##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings projectR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/projectR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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:
  .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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
projectR-methods 31.078  0.248  31.328
* 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-3.13-bioc/meat/projectR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL projectR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 3.12.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 355 
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: 191(A), 138(P), ChiSq: 53869, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 206(A), 192(P), ChiSq: 39846, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 236(A), 203(P), ChiSq: 36662, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 256(A), 197(P), ChiSq: 36060, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 274(A), 210(P), ChiSq: 34848, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 265(A), 208(P), ChiSq: 34595, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 278(A), 224(P), ChiSq: 34006, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 289(A), 218(P), ChiSq: 33681, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 296(A), 227(P), ChiSq: 33326, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 315(A), 238(P), ChiSq: 33077, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 336(A), 249(P), ChiSq: 32563, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 343(A), 223(P), ChiSq: 31144, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 349(A), 231(P), ChiSq: 30756, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 373(A), 233(P), ChiSq: 30582, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 368(A), 228(P), ChiSq: 30583, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 386(A), 230(P), ChiSq: 30385, Time: 00:00:04 / 00:00:30
17000 of 50000, Atoms: 367(A), 263(P), ChiSq: 30393, Time: 00:00:04 / 00:00:28
18000 of 50000, Atoms: 347(A), 251(P), ChiSq: 30313, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 380(A), 253(P), ChiSq: 30261, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 377(A), 245(P), ChiSq: 30313, Time: 00:00:05 / 00:00:29
21000 of 50000, Atoms: 373(A), 263(P), ChiSq: 30133, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 399(A), 244(P), ChiSq: 30147, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 408(A), 251(P), ChiSq: 30130, Time: 00:00:06 / 00:00:30
24000 of 50000, Atoms: 393(A), 244(P), ChiSq: 30057, Time: 00:00:06 / 00:00:28
25000 of 50000, Atoms: 394(A), 262(P), ChiSq: 30046, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 395(A), 248(P), ChiSq: 29986, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 409(A), 246(P), ChiSq: 29966, Time: 00:00:07 / 00:00:29
28000 of 50000, Atoms: 394(A), 248(P), ChiSq: 30003, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 388(A), 248(P), ChiSq: 30051, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 412(A), 256(P), ChiSq: 29963, Time: 00:00:08 / 00:00:30
31000 of 50000, Atoms: 404(A), 254(P), ChiSq: 29972, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 399(A), 250(P), ChiSq: 30036, Time: 00:00:08 / 00:00:28
33000 of 50000, Atoms: 405(A), 248(P), ChiSq: 29963, Time: 00:00:09 / 00:00:30
34000 of 50000, Atoms: 396(A), 245(P), ChiSq: 30022, Time: 00:00:09 / 00:00:29
35000 of 50000, Atoms: 409(A), 251(P), ChiSq: 29973, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 407(A), 248(P), ChiSq: 29980, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 398(A), 253(P), ChiSq: 29949, Time: 00:00:10 / 00:00:29
38000 of 50000, Atoms: 400(A), 250(P), ChiSq: 29918, Time: 00:00:10 / 00:00:28
39000 of 50000, Atoms: 412(A), 254(P), ChiSq: 29932, Time: 00:00:10 / 00:00:28
40000 of 50000, Atoms: 413(A), 258(P), ChiSq: 29966, Time: 00:00:11 / 00:00:30
41000 of 50000, Atoms: 407(A), 262(P), ChiSq: 30008, Time: 00:00:11 / 00:00:29
42000 of 50000, Atoms: 396(A), 260(P), ChiSq: 29977, Time: 00:00:11 / 00:00:28
43000 of 50000, Atoms: 415(A), 262(P), ChiSq: 29985, Time: 00:00:11 / 00:00:27
44000 of 50000, Atoms: 412(A), 249(P), ChiSq: 30035, Time: 00:00:12 / 00:00:29
45000 of 50000, Atoms: 406(A), 267(P), ChiSq: 29898, Time: 00:00:12 / 00:00:28
46000 of 50000, Atoms: 391(A), 251(P), ChiSq: 29991, Time: 00:00:12 / 00:00:28
47000 of 50000, Atoms: 388(A), 258(P), ChiSq: 29985, Time: 00:00:13 / 00:00:29
48000 of 50000, Atoms: 406(A), 268(P), ChiSq: 29955, Time: 00:00:13 / 00:00:29
49000 of 50000, Atoms: 396(A), 263(P), ChiSq: 29941, Time: 00:00:13 / 00:00:28
50000 of 50000, Atoms: 400(A), 247(P), ChiSq: 29960, Time: 00:00:14 / 00:00:29
-- Sampling Phase --
1000 of 50000, Atoms: 413(A), 256(P), ChiSq: 29960, Time: 00:00:14 / 00:00:29
2000 of 50000, Atoms: 426(A), 268(P), ChiSq: 29983, Time: 00:00:14 / 00:00:28
3000 of 50000, Atoms: 428(A), 241(P), ChiSq: 29913, Time: 00:00:15 / 00:00:30
4000 of 50000, Atoms: 393(A), 246(P), ChiSq: 29998, Time: 00:00:15 / 00:00:29
5000 of 50000, Atoms: 401(A), 262(P), ChiSq: 29931, Time: 00:00:15 / 00:00:28
6000 of 50000, Atoms: 403(A), 254(P), ChiSq: 29998, Time: 00:00:16 / 00:00:30
7000 of 50000, Atoms: 402(A), 250(P), ChiSq: 30073, Time: 00:00:16 / 00:00:29
8000 of 50000, Atoms: 412(A), 250(P), ChiSq: 30001, Time: 00:00:16 / 00:00:29
9000 of 50000, Atoms: 405(A), 238(P), ChiSq: 30064, Time: 00:00:16 / 00:00:28
10000 of 50000, Atoms: 412(A), 254(P), ChiSq: 29971, Time: 00:00:17 / 00:00:29
11000 of 50000, Atoms: 418(A), 251(P), ChiSq: 29971, Time: 00:00:17 / 00:00:29
12000 of 50000, Atoms: 390(A), 253(P), ChiSq: 30000, Time: 00:00:17 / 00:00:28
13000 of 50000, Atoms: 374(A), 252(P), ChiSq: 29985, Time: 00:00:18 / 00:00:29
14000 of 50000, Atoms: 400(A), 246(P), ChiSq: 30057, Time: 00:00:18 / 00:00:29
15000 of 50000, Atoms: 412(A), 253(P), ChiSq: 29961, Time: 00:00:18 / 00:00:28
16000 of 50000, Atoms: 412(A), 251(P), ChiSq: 29997, Time: 00:00:19 / 00:00:29
17000 of 50000, Atoms: 394(A), 259(P), ChiSq: 30029, Time: 00:00:19 / 00:00:29
18000 of 50000, Atoms: 415(A), 253(P), ChiSq: 29930, Time: 00:00:19 / 00:00:29
19000 of 50000, Atoms: 392(A), 261(P), ChiSq: 29967, Time: 00:00:20 / 00:00:30
20000 of 50000, Atoms: 394(A), 249(P), ChiSq: 29964, Time: 00:00:20 / 00:00:29
21000 of 50000, Atoms: 408(A), 253(P), ChiSq: 29971, Time: 00:00:20 / 00:00:29
22000 of 50000, Atoms: 404(A), 256(P), ChiSq: 29976, Time: 00:00:21 / 00:00:30
23000 of 50000, Atoms: 438(A), 260(P), ChiSq: 29524, Time: 00:00:21 / 00:00:29
24000 of 50000, Atoms: 459(A), 248(P), ChiSq: 29393, Time: 00:00:21 / 00:00:29
25000 of 50000, Atoms: 472(A), 230(P), ChiSq: 28721, Time: 00:00:22 / 00:00:30
26000 of 50000, Atoms: 496(A), 223(P), ChiSq: 28239, Time: 00:00:22 / 00:00:29
27000 of 50000, Atoms: 507(A), 209(P), ChiSq: 28117, Time: 00:00:22 / 00:00:29
28000 of 50000, Atoms: 468(A), 230(P), ChiSq: 28134, Time: 00:00:23 / 00:00:30
29000 of 50000, Atoms: 478(A), 223(P), ChiSq: 28206, Time: 00:00:23 / 00:00:29
30000 of 50000, Atoms: 458(A), 217(P), ChiSq: 28177, Time: 00:00:23 / 00:00:29
31000 of 50000, Atoms: 464(A), 225(P), ChiSq: 28152, Time: 00:00:24 / 00:00:30
32000 of 50000, Atoms: 462(A), 234(P), ChiSq: 28214, Time: 00:00:24 / 00:00:29
33000 of 50000, Atoms: 473(A), 225(P), ChiSq: 28147, Time: 00:00:24 / 00:00:29
34000 of 50000, Atoms: 478(A), 234(P), ChiSq: 28186, Time: 00:00:25 / 00:00:30
35000 of 50000, Atoms: 454(A), 230(P), ChiSq: 28249, Time: 00:00:25 / 00:00:29
36000 of 50000, Atoms: 478(A), 233(P), ChiSq: 28155, Time: 00:00:25 / 00:00:29
37000 of 50000, Atoms: 492(A), 232(P), ChiSq: 28239, Time: 00:00:26 / 00:00:30
38000 of 50000, Atoms: 458(A), 236(P), ChiSq: 28211, Time: 00:00:26 / 00:00:29
39000 of 50000, Atoms: 482(A), 233(P), ChiSq: 28245, Time: 00:00:26 / 00:00:29
40000 of 50000, Atoms: 470(A), 233(P), ChiSq: 28201, Time: 00:00:27 / 00:00:30
41000 of 50000, Atoms: 482(A), 237(P), ChiSq: 28191, Time: 00:00:27 / 00:00:29
42000 of 50000, Atoms: 471(A), 238(P), ChiSq: 28202, Time: 00:00:27 / 00:00:29
43000 of 50000, Atoms: 479(A), 223(P), ChiSq: 28188, Time: 00:00:28 / 00:00:30
44000 of 50000, Atoms: 480(A), 225(P), ChiSq: 28200, Time: 00:00:28 / 00:00:29
45000 of 50000, Atoms: 459(A), 235(P), ChiSq: 28226, Time: 00:00:28 / 00:00:29
46000 of 50000, Atoms: 478(A), 235(P), ChiSq: 28122, Time: 00:00:28 / 00:00:29
47000 of 50000, Atoms: 480(A), 240(P), ChiSq: 28190, Time: 00:00:29 / 00:00:29
48000 of 50000, Atoms: 469(A), 238(P), ChiSq: 28204, Time: 00:00:29 / 00:00:29
49000 of 50000, Atoms: 476(A), 229(P), ChiSq: 28216, Time: 00:00:29 / 00:00:29
50000 of 50000, Atoms: 459(A), 240(P), ChiSq: 28231, 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 ]
> 
> proc.time()
   user  system elapsed 
 38.737   0.445  39.173