##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings projectR_1.4.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/projectR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.4.0’
* 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 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 38.663  0.055  38.871
* 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-3.11-bioc/meat/projectR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL projectR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 3.8.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 281 
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: 194(A), 99(P), ChiSq: 55137, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 248(A), 135(P), ChiSq: 40748, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 264(A), 150(P), ChiSq: 36606, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 299(A), 161(P), ChiSq: 34684, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 299(A), 170(P), ChiSq: 33466, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 309(A), 187(P), ChiSq: 32721, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 303(A), 190(P), ChiSq: 32277, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 337(A), 188(P), ChiSq: 31842, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 336(A), 186(P), ChiSq: 31669, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 351(A), 195(P), ChiSq: 31039, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 361(A), 189(P), ChiSq: 30442, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 401(A), 212(P), ChiSq: 30298, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 385(A), 212(P), ChiSq: 30258, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 385(A), 221(P), ChiSq: 30116, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 386(A), 204(P), ChiSq: 30144, Time: 00:00:04 / 00:00:32
16000 of 50000, Atoms: 401(A), 214(P), ChiSq: 30039, Time: 00:00:04 / 00:00:30
17000 of 50000, Atoms: 398(A), 217(P), ChiSq: 29937, Time: 00:00:05 / 00:00:35
18000 of 50000, Atoms: 405(A), 211(P), ChiSq: 29912, Time: 00:00:05 / 00:00:33
19000 of 50000, Atoms: 406(A), 212(P), ChiSq: 29875, Time: 00:00:05 / 00:00:31
20000 of 50000, Atoms: 409(A), 234(P), ChiSq: 29785, Time: 00:00:06 / 00:00:35
21000 of 50000, Atoms: 415(A), 220(P), ChiSq: 29678, Time: 00:00:06 / 00:00:33
22000 of 50000, Atoms: 418(A), 220(P), ChiSq: 29499, Time: 00:00:06 / 00:00:31
23000 of 50000, Atoms: 458(A), 239(P), ChiSq: 29215, Time: 00:00:07 / 00:00:35
24000 of 50000, Atoms: 489(A), 232(P), ChiSq: 28523, Time: 00:00:07 / 00:00:33
25000 of 50000, Atoms: 484(A), 229(P), ChiSq: 28506, Time: 00:00:08 / 00:00:36
26000 of 50000, Atoms: 461(A), 231(P), ChiSq: 28176, Time: 00:00:08 / 00:00:35
27000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28162, Time: 00:00:08 / 00:00:33
28000 of 50000, Atoms: 489(A), 234(P), ChiSq: 28198, Time: 00:00:09 / 00:00:36
29000 of 50000, Atoms: 483(A), 227(P), ChiSq: 28216, Time: 00:00:09 / 00:00:35
30000 of 50000, Atoms: 476(A), 224(P), ChiSq: 28102, Time: 00:00:10 / 00:00:37
31000 of 50000, Atoms: 474(A), 225(P), ChiSq: 28187, Time: 00:00:10 / 00:00:36
32000 of 50000, Atoms: 458(A), 237(P), ChiSq: 28145, Time: 00:00:10 / 00:00:35
33000 of 50000, Atoms: 458(A), 224(P), ChiSq: 28199, Time: 00:00:11 / 00:00:37
34000 of 50000, Atoms: 464(A), 218(P), ChiSq: 28208, Time: 00:00:11 / 00:00:36
35000 of 50000, Atoms: 477(A), 233(P), ChiSq: 28183, Time: 00:00:12 / 00:00:38
36000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28218, Time: 00:00:12 / 00:00:36
37000 of 50000, Atoms: 463(A), 221(P), ChiSq: 28194, Time: 00:00:12 / 00:00:35
38000 of 50000, Atoms: 467(A), 222(P), ChiSq: 28187, Time: 00:00:13 / 00:00:37
39000 of 50000, Atoms: 466(A), 238(P), ChiSq: 28210, Time: 00:00:13 / 00:00:36
40000 of 50000, Atoms: 477(A), 243(P), ChiSq: 28142, Time: 00:00:14 / 00:00:38
41000 of 50000, Atoms: 459(A), 239(P), ChiSq: 28158, Time: 00:00:14 / 00:00:37
42000 of 50000, Atoms: 470(A), 225(P), ChiSq: 28174, Time: 00:00:14 / 00:00:36
43000 of 50000, Atoms: 453(A), 239(P), ChiSq: 28195, Time: 00:00:15 / 00:00:37
44000 of 50000, Atoms: 466(A), 229(P), ChiSq: 28178, Time: 00:00:15 / 00:00:36
45000 of 50000, Atoms: 467(A), 232(P), ChiSq: 28212, Time: 00:00:16 / 00:00:38
46000 of 50000, Atoms: 473(A), 234(P), ChiSq: 28208, Time: 00:00:16 / 00:00:37
47000 of 50000, Atoms: 467(A), 233(P), ChiSq: 28185, Time: 00:00:17 / 00:00:38
48000 of 50000, Atoms: 466(A), 229(P), ChiSq: 28214, Time: 00:00:17 / 00:00:38
49000 of 50000, Atoms: 471(A), 234(P), ChiSq: 28218, Time: 00:00:17 / 00:00:37
50000 of 50000, Atoms: 477(A), 219(P), ChiSq: 28178, Time: 00:00:18 / 00:00:38
-- Sampling Phase --
1000 of 50000, Atoms: 460(A), 244(P), ChiSq: 28270, Time: 00:00:18 / 00:00:37
2000 of 50000, Atoms: 467(A), 233(P), ChiSq: 28242, Time: 00:00:19 / 00:00:38
3000 of 50000, Atoms: 470(A), 223(P), ChiSq: 28192, Time: 00:00:19 / 00:00:38
4000 of 50000, Atoms: 476(A), 226(P), ChiSq: 28132, Time: 00:00:19 / 00:00:37
5000 of 50000, Atoms: 485(A), 234(P), ChiSq: 28199, Time: 00:00:20 / 00:00:38
6000 of 50000, Atoms: 473(A), 234(P), ChiSq: 28255, Time: 00:00:20 / 00:00:37
7000 of 50000, Atoms: 470(A), 247(P), ChiSq: 28126, Time: 00:00:21 / 00:00:38
8000 of 50000, Atoms: 477(A), 225(P), ChiSq: 28172, Time: 00:00:21 / 00:00:38
9000 of 50000, Atoms: 474(A), 227(P), ChiSq: 28154, Time: 00:00:22 / 00:00:39
10000 of 50000, Atoms: 469(A), 227(P), ChiSq: 28199, Time: 00:00:22 / 00:00:38
11000 of 50000, Atoms: 469(A), 228(P), ChiSq: 28176, Time: 00:00:22 / 00:00:37
12000 of 50000, Atoms: 476(A), 222(P), ChiSq: 28175, Time: 00:00:23 / 00:00:38
13000 of 50000, Atoms: 462(A), 229(P), ChiSq: 28154, Time: 00:00:23 / 00:00:38
14000 of 50000, Atoms: 481(A), 227(P), ChiSq: 28188, Time: 00:00:24 / 00:00:39
15000 of 50000, Atoms: 462(A), 226(P), ChiSq: 28160, Time: 00:00:24 / 00:00:38
16000 of 50000, Atoms: 465(A), 224(P), ChiSq: 28196, Time: 00:00:24 / 00:00:37
17000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28240, Time: 00:00:25 / 00:00:38
18000 of 50000, Atoms: 465(A), 241(P), ChiSq: 28231, Time: 00:00:25 / 00:00:38
19000 of 50000, Atoms: 459(A), 233(P), ChiSq: 28159, Time: 00:00:26 / 00:00:39
20000 of 50000, Atoms: 478(A), 225(P), ChiSq: 28181, Time: 00:00:26 / 00:00:38
21000 of 50000, Atoms: 458(A), 224(P), ChiSq: 28202, Time: 00:00:27 / 00:00:39
22000 of 50000, Atoms: 499(A), 231(P), ChiSq: 28227, Time: 00:00:27 / 00:00:38
23000 of 50000, Atoms: 470(A), 237(P), ChiSq: 28246, Time: 00:00:27 / 00:00:38
24000 of 50000, Atoms: 476(A), 242(P), ChiSq: 28159, Time: 00:00:28 / 00:00:38
25000 of 50000, Atoms: 470(A), 243(P), ChiSq: 28141, Time: 00:00:28 / 00:00:38
26000 of 50000, Atoms: 463(A), 233(P), ChiSq: 28187, Time: 00:00:29 / 00:00:39
27000 of 50000, Atoms: 486(A), 228(P), ChiSq: 28182, Time: 00:00:29 / 00:00:38
28000 of 50000, Atoms: 472(A), 227(P), ChiSq: 28156, Time: 00:00:30 / 00:00:39
29000 of 50000, Atoms: 475(A), 238(P), ChiSq: 28140, Time: 00:00:30 / 00:00:38
30000 of 50000, Atoms: 480(A), 242(P), ChiSq: 28200, Time: 00:00:30 / 00:00:38
31000 of 50000, Atoms: 469(A), 228(P), ChiSq: 28249, Time: 00:00:31 / 00:00:39
32000 of 50000, Atoms: 464(A), 241(P), ChiSq: 28243, Time: 00:00:31 / 00:00:38
33000 of 50000, Atoms: 458(A), 233(P), ChiSq: 28225, Time: 00:00:32 / 00:00:39
34000 of 50000, Atoms: 459(A), 236(P), ChiSq: 28263, Time: 00:00:32 / 00:00:38
35000 of 50000, Atoms: 469(A), 239(P), ChiSq: 28253, Time: 00:00:32 / 00:00:38
36000 of 50000, Atoms: 475(A), 239(P), ChiSq: 28182, Time: 00:00:33 / 00:00:38
37000 of 50000, Atoms: 471(A), 221(P), ChiSq: 28145, Time: 00:00:33 / 00:00:38
38000 of 50000, Atoms: 464(A), 228(P), ChiSq: 28257, Time: 00:00:34 / 00:00:39
39000 of 50000, Atoms: 473(A), 236(P), ChiSq: 28214, Time: 00:00:34 / 00:00:38
40000 of 50000, Atoms: 482(A), 228(P), ChiSq: 28203, Time: 00:00:34 / 00:00:38
41000 of 50000, Atoms: 477(A), 225(P), ChiSq: 28183, Time: 00:00:35 / 00:00:38
42000 of 50000, Atoms: 452(A), 226(P), ChiSq: 28213, Time: 00:00:35 / 00:00:38
43000 of 50000, Atoms: 473(A), 228(P), ChiSq: 28197, Time: 00:00:36 / 00:00:38
44000 of 50000, Atoms: 469(A), 238(P), ChiSq: 28160, Time: 00:00:36 / 00:00:38
45000 of 50000, Atoms: 461(A), 251(P), ChiSq: 28235, Time: 00:00:36 / 00:00:38
46000 of 50000, Atoms: 478(A), 228(P), ChiSq: 28207, Time: 00:00:37 / 00:00:38
47000 of 50000, Atoms: 468(A), 225(P), ChiSq: 28211, Time: 00:00:37 / 00:00:38
48000 of 50000, Atoms: 466(A), 245(P), ChiSq: 28224, Time: 00:00:38 / 00:00:38
49000 of 50000, Atoms: 447(A), 237(P), ChiSq: 28188, Time: 00:00:38 / 00:00:38
50000 of 50000, Atoms: 461(A), 235(P), ChiSq: 28216, Time: 00:00:39 / 00:00:39
[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"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 52.222   0.687  52.918