000 of 50000, Atoms: 442(A), 237(P), ChiSq: 28346, Time: 00:00:08 / 00:00:42
23000 of 50000, Atoms: 465(A), 227(P), ChiSq: 28333, Time: 00:00:08 / 00:00:40
24000 of 50000, Atoms: 468(A), 238(P), ChiSq: 28249, Time: 00:00:09 / 00:00:43
25000 of 50000, Atoms: 454(A), 220(P), ChiSq: 28242, Time: 00:00:09 / 00:00:41
26000 of 50000, Atoms: 454(A), 228(P), ChiSq: 28256, Time: 00:00:10 / 00:00:44
27000 of 50000, Atoms: 471(A), 225(P), ChiSq: 28262, Time: 00:00:10 / 00:00:42
28000 of 50000, Atoms: 466(A), 232(P), ChiSq: 28295, Time: 00:00:11 / 00:00:44
29000 of 50000, Atoms: 469(A), 225(P), ChiSq: 28294, Time: 00:00:11 / 00:00:42
30000 of 50000, Atoms: 443(A), 249(P), ChiSq: 28193, Time: 00:00:12 / 00:00:45
31000 of 50000, Atoms: 474(A), 237(P), ChiSq: 28276, Time: 00:00:12 / 00:00:43
32000 of 50000, Atoms: 478(A), 242(P), ChiSq: 28200, Time: 00:00:12 / 00:00:42
33000 of 50000, Atoms: 481(A), 229(P), ChiSq: 28235, Time: 00:00:13 / 00:00:44
34000 of 50000, Atoms: 484(A), 221(P), ChiSq: 28209, Time: 00:00:13 / 00:00:42
35000 of 50000, Atoms: 475(A), 230(P), ChiSq: 28171, Time: 00:00:14 / 00:00:44
36000 of 50000, Atoms: 464(A), 243(P), ChiSq: 28188, Time: 00:00:14 / 00:00:43
37000 of 50000, Atoms: 475(A), 233(P), ChiSq: 28176, Time: 00:00:15 / 00:00:44
38000 of 50000, Atoms: 465(A), 229(P), ChiSq: 28220, Time: 00:00:15 / 00:00:43
39000 of 50000, Atoms: 472(A), 231(P), ChiSq: 28239, Time: 00:00:15 / 00:00:42
40000 of 50000, Atoms: 449(A), 246(P), ChiSq: 28265, Time: 00:00:16 / 00:00:43
41000 of 50000, Atoms: 459(A), 234(P), ChiSq: 28200, Time: 00:00:16 / 00:00:42
42000 of 50000, Atoms: 466(A), 237(P), ChiSq: 28208, Time: 00:00:17 / 00:00:44
43000 of 50000, Atoms: 456(A), 240(P), ChiSq: 28274, Time: 00:00:17 / 00:00:42
44000 of 50000, Atoms: 446(A), 232(P), ChiSq: 28231, Time: 00:00:18 / 00:00:44
45000 of 50000, Atoms: 454(A), 225(P), ChiSq: 28227, Time: 00:00:18 / 00:00:43
46000 of 50000, Atoms: 455(A), 240(P), ChiSq: 28239, Time: 00:00:18 / 00:00:42
47000 of 50000, Atoms: 455(A), 247(P), ChiSq: 28290, Time: 00:00:19 / 00:00:43
48000 of 50000, Atoms: 461(A), 246(P), ChiSq: 28243, Time: 00:00:19 / 00:00:42
49000 of 50000, Atoms: 472(A), 229(P), ChiSq: 28290, Time: 00:00:20 / 00:00:43
50000 of 50000, Atoms: 474(A), 236(P), ChiSq: 28221, Time: 00:00:20 / 00:00:42
-- Sampling Phase --
1000 of 50000, Atoms: 463(A), 236(P), ChiSq: 28129, Time: 00:00:21 / 00:00:43
2000 of 50000, Atoms: 466(A), 235(P), ChiSq: 28262, Time: 00:00:21 / 00:00:43
3000 of 50000, Atoms: 458(A), 223(P), ChiSq: 28266, Time: 00:00:22 / 00:00:44
4000 of 50000, Atoms: 480(A), 235(P), ChiSq: 28181, Time: 00:00:22 / 00:00:43
5000 of 50000, Atoms: 465(A), 244(P), ChiSq: 28261, Time: 00:00:23 / 00:00:44
6000 of 50000, Atoms: 467(A), 231(P), ChiSq: 28258, Time: 00:00:23 / 00:00:43
7000 of 50000, Atoms: 468(A), 223(P), ChiSq: 28265, Time: 00:00:23 / 00:00:42
8000 of 50000, Atoms: 465(A), 226(P), ChiSq: 28206, Time: 00:00:24 / 00:00:43
9000 of 50000, Atoms: 457(A), 234(P), ChiSq: 28263, Time: 00:00:24 / 00:00:42
10000 of 50000, Atoms: 452(A), 234(P), ChiSq: 28182, Time: 00:00:25 / 00:00:43
11000 of 50000, Atoms: 456(A), 229(P), ChiSq: 28229, Time: 00:00:25 / 00:00:43
12000 of 50000, Atoms: 467(A), 233(P), ChiSq: 28220, Time: 00:00:26 / 00:00:43
13000 of 50000, Atoms: 480(A), 231(P), ChiSq: 28186, Time: 00:00:26 / 00:00:43
14000 of 50000, Atoms: 463(A), 221(P), ChiSq: 28239, Time: 00:00:27 / 00:00:44
15000 of 50000, Atoms: 468(A), 224(P), ChiSq: 28241, Time: 00:00:27 / 00:00:43
16000 of 50000, Atoms: 433(A), 223(P), ChiSq: 28232, Time: 00:00:28 / 00:00:44
17000 of 50000, Atoms: 450(A), 235(P), ChiSq: 28229, Time: 00:00:28 / 00:00:43
18000 of 50000, Atoms: 457(A), 232(P), ChiSq: 28206, Time: 00:00:28 / 00:00:42
19000 of 50000, Atoms: 468(A), 238(P), ChiSq: 28250, Time: 00:00:29 / 00:00:43
20000 of 50000, Atoms: 476(A), 219(P), ChiSq: 28254, Time: 00:00:29 / 00:00:42
21000 of 50000, Atoms: 463(A), 226(P), ChiSq: 28212, Time: 00:00:30 / 00:00:43
22000 of 50000, Atoms: 472(A), 236(P), ChiSq: 28216, Time: 00:00:30 / 00:00:43
23000 of 50000, Atoms: 471(A), 230(P), ChiSq: 28252, Time: 00:00:31 / 00:00:43
24000 of 50000, Atoms: 462(A), 241(P), ChiSq: 28239, Time: 00:00:31 / 00:00:43
25000 of 50000, Atoms: 459(A), 243(P), ChiSq: 28277, Time: 00:00:32 / 00:00:43
26000 of 50000, Atoms: 463(A), 232(P), ChiSq: 28236, Time: 00:00:32 / 00:00:43
27000 of 50000, Atoms: 451(A), 240(P), ChiSq: 28288, Time: 00:00:32 / 00:00:42
28000 of 50000, Atoms: 456(A), 221(P), ChiSq: 28221, Time: 00:00:33 / 00:00:43
29000 of 50000, Atoms: 474(A), 225(P), ChiSq: 28241, Time: 00:00:33 / 00:00:42
30000 of 50000, Atoms: 461(A), 221(P), ChiSq: 28329, Time: 00:00:34 / 00:00:43
31000 of 50000, Atoms: 441(A), 238(P), ChiSq: 28291, Time: 00:00:34 / 00:00:42
32000 of 50000, Atoms: 469(A), 233(P), ChiSq: 28251, Time: 00:00:35 / 00:00:43
33000 of 50000, Atoms: 457(A), 215(P), ChiSq: 28238, Time: 00:00:35 / 00:00:42
34000 of 50000, Atoms: 463(A), 225(P), ChiSq: 28184, Time: 00:00:36 / 00:00:43
35000 of 50000, Atoms: 467(A), 226(P), ChiSq: 28281, Time: 00:00:36 / 00:00:43
36000 of 50000, Atoms: 471(A), 219(P), ChiSq: 28198, Time: 00:00:37 / 00:00:43
37000 of 50000, Atoms: 456(A), 222(P), ChiSq: 28153, Time: 00:00:37 / 00:00:43
38000 of 50000, Atoms: 470(A), 226(P), ChiSq: 28248, Time: 00:00:37 / 00:00:42
39000 of 50000, Atoms: 474(A), 239(P), ChiSq: 28311, Time: 00:00:38 / 00:00:43
40000 of 50000, Atoms: 452(A), 232(P), ChiSq: 28233, Time: 00:00:38 / 00:00:42
41000 of 50000, Atoms: 460(A), 237(P), ChiSq: 28259, Time: 00:00:39 / 00:00:43
42000 of 50000, Atoms: 481(A), 221(P), ChiSq: 28339, Time: 00:00:39 / 00:00:42
43000 of 50000, Atoms: 484(A), 232(P), ChiSq: 28224, Time: 00:00:40 / 00:00:43
44000 of 50000, Atoms: 477(A), 253(P), ChiSq: 28223, Time: 00:00:40 / 00:00:42
45000 of 50000, Atoms: 478(A), 229(P), ChiSq: 28169, Time: 00:00:41 / 00:00:43
46000 of 50000, Atoms: 482(A), 224(P), ChiSq: 28310, Time: 00:00:41 / 00:00:42
47000 of 50000, Atoms: 464(A), 235(P), ChiSq: 28278, Time: 00:00:42 / 00:00:43
48000 of 50000, Atoms: 445(A), 228(P), ChiSq: 28285, Time: 00:00:42 / 00:00:42
49000 of 50000, Atoms: 451(A), 232(P), ChiSq: 28263, Time: 00:00:42 / 00:00:42
50000 of 50000, Atoms: 471(A), 223(P), ChiSq: 28261, Time: 00:00:43 / 00:00:43
[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 
 59.843   0.763  60.679