##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings projectR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/projectR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
projectR-methods 49.097  1.543  50.665
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/projectR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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-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 3.8.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 637 
sparseOptimization   FALSE 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

Data Model: Dense, Normal
Sampler Type: Asynchronous
Loading Data...Done! (00:00:00)
Running on 1 out of 20 available threads
-- Equilibration Phase --
1000 of 50000, Atoms: 185(A), 83(P), ChiSq: 52438, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 263(A), 139(P), ChiSq: 41438, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 291(A), 163(P), ChiSq: 35029, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 299(A), 180(P), ChiSq: 33467, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 322(A), 193(P), ChiSq: 31956, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 385(A), 188(P), ChiSq: 30655, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 392(A), 183(P), ChiSq: 30267, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 397(A), 199(P), ChiSq: 29912, Time: 00:00:03 / 00:00:49
9000 of 50000, Atoms: 402(A), 197(P), ChiSq: 29637, Time: 00:00:03 / 00:00:43
10000 of 50000, Atoms: 431(A), 202(P), ChiSq: 29311, Time: 00:00:04 / 00:00:51
11000 of 50000, Atoms: 416(A), 208(P), ChiSq: 29148, Time: 00:00:04 / 00:00:46
12000 of 50000, Atoms: 422(A), 206(P), ChiSq: 29107, Time: 00:00:05 / 00:00:52
13000 of 50000, Atoms: 433(A), 211(P), ChiSq: 29058, Time: 00:00:06 / 00:00:57
14000 of 50000, Atoms: 439(A), 215(P), ChiSq: 28793, Time: 00:00:06 / 00:00:52
15000 of 50000, Atoms: 458(A), 208(P), ChiSq: 28810, Time: 00:00:07 / 00:00:56
16000 of 50000, Atoms: 477(A), 206(P), ChiSq: 28714, Time: 00:00:07 / 00:00:52
17000 of 50000, Atoms: 456(A), 226(P), ChiSq: 28523, Time: 00:00:08 / 00:00:56
18000 of 50000, Atoms: 470(A), 224(P), ChiSq: 28566, Time: 00:00:08 / 00:00:53
19000 of 50000, Atoms: 480(A), 226(P), ChiSq: 28526, Time: 00:00:09 / 00:00:56
20000 of 50000, Atoms: 466(A), 217(P), ChiSq: 28462, Time: 00:00:09 / 00:00:53
21000 of 50000, Atoms: 470(A), 230(P), ChiSq: 28419, Time: 00:00:09 / 00:00:50
22000 of 50000, Atoms: 490(A), 223(P), ChiSq: 28345, Time: 00:00:10 / 00:00:53
23000 of 50000, Atoms: 480(A), 218(P), ChiSq: 28316, Time: 00:00:11 / 00:00:55
24000 of 50000, Atoms: 498(A), 242(P), ChiSq: 28287, Time: 00:00:11 / 00:00:53
25000 of 50000, Atoms: 482(A), 228(P), ChiSq: 28202, Time: 00:00:12 / 00:00:55
26000 of 50000, Atoms: 480(A), 232(P), ChiSq: 28245, Time: 00:00:12 / 00:00:52
27000 of 50000, Atoms: 501(A), 230(P), ChiSq: 28175, Time: 00:00:13 / 00:00:54
28000 of 50000, Atoms: 480(A), 242(P), ChiSq: 28275, Time: 00:00:14 / 00:00:56
29000 of 50000, Atoms: 476(A), 231(P), ChiSq: 28252, Time: 00:00:14 / 00:00:54
30000 of 50000, Atoms: 509(A), 231(P), ChiSq: 28290, Time: 00:00:15 / 00:00:56
31000 of 50000, Atoms: 496(A), 217(P), ChiSq: 28232, Time: 00:00:16 / 00:00:58
32000 of 50000, Atoms: 485(A), 228(P), ChiSq: 28251, Time: 00:00:16 / 00:00:56
33000 of 50000, Atoms: 481(A), 221(P), ChiSq: 28253, Time: 00:00:17 / 00:00:57
34000 of 50000, Atoms: 514(A), 236(P), ChiSq: 28223, Time: 00:00:17 / 00:00:55
35000 of 50000, Atoms: 516(A), 224(P), ChiSq: 28135, Time: 00:00:18 / 00:00:57
36000 of 50000, Atoms: 477(A), 224(P), ChiSq: 28259, Time: 00:00:18 / 00:00:55
37000 of 50000, Atoms: 493(A), 241(P), ChiSq: 28250, Time: 00:00:19 / 00:00:56
38000 of 50000, Atoms: 499(A), 233(P), ChiSq: 28243, Time: 00:00:20 / 00:00:57
39000 of 50000, Atoms: 486(A), 235(P), ChiSq: 28232, Time: 00:00:20 / 00:00:56
40000 of 50000, Atoms: 482(A), 246(P), ChiSq: 28285, Time: 00:00:21 / 00:00:57
41000 of 50000, Atoms: 492(A), 248(P), ChiSq: 28266, Time: 00:00:21 / 00:00:55
42000 of 50000, Atoms: 486(A), 226(P), ChiSq: 28175, Time: 00:00:22 / 00:00:57
43000 of 50000, Atoms: 497(A), 227(P), ChiSq: 28258, Time: 00:00:23 / 00:00:58
44000 of 50000, Atoms: 491(A), 227(P), ChiSq: 28207, Time: 00:00:23 / 00:00:56
45000 of 50000, Atoms: 493(A), 221(P), ChiSq: 28249, Time: 00:00:24 / 00:00:57
46000 of 50000, Atoms: 483(A), 233(P), ChiSq: 28225, Time: 00:00:24 / 00:00:56
47000 of 50000, Atoms: 497(A), 235(P), ChiSq: 28272, Time: 00:00:24 / 00:00:55
48000 of 50000, Atoms: 501(A), 233(P), ChiSq: 28227, Time: 00:00:25 / 00:00:55
49000 of 50000, Atoms: 490(A), 222(P), ChiSq: 28251, Time: 00:00:25 / 00:00:54
50000 of 50000, Atoms: 495(A), 237(P), ChiSq: 28262, Time: 00:00:26 / 00:00:55
-- Sampling Phase --
1000 of 50000, Atoms: 465(A), 234(P), ChiSq: 28313, Time: 00:00:27 / 00:00:56
2000 of 50000, Atoms: 481(A), 241(P), ChiSq: 28222, Time: 00:00:27 / 00:00:55
3000 of 50000, Atoms: 486(A), 237(P), ChiSq: 28284, Time: 00:00:28 / 00:00:56
4000 of 50000, Atoms: 509(A), 234(P), ChiSq: 28223, Time: 00:00:28 / 00:00:55
5000 of 50000, Atoms: 476(A), 223(P), ChiSq: 28273, Time: 00:00:29 / 00:00:55
6000 of 50000, Atoms: 508(A), 239(P), ChiSq: 28235, Time: 00:00:29 / 00:00:54
7000 of 50000, Atoms: 498(A), 231(P), ChiSq: 28268, Time: 00:00:30 / 00:00:55
8000 of 50000, Atoms: 523(A), 221(P), ChiSq: 28195, Time: 00:00:31 / 00:00:56
9000 of 50000, Atoms: 504(A), 231(P), ChiSq: 28207, Time: 00:00:31 / 00:00:55
10000 of 50000, Atoms: 490(A), 230(P), ChiSq: 28272, Time: 00:00:32 / 00:00:56
11000 of 50000, Atoms: 495(A), 251(P), ChiSq: 28195, Time: 00:00:33 / 00:00:56
12000 of 50000, Atoms: 520(A), 224(P), ChiSq: 28177, Time: 00:00:33 / 00:00:55
13000 of 50000, Atoms: 495(A), 231(P), ChiSq: 28298, Time: 00:00:33 / 00:00:54
14000 of 50000, Atoms: 497(A), 225(P), ChiSq: 28245, Time: 00:00:34 / 00:00:55
15000 of 50000, Atoms: 493(A), 229(P), ChiSq: 28172, Time: 00:00:35 / 00:00:56
16000 of 50000, Atoms: 481(A), 227(P), ChiSq: 28300, Time: 00:00:35 / 00:00:55
17000 of 50000, Atoms: 494(A), 225(P), ChiSq: 28272, Time: 00:00:36 / 00:00:55
18000 of 50000, Atoms: 489(A), 222(P), ChiSq: 28279, Time: 00:00:36 / 00:00:54
19000 of 50000, Atoms: 489(A), 229(P), ChiSq: 28238, Time: 00:00:37 / 00:00:55
20000 of 50000, Atoms: 502(A), 220(P), ChiSq: 28218, Time: 00:00:37 / 00:00:54
21000 of 50000, Atoms: 503(A), 234(P), ChiSq: 28255, Time: 00:00:38 / 00:00:55
22000 of 50000, Atoms: 504(A), 221(P), ChiSq: 28229, Time: 00:00:38 / 00:00:54
23000 of 50000, Atoms: 508(A), 219(P), ChiSq: 28260, Time: 00:00:39 / 00:00:55
24000 of 50000, Atoms: 484(A), 230(P), ChiSq: 28222, Time: 00:00:39 / 00:00:54
25000 of 50000, Atoms: 502(A), 221(P), ChiSq: 28230, Time: 00:00:40 / 00:00:54
26000 of 50000, Atoms: 494(A), 233(P), ChiSq: 28158, Time: 00:00:40 / 00:00:54
27000 of 50000, Atoms: 504(A), 235(P), ChiSq: 28207, Time: 00:00:41 / 00:00:54
28000 of 50000, Atoms: 500(A), 233(P), ChiSq: 28282, Time: 00:00:41 / 00:00:53
29000 of 50000, Atoms: 497(A), 217(P), ChiSq: 28302, Time: 00:00:41 / 00:00:53
30000 of 50000, Atoms: 466(A), 238(P), ChiSq: 28227, Time: 00:00:42 / 00:00:53
31000 of 50000, Atoms: 504(A), 236(P), ChiSq: 28242, Time: 00:00:42 / 00:00:52
32000 of 50000, Atoms: 481(A), 245(P), ChiSq: 28282, Time: 00:00:43 / 00:00:53
33000 of 50000, Atoms: 496(A), 229(P), ChiSq: 28318, Time: 00:00:43 / 00:00:52
34000 of 50000, Atoms: 482(A), 241(P), ChiSq: 28275, Time: 00:00:44 / 00:00:53
35000 of 50000, Atoms: 483(A), 228(P), ChiSq: 28190, Time: 00:00:44 / 00:00:52
36000 of 50000, Atoms: 492(A), 231(P), ChiSq: 28285, Time: 00:00:45 / 00:00:53
37000 of 50000, Atoms: 487(A), 225(P), ChiSq: 28226, Time: 00:00:46 / 00:00:53
38000 of 50000, Atoms: 490(A), 249(P), ChiSq: 28214, Time: 00:00:46 / 00:00:52
39000 of 50000, Atoms: 492(A), 241(P), ChiSq: 28238, Time: 00:00:47 / 00:00:53
40000 of 50000, Atoms: 488(A), 236(P), ChiSq: 28168, Time: 00:00:47 / 00:00:52
41000 of 50000, Atoms: 485(A), 229(P), ChiSq: 28205, Time: 00:00:48 / 00:00:53
42000 of 50000, Atoms: 486(A), 231(P), ChiSq: 28249, Time: 00:00:48 / 00:00:52
43000 of 50000, Atoms: 494(A), 220(P), ChiSq: 28166, Time: 00:00:49 / 00:00:53
44000 of 50000, Atoms: 500(A), 219(P), ChiSq: 28274, Time: 00:00:49 / 00:00:52
45000 of 50000, Atoms: 504(A), 244(P), ChiSq: 28184, Time: 00:00:50 / 00:00:52
46000 of 50000, Atoms: 493(A), 229(P), ChiSq: 28267, Time: 00:00:50 / 00:00:52
47000 of 50000, Atoms: 501(A), 234(P), ChiSq: 28234, Time: 00:00:51 / 00:00:52
48000 of 50000, Atoms: 488(A), 232(P), ChiSq: 28215, Time: 00:00:51 / 00:00:52
49000 of 50000, Atoms: 510(A), 232(P), ChiSq: 28204, Time: 00:00:52 / 00:00:52
50000 of 50000, Atoms: 492(A), 222(P), ChiSq: 28209, Time: 00:00:52 / 00:00:52
[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 
 61.733   1.960  63.689