##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings projectR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/projectR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘projectR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘projectR’ version ‘1.16.0’
* 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 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 29.604  0.194  45.609
* 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-3.17-bioc-mac-arm64/meat/projectR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL projectR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 3.20.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 313 
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: 192(A), 117(P), ChiSq: 54619, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 275(A), 131(P), ChiSq: 40438, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 298(A), 147(P), ChiSq: 36670, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 336(A), 170(P), ChiSq: 33701, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 343(A), 163(P), ChiSq: 32844, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 357(A), 181(P), ChiSq: 32226, Time: 00:00:02 / 00:00:45
7000 of 50000, Atoms: 362(A), 196(P), ChiSq: 31440, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 366(A), 202(P), ChiSq: 30861, Time: 00:00:03 / 00:00:49
9000 of 50000, Atoms: 380(A), 208(P), ChiSq: 30621, Time: 00:00:03 / 00:00:43
10000 of 50000, Atoms: 379(A), 207(P), ChiSq: 30556, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 391(A), 215(P), ChiSq: 30302, Time: 00:00:04 / 00:00:46
12000 of 50000, Atoms: 376(A), 221(P), ChiSq: 30363, Time: 00:00:04 / 00:00:41
13000 of 50000, Atoms: 388(A), 218(P), ChiSq: 30240, Time: 00:00:05 / 00:00:47
14000 of 50000, Atoms: 392(A), 228(P), ChiSq: 29944, Time: 00:00:05 / 00:00:43
15000 of 50000, Atoms: 419(A), 231(P), ChiSq: 29882, Time: 00:00:06 / 00:00:48
16000 of 50000, Atoms: 419(A), 228(P), ChiSq: 29735, Time: 00:00:06 / 00:00:45
17000 of 50000, Atoms: 417(A), 231(P), ChiSq: 29654, Time: 00:00:07 / 00:00:49
18000 of 50000, Atoms: 417(A), 241(P), ChiSq: 29531, Time: 00:00:07 / 00:00:46
19000 of 50000, Atoms: 435(A), 243(P), ChiSq: 29419, Time: 00:00:08 / 00:00:50
20000 of 50000, Atoms: 459(A), 246(P), ChiSq: 29229, Time: 00:00:08 / 00:00:47
21000 of 50000, Atoms: 481(A), 238(P), ChiSq: 28695, Time: 00:00:09 / 00:00:50
22000 of 50000, Atoms: 459(A), 238(P), ChiSq: 28309, Time: 00:00:09 / 00:00:47
23000 of 50000, Atoms: 448(A), 247(P), ChiSq: 28217, Time: 00:00:10 / 00:00:50
24000 of 50000, Atoms: 476(A), 241(P), ChiSq: 28215, Time: 00:00:10 / 00:00:48
25000 of 50000, Atoms: 480(A), 233(P), ChiSq: 28308, Time: 00:00:11 / 00:00:50
26000 of 50000, Atoms: 477(A), 230(P), ChiSq: 28197, Time: 00:00:11 / 00:00:48
27000 of 50000, Atoms: 454(A), 231(P), ChiSq: 28177, Time: 00:00:12 / 00:00:50
28000 of 50000, Atoms: 470(A), 224(P), ChiSq: 28244, Time: 00:00:12 / 00:00:48
29000 of 50000, Atoms: 461(A), 220(P), ChiSq: 28251, Time: 00:00:13 / 00:00:50
30000 of 50000, Atoms: 464(A), 232(P), ChiSq: 28248, Time: 00:00:13 / 00:00:48
31000 of 50000, Atoms: 473(A), 240(P), ChiSq: 28213, Time: 00:00:14 / 00:00:50
32000 of 50000, Atoms: 440(A), 224(P), ChiSq: 28188, Time: 00:00:14 / 00:00:49
33000 of 50000, Atoms: 456(A), 229(P), ChiSq: 28162, Time: 00:00:15 / 00:00:50
34000 of 50000, Atoms: 469(A), 240(P), ChiSq: 28240, Time: 00:00:15 / 00:00:49
35000 of 50000, Atoms: 482(A), 237(P), ChiSq: 28251, Time: 00:00:16 / 00:00:50
36000 of 50000, Atoms: 480(A), 244(P), ChiSq: 28186, Time: 00:00:16 / 00:00:49
37000 of 50000, Atoms: 465(A), 245(P), ChiSq: 28165, Time: 00:00:17 / 00:00:50
38000 of 50000, Atoms: 458(A), 231(P), ChiSq: 28260, Time: 00:00:17 / 00:00:49
39000 of 50000, Atoms: 474(A), 239(P), ChiSq: 28236, Time: 00:00:18 / 00:00:50
40000 of 50000, Atoms: 479(A), 237(P), ChiSq: 28190, Time: 00:00:18 / 00:00:49
41000 of 50000, Atoms: 479(A), 238(P), ChiSq: 28249, Time: 00:00:19 / 00:00:50
42000 of 50000, Atoms: 486(A), 243(P), ChiSq: 28213, Time: 00:00:19 / 00:00:49
43000 of 50000, Atoms: 470(A), 234(P), ChiSq: 28277, Time: 00:00:20 / 00:00:50
44000 of 50000, Atoms: 468(A), 220(P), ChiSq: 28225, Time: 00:00:20 / 00:00:49
45000 of 50000, Atoms: 467(A), 242(P), ChiSq: 28198, Time: 00:00:21 / 00:00:50
46000 of 50000, Atoms: 470(A), 241(P), ChiSq: 28262, Time: 00:00:21 / 00:00:49
47000 of 50000, Atoms: 465(A), 234(P), ChiSq: 28269, Time: 00:00:22 / 00:00:50
48000 of 50000, Atoms: 471(A), 230(P), ChiSq: 28227, Time: 00:00:22 / 00:00:49
49000 of 50000, Atoms: 462(A), 231(P), ChiSq: 28149, Time: 00:00:22 / 00:00:48
50000 of 50000, Atoms: 462(A), 233(P), ChiSq: 28144, Time: 00:00:23 / 00:00:49
-- Sampling Phase --
1000 of 50000, Atoms: 477(A), 234(P), ChiSq: 28240, Time: 00:00:24 / 00:00:50
2000 of 50000, Atoms: 483(A), 233(P), ChiSq: 28189, Time: 00:00:24 / 00:00:49
3000 of 50000, Atoms: 443(A), 243(P), ChiSq: 28220, Time: 00:00:25 / 00:00:50
4000 of 50000, Atoms: 482(A), 221(P), ChiSq: 28215, Time: 00:00:25 / 00:00:49
5000 of 50000, Atoms: 442(A), 235(P), ChiSq: 28216, Time: 00:00:26 / 00:00:50
6000 of 50000, Atoms: 461(A), 242(P), ChiSq: 28183, Time: 00:00:26 / 00:00:49
7000 of 50000, Atoms: 466(A), 235(P), ChiSq: 28220, Time: 00:00:27 / 00:00:50
8000 of 50000, Atoms: 493(A), 223(P), ChiSq: 28238, Time: 00:00:27 / 00:00:49
9000 of 50000, Atoms: 459(A), 227(P), ChiSq: 28240, Time: 00:00:28 / 00:00:49
10000 of 50000, Atoms: 472(A), 235(P), ChiSq: 28220, Time: 00:00:28 / 00:00:49
11000 of 50000, Atoms: 471(A), 240(P), ChiSq: 28195, Time: 00:00:29 / 00:00:49
12000 of 50000, Atoms: 464(A), 232(P), ChiSq: 28191, Time: 00:00:29 / 00:00:49
13000 of 50000, Atoms: 450(A), 219(P), ChiSq: 28300, Time: 00:00:30 / 00:00:49
14000 of 50000, Atoms: 464(A), 230(P), ChiSq: 28218, Time: 00:00:30 / 00:00:48
15000 of 50000, Atoms: 498(A), 238(P), ChiSq: 28158, Time: 00:00:31 / 00:00:49
16000 of 50000, Atoms: 455(A), 238(P), ChiSq: 28207, Time: 00:00:31 / 00:00:48
17000 of 50000, Atoms: 483(A), 234(P), ChiSq: 28266, Time: 00:00:31 / 00:00:48
18000 of 50000, Atoms: 482(A), 231(P), ChiSq: 28205, Time: 00:00:32 / 00:00:48
19000 of 50000, Atoms: 464(A), 226(P), ChiSq: 28238, Time: 00:00:32 / 00:00:48
20000 of 50000, Atoms: 468(A), 251(P), ChiSq: 28245, Time: 00:00:33 / 00:00:48
21000 of 50000, Atoms: 474(A), 231(P), ChiSq: 28192, Time: 00:00:33 / 00:00:48
22000 of 50000, Atoms: 470(A), 239(P), ChiSq: 28216, Time: 00:00:34 / 00:00:48
23000 of 50000, Atoms: 467(A), 237(P), ChiSq: 28189, Time: 00:00:34 / 00:00:48
24000 of 50000, Atoms: 459(A), 236(P), ChiSq: 28167, Time: 00:00:35 / 00:00:48
25000 of 50000, Atoms: 464(A), 227(P), ChiSq: 28211, Time: 00:00:35 / 00:00:47
26000 of 50000, Atoms: 457(A), 254(P), ChiSq: 28274, Time: 00:00:35 / 00:00:47
27000 of 50000, Atoms: 458(A), 254(P), ChiSq: 28200, Time: 00:00:36 / 00:00:47
28000 of 50000, Atoms: 456(A), 242(P), ChiSq: 28212, Time: 00:00:36 / 00:00:47
29000 of 50000, Atoms: 470(A), 226(P), ChiSq: 28281, Time: 00:00:37 / 00:00:47
30000 of 50000, Atoms: 462(A), 225(P), ChiSq: 28182, Time: 00:00:37 / 00:00:47
31000 of 50000, Atoms: 469(A), 235(P), ChiSq: 28168, Time: 00:00:38 / 00:00:47
32000 of 50000, Atoms: 463(A), 232(P), ChiSq: 28208, Time: 00:00:38 / 00:00:47
33000 of 50000, Atoms: 460(A), 216(P), ChiSq: 28269, Time: 00:00:38 / 00:00:46
34000 of 50000, Atoms: 485(A), 234(P), ChiSq: 28256, Time: 00:00:39 / 00:00:47
35000 of 50000, Atoms: 479(A), 235(P), ChiSq: 28245, Time: 00:00:39 / 00:00:46
36000 of 50000, Atoms: 483(A), 235(P), ChiSq: 28232, Time: 00:00:40 / 00:00:47
37000 of 50000, Atoms: 455(A), 228(P), ChiSq: 28280, Time: 00:00:40 / 00:00:46
38000 of 50000, Atoms: 477(A), 232(P), ChiSq: 28222, Time: 00:00:41 / 00:00:47
39000 of 50000, Atoms: 474(A), 237(P), ChiSq: 28242, Time: 00:00:41 / 00:00:46
40000 of 50000, Atoms: 486(A), 234(P), ChiSq: 28200, Time: 00:00:41 / 00:00:46
41000 of 50000, Atoms: 467(A), 244(P), ChiSq: 28214, Time: 00:00:42 / 00:00:46
42000 of 50000, Atoms: 468(A), 244(P), ChiSq: 28184, Time: 00:00:42 / 00:00:46
43000 of 50000, Atoms: 479(A), 241(P), ChiSq: 28172, Time: 00:00:43 / 00:00:46
44000 of 50000, Atoms: 480(A), 249(P), ChiSq: 28234, Time: 00:00:43 / 00:00:46
45000 of 50000, Atoms: 461(A), 236(P), ChiSq: 28233, Time: 00:00:44 / 00:00:46
46000 of 50000, Atoms: 470(A), 223(P), ChiSq: 28270, Time: 00:00:44 / 00:00:46
47000 of 50000, Atoms: 470(A), 232(P), ChiSq: 28216, Time: 00:00:45 / 00:00:46
48000 of 50000, Atoms: 475(A), 232(P), ChiSq: 28187, Time: 00:00:45 / 00:00:46
49000 of 50000, Atoms: 471(A), 234(P), ChiSq: 28119, Time: 00:00:46 / 00:00:46
50000 of 50000, Atoms: 483(A), 240(P), ChiSq: 28134, Time: 00:00:46 / 00:00:46
[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 
 45.126   0.860  67.725