##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings projectR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/projectR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
projectR-methods 31.297  0.107  31.405
* 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 ...
  ‘projectR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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-pc-linux-gnu (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                 296 
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: 210(A), 127(P), ChiSq: 47011, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 256(A), 148(P), ChiSq: 37624, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 276(A), 164(P), ChiSq: 35092, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 304(A), 186(P), ChiSq: 33367, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 332(A), 180(P), ChiSq: 32080, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 356(A), 187(P), ChiSq: 30722, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 372(A), 199(P), ChiSq: 30288, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 374(A), 205(P), ChiSq: 29976, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 393(A), 198(P), ChiSq: 29506, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 388(A), 207(P), ChiSq: 29294, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 397(A), 209(P), ChiSq: 29287, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 415(A), 220(P), ChiSq: 29025, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 416(A), 222(P), ChiSq: 28822, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 418(A), 226(P), ChiSq: 28850, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 448(A), 218(P), ChiSq: 28787, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 433(A), 201(P), ChiSq: 28704, Time: 00:00:04 / 00:00:30
17000 of 50000, Atoms: 430(A), 221(P), ChiSq: 28642, Time: 00:00:04 / 00:00:28
18000 of 50000, Atoms: 443(A), 230(P), ChiSq: 28461, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 436(A), 229(P), ChiSq: 28456, Time: 00:00:05 / 00:00:31
20000 of 50000, Atoms: 428(A), 223(P), ChiSq: 28400, Time: 00:00:05 / 00:00:29
21000 of 50000, Atoms: 455(A), 222(P), ChiSq: 28360, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 480(A), 237(P), ChiSq: 28364, Time: 00:00:06 / 00:00:31
23000 of 50000, Atoms: 448(A), 230(P), ChiSq: 28414, Time: 00:00:06 / 00:00:30
24000 of 50000, Atoms: 452(A), 238(P), ChiSq: 28293, Time: 00:00:06 / 00:00:28
25000 of 50000, Atoms: 462(A), 220(P), ChiSq: 28244, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 442(A), 237(P), ChiSq: 28259, Time: 00:00:07 / 00:00:30
27000 of 50000, Atoms: 460(A), 223(P), ChiSq: 28249, Time: 00:00:07 / 00:00:29
28000 of 50000, Atoms: 465(A), 224(P), ChiSq: 28232, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 466(A), 241(P), ChiSq: 28244, Time: 00:00:08 / 00:00:31
30000 of 50000, Atoms: 451(A), 237(P), ChiSq: 28271, Time: 00:00:08 / 00:00:30
31000 of 50000, Atoms: 448(A), 235(P), ChiSq: 28193, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 455(A), 234(P), ChiSq: 28255, Time: 00:00:09 / 00:00:31
33000 of 50000, Atoms: 441(A), 231(P), ChiSq: 28261, Time: 00:00:09 / 00:00:30
34000 of 50000, Atoms: 450(A), 236(P), ChiSq: 28183, Time: 00:00:09 / 00:00:29
35000 of 50000, Atoms: 457(A), 234(P), ChiSq: 28263, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 454(A), 237(P), ChiSq: 28294, Time: 00:00:10 / 00:00:30
37000 of 50000, Atoms: 450(A), 244(P), ChiSq: 28283, Time: 00:00:10 / 00:00:29
38000 of 50000, Atoms: 461(A), 224(P), ChiSq: 28320, Time: 00:00:10 / 00:00:28
39000 of 50000, Atoms: 464(A), 223(P), ChiSq: 28267, Time: 00:00:11 / 00:00:30
40000 of 50000, Atoms: 462(A), 233(P), ChiSq: 28147, Time: 00:00:11 / 00:00:30
41000 of 50000, Atoms: 465(A), 226(P), ChiSq: 28305, Time: 00:00:11 / 00:00:29
42000 of 50000, Atoms: 465(A), 239(P), ChiSq: 28219, Time: 00:00:12 / 00:00:31
43000 of 50000, Atoms: 451(A), 231(P), ChiSq: 28201, Time: 00:00:12 / 00:00:30
44000 of 50000, Atoms: 459(A), 228(P), ChiSq: 28274, Time: 00:00:12 / 00:00:29
45000 of 50000, Atoms: 468(A), 232(P), ChiSq: 28192, Time: 00:00:13 / 00:00:31
46000 of 50000, Atoms: 455(A), 233(P), ChiSq: 28240, Time: 00:00:13 / 00:00:30
47000 of 50000, Atoms: 457(A), 235(P), ChiSq: 28201, Time: 00:00:13 / 00:00:29
48000 of 50000, Atoms: 463(A), 228(P), ChiSq: 28178, Time: 00:00:13 / 00:00:29
49000 of 50000, Atoms: 449(A), 239(P), ChiSq: 28248, Time: 00:00:14 / 00:00:30
50000 of 50000, Atoms: 485(A), 225(P), ChiSq: 28285, Time: 00:00:14 / 00:00:29
-- Sampling Phase --
1000 of 50000, Atoms: 473(A), 237(P), ChiSq: 28182, Time: 00:00:14 / 00:00:29
2000 of 50000, Atoms: 482(A), 240(P), ChiSq: 28298, Time: 00:00:15 / 00:00:30
3000 of 50000, Atoms: 468(A), 229(P), ChiSq: 28227, Time: 00:00:15 / 00:00:30
4000 of 50000, Atoms: 464(A), 233(P), ChiSq: 28242, Time: 00:00:15 / 00:00:29
5000 of 50000, Atoms: 481(A), 233(P), ChiSq: 28231, Time: 00:00:16 / 00:00:30
6000 of 50000, Atoms: 465(A), 215(P), ChiSq: 28280, Time: 00:00:16 / 00:00:30
7000 of 50000, Atoms: 462(A), 231(P), ChiSq: 28316, Time: 00:00:16 / 00:00:29
8000 of 50000, Atoms: 481(A), 244(P), ChiSq: 28282, Time: 00:00:17 / 00:00:30
9000 of 50000, Atoms: 474(A), 247(P), ChiSq: 28215, Time: 00:00:17 / 00:00:30
10000 of 50000, Atoms: 457(A), 255(P), ChiSq: 28235, Time: 00:00:17 / 00:00:29
11000 of 50000, Atoms: 467(A), 235(P), ChiSq: 28227, Time: 00:00:18 / 00:00:30
12000 of 50000, Atoms: 458(A), 218(P), ChiSq: 28231, Time: 00:00:18 / 00:00:30
13000 of 50000, Atoms: 471(A), 221(P), ChiSq: 28253, Time: 00:00:18 / 00:00:29
14000 of 50000, Atoms: 445(A), 228(P), ChiSq: 28209, Time: 00:00:19 / 00:00:31
15000 of 50000, Atoms: 450(A), 231(P), ChiSq: 28245, Time: 00:00:19 / 00:00:30
16000 of 50000, Atoms: 453(A), 222(P), ChiSq: 28332, Time: 00:00:19 / 00:00:29
17000 of 50000, Atoms: 471(A), 225(P), ChiSq: 28284, Time: 00:00:20 / 00:00:31
18000 of 50000, Atoms: 453(A), 224(P), ChiSq: 28223, Time: 00:00:20 / 00:00:30
19000 of 50000, Atoms: 451(A), 237(P), ChiSq: 28233, Time: 00:00:20 / 00:00:30
20000 of 50000, Atoms: 456(A), 237(P), ChiSq: 28265, Time: 00:00:21 / 00:00:31
21000 of 50000, Atoms: 475(A), 243(P), ChiSq: 28212, Time: 00:00:21 / 00:00:30
22000 of 50000, Atoms: 467(A), 225(P), ChiSq: 28285, Time: 00:00:21 / 00:00:30
23000 of 50000, Atoms: 463(A), 215(P), ChiSq: 28342, Time: 00:00:22 / 00:00:31
24000 of 50000, Atoms: 441(A), 239(P), ChiSq: 28253, Time: 00:00:22 / 00:00:30
25000 of 50000, Atoms: 467(A), 243(P), ChiSq: 28197, Time: 00:00:22 / 00:00:30
26000 of 50000, Atoms: 471(A), 220(P), ChiSq: 28188, Time: 00:00:23 / 00:00:31
27000 of 50000, Atoms: 464(A), 225(P), ChiSq: 28174, Time: 00:00:23 / 00:00:30
28000 of 50000, Atoms: 465(A), 225(P), ChiSq: 28272, Time: 00:00:23 / 00:00:30
29000 of 50000, Atoms: 465(A), 240(P), ChiSq: 28240, Time: 00:00:24 / 00:00:31
30000 of 50000, Atoms: 473(A), 236(P), ChiSq: 28208, Time: 00:00:24 / 00:00:30
31000 of 50000, Atoms: 470(A), 230(P), ChiSq: 28226, Time: 00:00:24 / 00:00:30
32000 of 50000, Atoms: 450(A), 230(P), ChiSq: 28233, Time: 00:00:25 / 00:00:31
33000 of 50000, Atoms: 477(A), 234(P), ChiSq: 28249, Time: 00:00:25 / 00:00:30
34000 of 50000, Atoms: 450(A), 235(P), ChiSq: 28230, Time: 00:00:25 / 00:00:30
35000 of 50000, Atoms: 475(A), 235(P), ChiSq: 28283, Time: 00:00:26 / 00:00:31
36000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28257, Time: 00:00:26 / 00:00:30
37000 of 50000, Atoms: 455(A), 240(P), ChiSq: 28219, Time: 00:00:26 / 00:00:30
38000 of 50000, Atoms: 456(A), 250(P), ChiSq: 28285, Time: 00:00:27 / 00:00:31
39000 of 50000, Atoms: 475(A), 233(P), ChiSq: 28192, Time: 00:00:27 / 00:00:30
40000 of 50000, Atoms: 445(A), 230(P), ChiSq: 28251, Time: 00:00:27 / 00:00:30
41000 of 50000, Atoms: 456(A), 226(P), ChiSq: 28197, Time: 00:00:27 / 00:00:29
42000 of 50000, Atoms: 466(A), 236(P), ChiSq: 28248, Time: 00:00:28 / 00:00:30
43000 of 50000, Atoms: 476(A), 216(P), ChiSq: 28212, Time: 00:00:28 / 00:00:30
44000 of 50000, Atoms: 457(A), 227(P), ChiSq: 28206, Time: 00:00:28 / 00:00:29
45000 of 50000, Atoms: 451(A), 224(P), ChiSq: 28293, Time: 00:00:29 / 00:00:30
46000 of 50000, Atoms: 483(A), 219(P), ChiSq: 28210, Time: 00:00:29 / 00:00:30
47000 of 50000, Atoms: 459(A), 239(P), ChiSq: 28230, Time: 00:00:29 / 00:00:29
48000 of 50000, Atoms: 482(A), 238(P), ChiSq: 28172, Time: 00:00:30 / 00:00:30
49000 of 50000, Atoms: 472(A), 226(P), ChiSq: 28253, Time: 00:00:30 / 00:00:30
50000 of 50000, Atoms: 482(A), 223(P), ChiSq: 28221, Time: 00:00:30 / 00:00:30
[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 
 39.999   0.544  40.526