##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:projectR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings projectR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/projectR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 28.15   0.03   28.17
* 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
  'F:/biocbuild/bbs-3.17-bioc/meat/projectR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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                 633 
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: 161(A), 151(P), ChiSq: 53807, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 207(A), 175(P), ChiSq: 39950, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 257(A), 187(P), ChiSq: 35985, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 266(A), 194(P), ChiSq: 33810, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 294(A), 210(P), ChiSq: 32772, Time: 00:00:00 / 00:00:00
6000 of 50000, Atoms: 284(A), 226(P), ChiSq: 32074, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 335(A), 214(P), ChiSq: 31622, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 331(A), 220(P), ChiSq: 31369, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 326(A), 230(P), ChiSq: 31142, Time: 00:00:01 / 00:00:14
10000 of 50000, Atoms: 322(A), 233(P), ChiSq: 31052, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 330(A), 236(P), ChiSq: 30824, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 350(A), 223(P), ChiSq: 30696, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 362(A), 233(P), ChiSq: 30593, Time: 00:00:02 / 00:00:19
14000 of 50000, Atoms: 357(A), 242(P), ChiSq: 30474, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 371(A), 240(P), ChiSq: 30515, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 380(A), 234(P), ChiSq: 30459, Time: 00:00:03 / 00:00:22
17000 of 50000, Atoms: 367(A), 262(P), ChiSq: 30295, Time: 00:00:03 / 00:00:21
18000 of 50000, Atoms: 364(A), 239(P), ChiSq: 30284, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 376(A), 246(P), ChiSq: 30220, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 382(A), 246(P), ChiSq: 30204, Time: 00:00:04 / 00:00:23
21000 of 50000, Atoms: 387(A), 256(P), ChiSq: 30086, Time: 00:00:04 / 00:00:22
22000 of 50000, Atoms: 376(A), 255(P), ChiSq: 30073, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 398(A), 249(P), ChiSq: 30065, Time: 00:00:05 / 00:00:25
24000 of 50000, Atoms: 401(A), 253(P), ChiSq: 30017, Time: 00:00:05 / 00:00:24
25000 of 50000, Atoms: 409(A), 263(P), ChiSq: 30021, Time: 00:00:05 / 00:00:23
26000 of 50000, Atoms: 412(A), 252(P), ChiSq: 29961, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 416(A), 252(P), ChiSq: 29986, Time: 00:00:06 / 00:00:25
28000 of 50000, Atoms: 406(A), 259(P), ChiSq: 29942, Time: 00:00:06 / 00:00:24
29000 of 50000, Atoms: 380(A), 253(P), ChiSq: 30029, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 392(A), 260(P), ChiSq: 29971, Time: 00:00:07 / 00:00:26
31000 of 50000, Atoms: 406(A), 258(P), ChiSq: 30003, Time: 00:00:07 / 00:00:25
32000 of 50000, Atoms: 419(A), 267(P), ChiSq: 29961, Time: 00:00:07 / 00:00:24
33000 of 50000, Atoms: 419(A), 257(P), ChiSq: 29965, Time: 00:00:08 / 00:00:27
34000 of 50000, Atoms: 422(A), 256(P), ChiSq: 29958, Time: 00:00:08 / 00:00:26
35000 of 50000, Atoms: 408(A), 259(P), ChiSq: 29944, Time: 00:00:08 / 00:00:25
36000 of 50000, Atoms: 381(A), 257(P), ChiSq: 30000, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 387(A), 262(P), ChiSq: 29963, Time: 00:00:09 / 00:00:26
38000 of 50000, Atoms: 397(A), 276(P), ChiSq: 29988, Time: 00:00:09 / 00:00:26
39000 of 50000, Atoms: 391(A), 242(P), ChiSq: 30035, Time: 00:00:09 / 00:00:25
40000 of 50000, Atoms: 387(A), 247(P), ChiSq: 29940, Time: 00:00:10 / 00:00:27
41000 of 50000, Atoms: 408(A), 279(P), ChiSq: 30004, Time: 00:00:10 / 00:00:26
42000 of 50000, Atoms: 401(A), 256(P), ChiSq: 29945, Time: 00:00:10 / 00:00:25
43000 of 50000, Atoms: 403(A), 238(P), ChiSq: 29934, Time: 00:00:10 / 00:00:25
44000 of 50000, Atoms: 408(A), 257(P), ChiSq: 29931, Time: 00:00:11 / 00:00:27
45000 of 50000, Atoms: 411(A), 243(P), ChiSq: 29939, Time: 00:00:11 / 00:00:26
46000 of 50000, Atoms: 408(A), 261(P), ChiSq: 29989, Time: 00:00:11 / 00:00:25
47000 of 50000, Atoms: 390(A), 248(P), ChiSq: 29999, Time: 00:00:11 / 00:00:25
48000 of 50000, Atoms: 392(A), 261(P), ChiSq: 29979, Time: 00:00:12 / 00:00:26
49000 of 50000, Atoms: 408(A), 258(P), ChiSq: 30002, Time: 00:00:12 / 00:00:26
50000 of 50000, Atoms: 396(A), 248(P), ChiSq: 30003, Time: 00:00:12 / 00:00:25
-- Sampling Phase --
1000 of 50000, Atoms: 409(A), 246(P), ChiSq: 29922, Time: 00:00:13 / 00:00:27
2000 of 50000, Atoms: 402(A), 256(P), ChiSq: 30033, Time: 00:00:13 / 00:00:26
3000 of 50000, Atoms: 423(A), 252(P), ChiSq: 30015, Time: 00:00:13 / 00:00:26
4000 of 50000, Atoms: 417(A), 256(P), ChiSq: 29940, Time: 00:00:13 / 00:00:25
5000 of 50000, Atoms: 403(A), 250(P), ChiSq: 29978, Time: 00:00:14 / 00:00:26
6000 of 50000, Atoms: 417(A), 267(P), ChiSq: 30072, Time: 00:00:14 / 00:00:26
7000 of 50000, Atoms: 393(A), 254(P), ChiSq: 29978, Time: 00:00:14 / 00:00:25
8000 of 50000, Atoms: 401(A), 253(P), ChiSq: 29980, Time: 00:00:14 / 00:00:25
9000 of 50000, Atoms: 403(A), 268(P), ChiSq: 29993, Time: 00:00:15 / 00:00:26
10000 of 50000, Atoms: 403(A), 255(P), ChiSq: 29979, Time: 00:00:15 / 00:00:26
11000 of 50000, Atoms: 396(A), 263(P), ChiSq: 29983, Time: 00:00:15 / 00:00:25
12000 of 50000, Atoms: 406(A), 248(P), ChiSq: 29976, Time: 00:00:16 / 00:00:27
13000 of 50000, Atoms: 425(A), 252(P), ChiSq: 29924, Time: 00:00:16 / 00:00:26
14000 of 50000, Atoms: 417(A), 263(P), ChiSq: 30020, Time: 00:00:16 / 00:00:26
15000 of 50000, Atoms: 419(A), 260(P), ChiSq: 30014, Time: 00:00:16 / 00:00:25
16000 of 50000, Atoms: 397(A), 269(P), ChiSq: 29967, Time: 00:00:17 / 00:00:26
17000 of 50000, Atoms: 405(A), 258(P), ChiSq: 29959, Time: 00:00:17 / 00:00:26
18000 of 50000, Atoms: 408(A), 243(P), ChiSq: 29996, Time: 00:00:17 / 00:00:25
19000 of 50000, Atoms: 397(A), 250(P), ChiSq: 29992, Time: 00:00:18 / 00:00:27
20000 of 50000, Atoms: 400(A), 262(P), ChiSq: 29888, Time: 00:00:18 / 00:00:26
21000 of 50000, Atoms: 414(A), 268(P), ChiSq: 29981, Time: 00:00:18 / 00:00:26
22000 of 50000, Atoms: 399(A), 250(P), ChiSq: 29995, Time: 00:00:18 / 00:00:25
23000 of 50000, Atoms: 412(A), 256(P), ChiSq: 29994, Time: 00:00:19 / 00:00:26
24000 of 50000, Atoms: 421(A), 255(P), ChiSq: 29931, Time: 00:00:19 / 00:00:26
25000 of 50000, Atoms: 416(A), 260(P), ChiSq: 30022, Time: 00:00:19 / 00:00:26
26000 of 50000, Atoms: 399(A), 244(P), ChiSq: 30006, Time: 00:00:19 / 00:00:25
27000 of 50000, Atoms: 425(A), 258(P), ChiSq: 29928, Time: 00:00:20 / 00:00:26
28000 of 50000, Atoms: 392(A), 262(P), ChiSq: 30022, Time: 00:00:20 / 00:00:26
29000 of 50000, Atoms: 398(A), 248(P), ChiSq: 30018, Time: 00:00:20 / 00:00:25
30000 of 50000, Atoms: 390(A), 255(P), ChiSq: 30021, Time: 00:00:21 / 00:00:26
31000 of 50000, Atoms: 403(A), 254(P), ChiSq: 29964, Time: 00:00:21 / 00:00:26
32000 of 50000, Atoms: 416(A), 256(P), ChiSq: 29907, Time: 00:00:21 / 00:00:26
33000 of 50000, Atoms: 390(A), 254(P), ChiSq: 29985, Time: 00:00:21 / 00:00:25
34000 of 50000, Atoms: 408(A), 248(P), ChiSq: 29911, Time: 00:00:22 / 00:00:26
35000 of 50000, Atoms: 399(A), 247(P), ChiSq: 30019, Time: 00:00:22 / 00:00:26
36000 of 50000, Atoms: 400(A), 242(P), ChiSq: 29968, Time: 00:00:22 / 00:00:25
37000 of 50000, Atoms: 418(A), 261(P), ChiSq: 29965, Time: 00:00:23 / 00:00:26
38000 of 50000, Atoms: 394(A), 259(P), ChiSq: 30042, Time: 00:00:23 / 00:00:26
39000 of 50000, Atoms: 407(A), 245(P), ChiSq: 30015, Time: 00:00:23 / 00:00:26
40000 of 50000, Atoms: 414(A), 268(P), ChiSq: 30038, Time: 00:00:23 / 00:00:25
41000 of 50000, Atoms: 404(A), 271(P), ChiSq: 29980, Time: 00:00:24 / 00:00:26
42000 of 50000, Atoms: 400(A), 263(P), ChiSq: 29943, Time: 00:00:24 / 00:00:26
43000 of 50000, Atoms: 385(A), 258(P), ChiSq: 29957, Time: 00:00:24 / 00:00:25
44000 of 50000, Atoms: 385(A), 264(P), ChiSq: 29978, Time: 00:00:24 / 00:00:25
45000 of 50000, Atoms: 409(A), 251(P), ChiSq: 29921, Time: 00:00:25 / 00:00:26
46000 of 50000, Atoms: 411(A), 250(P), ChiSq: 29976, Time: 00:00:25 / 00:00:26
47000 of 50000, Atoms: 411(A), 261(P), ChiSq: 29982, Time: 00:00:25 / 00:00:25
48000 of 50000, Atoms: 412(A), 260(P), ChiSq: 29972, Time: 00:00:26 / 00:00:26
49000 of 50000, Atoms: 390(A), 249(P), ChiSq: 29948, Time: 00:00:26 / 00:00:26
50000 of 50000, Atoms: 390(A), 249(P), ChiSq: 29998, Time: 00:00:26 / 00:00:26
[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 
  37.34    0.70   38.03