##############################################################################
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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_1.8.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/projectR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  .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 36.562  0.096  36.695
* 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-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 3.12.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 596 
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: 204(A), 145(P), ChiSq: 53308, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 241(A), 187(P), ChiSq: 39406, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 259(A), 190(P), ChiSq: 35070, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 290(A), 201(P), ChiSq: 33563, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 300(A), 203(P), ChiSq: 32764, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 314(A), 218(P), ChiSq: 32082, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 356(A), 210(P), ChiSq: 30723, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 372(A), 195(P), ChiSq: 30048, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 383(A), 217(P), ChiSq: 29727, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 385(A), 206(P), ChiSq: 29459, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 407(A), 207(P), ChiSq: 29166, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 411(A), 213(P), ChiSq: 28933, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 414(A), 213(P), ChiSq: 28899, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 431(A), 213(P), ChiSq: 28845, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 413(A), 212(P), ChiSq: 28823, Time: 00:00:04 / 00:00:32
16000 of 50000, Atoms: 422(A), 211(P), ChiSq: 28797, Time: 00:00:04 / 00:00:30
17000 of 50000, Atoms: 427(A), 232(P), ChiSq: 28492, Time: 00:00:05 / 00:00:35
18000 of 50000, Atoms: 442(A), 219(P), ChiSq: 28541, Time: 00:00:05 / 00:00:33
19000 of 50000, Atoms: 456(A), 217(P), ChiSq: 28446, Time: 00:00:05 / 00:00:31
20000 of 50000, Atoms: 436(A), 229(P), ChiSq: 28453, Time: 00:00:06 / 00:00:35
21000 of 50000, Atoms: 443(A), 226(P), ChiSq: 28369, Time: 00:00:06 / 00:00:33
22000 of 50000, Atoms: 450(A), 222(P), ChiSq: 28272, Time: 00:00:06 / 00:00:31
23000 of 50000, Atoms: 482(A), 230(P), ChiSq: 28309, Time: 00:00:07 / 00:00:35
24000 of 50000, Atoms: 461(A), 220(P), ChiSq: 28298, Time: 00:00:07 / 00:00:33
25000 of 50000, Atoms: 452(A), 225(P), ChiSq: 28231, Time: 00:00:08 / 00:00:36
26000 of 50000, Atoms: 469(A), 235(P), ChiSq: 28185, Time: 00:00:08 / 00:00:35
27000 of 50000, Atoms: 468(A), 227(P), ChiSq: 28234, Time: 00:00:08 / 00:00:33
28000 of 50000, Atoms: 467(A), 241(P), ChiSq: 28268, Time: 00:00:09 / 00:00:36
29000 of 50000, Atoms: 483(A), 238(P), ChiSq: 28182, Time: 00:00:09 / 00:00:35
30000 of 50000, Atoms: 474(A), 241(P), ChiSq: 28207, Time: 00:00:09 / 00:00:33
31000 of 50000, Atoms: 477(A), 225(P), ChiSq: 28293, Time: 00:00:10 / 00:00:36
32000 of 50000, Atoms: 456(A), 227(P), ChiSq: 28249, Time: 00:00:10 / 00:00:35
33000 of 50000, Atoms: 465(A), 225(P), ChiSq: 28280, Time: 00:00:10 / 00:00:33
34000 of 50000, Atoms: 479(A), 221(P), ChiSq: 28240, Time: 00:00:11 / 00:00:36
35000 of 50000, Atoms: 459(A), 232(P), ChiSq: 28273, Time: 00:00:11 / 00:00:34
36000 of 50000, Atoms: 466(A), 242(P), ChiSq: 28160, Time: 00:00:11 / 00:00:33
37000 of 50000, Atoms: 465(A), 235(P), ChiSq: 28225, Time: 00:00:12 / 00:00:35
38000 of 50000, Atoms: 469(A), 217(P), ChiSq: 28266, Time: 00:00:12 / 00:00:34
39000 of 50000, Atoms: 475(A), 235(P), ChiSq: 28226, Time: 00:00:12 / 00:00:33
40000 of 50000, Atoms: 472(A), 220(P), ChiSq: 28172, Time: 00:00:13 / 00:00:35
41000 of 50000, Atoms: 482(A), 239(P), ChiSq: 28239, Time: 00:00:13 / 00:00:34
42000 of 50000, Atoms: 463(A), 242(P), ChiSq: 28217, Time: 00:00:13 / 00:00:33
43000 of 50000, Atoms: 461(A), 215(P), ChiSq: 28255, Time: 00:00:14 / 00:00:35
44000 of 50000, Atoms: 474(A), 228(P), ChiSq: 28312, Time: 00:00:14 / 00:00:34
45000 of 50000, Atoms: 477(A), 221(P), ChiSq: 28257, Time: 00:00:14 / 00:00:33
46000 of 50000, Atoms: 480(A), 216(P), ChiSq: 28211, Time: 00:00:15 / 00:00:35
47000 of 50000, Atoms: 455(A), 242(P), ChiSq: 28219, Time: 00:00:15 / 00:00:34
48000 of 50000, Atoms: 459(A), 233(P), ChiSq: 28242, Time: 00:00:15 / 00:00:33
49000 of 50000, Atoms: 471(A), 235(P), ChiSq: 28226, Time: 00:00:16 / 00:00:35
50000 of 50000, Atoms: 450(A), 222(P), ChiSq: 28255, Time: 00:00:16 / 00:00:34
-- Sampling Phase --
1000 of 50000, Atoms: 476(A), 234(P), ChiSq: 28278, Time: 00:00:17 / 00:00:35
2000 of 50000, Atoms: 475(A), 230(P), ChiSq: 28248, Time: 00:00:17 / 00:00:34
3000 of 50000, Atoms: 467(A), 234(P), ChiSq: 28244, Time: 00:00:17 / 00:00:34
4000 of 50000, Atoms: 464(A), 238(P), ChiSq: 28292, Time: 00:00:18 / 00:00:35
5000 of 50000, Atoms: 474(A), 227(P), ChiSq: 28210, Time: 00:00:18 / 00:00:34
6000 of 50000, Atoms: 480(A), 234(P), ChiSq: 28212, Time: 00:00:19 / 00:00:35
7000 of 50000, Atoms: 466(A), 230(P), ChiSq: 28243, Time: 00:00:19 / 00:00:35
8000 of 50000, Atoms: 437(A), 234(P), ChiSq: 28173, Time: 00:00:19 / 00:00:34
9000 of 50000, Atoms: 461(A), 225(P), ChiSq: 28255, Time: 00:00:20 / 00:00:35
10000 of 50000, Atoms: 484(A), 237(P), ChiSq: 28298, Time: 00:00:20 / 00:00:35
11000 of 50000, Atoms: 469(A), 235(P), ChiSq: 28265, Time: 00:00:21 / 00:00:36
12000 of 50000, Atoms: 467(A), 244(P), ChiSq: 28229, Time: 00:00:21 / 00:00:35
13000 of 50000, Atoms: 457(A), 230(P), ChiSq: 28283, Time: 00:00:21 / 00:00:34
14000 of 50000, Atoms: 501(A), 246(P), ChiSq: 28215, Time: 00:00:22 / 00:00:35
15000 of 50000, Atoms: 478(A), 232(P), ChiSq: 28272, Time: 00:00:22 / 00:00:35
16000 of 50000, Atoms: 466(A), 216(P), ChiSq: 28319, Time: 00:00:22 / 00:00:34
17000 of 50000, Atoms: 467(A), 233(P), ChiSq: 28245, Time: 00:00:23 / 00:00:35
18000 of 50000, Atoms: 471(A), 227(P), ChiSq: 28261, Time: 00:00:23 / 00:00:35
19000 of 50000, Atoms: 454(A), 225(P), ChiSq: 28205, Time: 00:00:24 / 00:00:36
20000 of 50000, Atoms: 464(A), 232(P), ChiSq: 28250, Time: 00:00:24 / 00:00:35
21000 of 50000, Atoms: 463(A), 228(P), ChiSq: 28234, Time: 00:00:24 / 00:00:34
22000 of 50000, Atoms: 469(A), 226(P), ChiSq: 28271, Time: 00:00:25 / 00:00:35
23000 of 50000, Atoms: 483(A), 231(P), ChiSq: 28226, Time: 00:00:25 / 00:00:35
24000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28230, Time: 00:00:26 / 00:00:36
25000 of 50000, Atoms: 480(A), 225(P), ChiSq: 28211, Time: 00:00:26 / 00:00:35
26000 of 50000, Atoms: 489(A), 222(P), ChiSq: 28239, Time: 00:00:26 / 00:00:35
27000 of 50000, Atoms: 464(A), 221(P), ChiSq: 28170, Time: 00:00:27 / 00:00:35
28000 of 50000, Atoms: 457(A), 235(P), ChiSq: 28212, Time: 00:00:27 / 00:00:35
29000 of 50000, Atoms: 470(A), 233(P), ChiSq: 28201, Time: 00:00:28 / 00:00:36
30000 of 50000, Atoms: 482(A), 221(P), ChiSq: 28181, Time: 00:00:28 / 00:00:35
31000 of 50000, Atoms: 468(A), 225(P), ChiSq: 28266, Time: 00:00:28 / 00:00:35
32000 of 50000, Atoms: 493(A), 216(P), ChiSq: 28301, Time: 00:00:29 / 00:00:36
33000 of 50000, Atoms: 476(A), 232(P), ChiSq: 28191, Time: 00:00:29 / 00:00:35
34000 of 50000, Atoms: 466(A), 238(P), ChiSq: 28180, Time: 00:00:30 / 00:00:36
35000 of 50000, Atoms: 460(A), 230(P), ChiSq: 28176, Time: 00:00:30 / 00:00:35
36000 of 50000, Atoms: 461(A), 237(P), ChiSq: 28257, Time: 00:00:31 / 00:00:36
37000 of 50000, Atoms: 462(A), 224(P), ChiSq: 28268, Time: 00:00:31 / 00:00:36
38000 of 50000, Atoms: 486(A), 224(P), ChiSq: 28259, Time: 00:00:31 / 00:00:35
39000 of 50000, Atoms: 464(A), 242(P), ChiSq: 28239, Time: 00:00:32 / 00:00:36
40000 of 50000, Atoms: 473(A), 229(P), ChiSq: 28262, Time: 00:00:32 / 00:00:35
41000 of 50000, Atoms: 484(A), 223(P), ChiSq: 28181, Time: 00:00:32 / 00:00:35
42000 of 50000, Atoms: 471(A), 234(P), ChiSq: 28262, Time: 00:00:33 / 00:00:36
43000 of 50000, Atoms: 482(A), 241(P), ChiSq: 28193, Time: 00:00:33 / 00:00:35
44000 of 50000, Atoms: 461(A), 232(P), ChiSq: 28216, Time: 00:00:34 / 00:00:36
45000 of 50000, Atoms: 489(A), 235(P), ChiSq: 28195, Time: 00:00:34 / 00:00:35
46000 of 50000, Atoms: 483(A), 220(P), ChiSq: 28193, Time: 00:00:34 / 00:00:35
47000 of 50000, Atoms: 477(A), 235(P), ChiSq: 28267, Time: 00:00:35 / 00:00:36
48000 of 50000, Atoms: 484(A), 242(P), ChiSq: 28248, Time: 00:00:35 / 00:00:35
49000 of 50000, Atoms: 481(A), 221(P), ChiSq: 28206, Time: 00:00:35 / 00:00:35
50000 of 50000, Atoms: 465(A), 229(P), ChiSq: 28245, Time: 00:00:36 / 00:00:36
[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 ]
> 
> proc.time()
   user  system elapsed 
 48.304   0.570  48.889