##############################################################################
##############################################################################
###
### 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/projectR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.15.0'
* 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 24.64   0.03   24.67
* 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-rtools43/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 3.19.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 801 
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: 176(A), 158(P), ChiSq: 52906, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 221(A), 162(P), ChiSq: 43316, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 239(A), 194(P), ChiSq: 35576, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 280(A), 206(P), ChiSq: 33793, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 279(A), 211(P), ChiSq: 33136, Time: 00:00:00 / 00:00:00
6000 of 50000, Atoms: 285(A), 223(P), ChiSq: 32564, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 304(A), 214(P), ChiSq: 32037, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 300(A), 216(P), ChiSq: 31576, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 316(A), 228(P), ChiSq: 31374, Time: 00:00:01 / 00:00:14
10000 of 50000, Atoms: 324(A), 226(P), ChiSq: 31210, Time: 00:00:01 / 00:00:12
11000 of 50000, Atoms: 339(A), 225(P), ChiSq: 30781, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 337(A), 239(P), ChiSq: 30727, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 337(A), 226(P), ChiSq: 30666, Time: 00:00:02 / 00:00:19
14000 of 50000, Atoms: 354(A), 242(P), ChiSq: 30556, Time: 00:00:02 / 00:00:17
15000 of 50000, Atoms: 352(A), 233(P), ChiSq: 30478, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 370(A), 245(P), ChiSq: 30477, Time: 00:00:03 / 00:00:22
17000 of 50000, Atoms: 360(A), 230(P), ChiSq: 30438, Time: 00:00:03 / 00:00:21
18000 of 50000, Atoms: 385(A), 225(P), ChiSq: 30316, Time: 00:00:03 / 00:00:19
19000 of 50000, Atoms: 372(A), 242(P), ChiSq: 30323, Time: 00:00:03 / 00:00:18
20000 of 50000, Atoms: 384(A), 252(P), ChiSq: 30202, Time: 00:00:04 / 00:00:23
21000 of 50000, Atoms: 395(A), 253(P), ChiSq: 30196, Time: 00:00:04 / 00:00:22
22000 of 50000, Atoms: 376(A), 252(P), ChiSq: 30113, Time: 00:00:04 / 00:00:21
23000 of 50000, Atoms: 374(A), 247(P), ChiSq: 30151, Time: 00:00:04 / 00:00:20
24000 of 50000, Atoms: 404(A), 244(P), ChiSq: 30066, Time: 00:00:05 / 00:00:24
25000 of 50000, Atoms: 411(A), 245(P), ChiSq: 30022, Time: 00:00:05 / 00:00:23
26000 of 50000, Atoms: 384(A), 258(P), ChiSq: 30027, Time: 00:00:05 / 00:00:22
27000 of 50000, Atoms: 394(A), 253(P), ChiSq: 29999, Time: 00:00:05 / 00:00:21
28000 of 50000, Atoms: 400(A), 258(P), ChiSq: 29993, Time: 00:00:06 / 00:00:24
29000 of 50000, Atoms: 381(A), 246(P), ChiSq: 30039, Time: 00:00:06 / 00:00:23
30000 of 50000, Atoms: 401(A), 258(P), ChiSq: 29919, Time: 00:00:06 / 00:00:22
31000 of 50000, Atoms: 381(A), 273(P), ChiSq: 30051, Time: 00:00:06 / 00:00:21
32000 of 50000, Atoms: 415(A), 250(P), ChiSq: 30010, Time: 00:00:06 / 00:00:21
33000 of 50000, Atoms: 399(A), 254(P), ChiSq: 30004, Time: 00:00:07 / 00:00:23
34000 of 50000, Atoms: 388(A), 261(P), ChiSq: 29991, Time: 00:00:07 / 00:00:22
35000 of 50000, Atoms: 427(A), 251(P), ChiSq: 29990, Time: 00:00:07 / 00:00:22
36000 of 50000, Atoms: 399(A), 261(P), ChiSq: 30017, Time: 00:00:07 / 00:00:21
37000 of 50000, Atoms: 410(A), 262(P), ChiSq: 29930, Time: 00:00:08 / 00:00:23
38000 of 50000, Atoms: 387(A), 281(P), ChiSq: 30055, Time: 00:00:08 / 00:00:23
39000 of 50000, Atoms: 411(A), 255(P), ChiSq: 29990, Time: 00:00:08 / 00:00:22
40000 of 50000, Atoms: 401(A), 249(P), ChiSq: 29938, Time: 00:00:08 / 00:00:21
41000 of 50000, Atoms: 415(A), 259(P), ChiSq: 29994, Time: 00:00:09 / 00:00:23
42000 of 50000, Atoms: 403(A), 247(P), ChiSq: 29985, Time: 00:00:09 / 00:00:23
43000 of 50000, Atoms: 400(A), 258(P), ChiSq: 30005, Time: 00:00:09 / 00:00:22
44000 of 50000, Atoms: 413(A), 251(P), ChiSq: 29967, Time: 00:00:09 / 00:00:22
45000 of 50000, Atoms: 408(A), 252(P), ChiSq: 29937, Time: 00:00:10 / 00:00:24
46000 of 50000, Atoms: 420(A), 247(P), ChiSq: 30039, Time: 00:00:10 / 00:00:23
47000 of 50000, Atoms: 413(A), 259(P), ChiSq: 29973, Time: 00:00:10 / 00:00:22
48000 of 50000, Atoms: 413(A), 262(P), ChiSq: 29962, Time: 00:00:10 / 00:00:22
49000 of 50000, Atoms: 409(A), 257(P), ChiSq: 29981, Time: 00:00:11 / 00:00:24
50000 of 50000, Atoms: 418(A), 251(P), ChiSq: 29993, Time: 00:00:11 / 00:00:23
-- Sampling Phase --
1000 of 50000, Atoms: 415(A), 257(P), ChiSq: 30065, Time: 00:00:11 / 00:00:23
2000 of 50000, Atoms: 419(A), 271(P), ChiSq: 29967, Time: 00:00:11 / 00:00:22
3000 of 50000, Atoms: 416(A), 250(P), ChiSq: 29954, Time: 00:00:12 / 00:00:24
4000 of 50000, Atoms: 407(A), 253(P), ChiSq: 29984, Time: 00:00:12 / 00:00:23
5000 of 50000, Atoms: 406(A), 243(P), ChiSq: 30010, Time: 00:00:12 / 00:00:23
6000 of 50000, Atoms: 416(A), 242(P), ChiSq: 29981, Time: 00:00:12 / 00:00:22
7000 of 50000, Atoms: 394(A), 274(P), ChiSq: 29972, Time: 00:00:13 / 00:00:24
8000 of 50000, Atoms: 399(A), 252(P), ChiSq: 30039, Time: 00:00:13 / 00:00:23
9000 of 50000, Atoms: 407(A), 259(P), ChiSq: 30054, Time: 00:00:13 / 00:00:23
10000 of 50000, Atoms: 397(A), 261(P), ChiSq: 29937, Time: 00:00:13 / 00:00:22
11000 of 50000, Atoms: 393(A), 262(P), ChiSq: 29977, Time: 00:00:14 / 00:00:24
12000 of 50000, Atoms: 384(A), 265(P), ChiSq: 29967, Time: 00:00:14 / 00:00:23
13000 of 50000, Atoms: 414(A), 251(P), ChiSq: 29964, Time: 00:00:14 / 00:00:23
14000 of 50000, Atoms: 381(A), 259(P), ChiSq: 30001, Time: 00:00:14 / 00:00:22
15000 of 50000, Atoms: 409(A), 241(P), ChiSq: 29924, Time: 00:00:15 / 00:00:24
16000 of 50000, Atoms: 414(A), 241(P), ChiSq: 29918, Time: 00:00:15 / 00:00:23
17000 of 50000, Atoms: 398(A), 244(P), ChiSq: 30005, Time: 00:00:15 / 00:00:23
18000 of 50000, Atoms: 418(A), 244(P), ChiSq: 29974, Time: 00:00:15 / 00:00:22
19000 of 50000, Atoms: 406(A), 262(P), ChiSq: 30032, Time: 00:00:16 / 00:00:24
20000 of 50000, Atoms: 405(A), 258(P), ChiSq: 29996, Time: 00:00:16 / 00:00:23
21000 of 50000, Atoms: 410(A), 269(P), ChiSq: 29948, Time: 00:00:16 / 00:00:23
22000 of 50000, Atoms: 410(A), 255(P), ChiSq: 29954, Time: 00:00:16 / 00:00:22
23000 of 50000, Atoms: 414(A), 246(P), ChiSq: 29951, Time: 00:00:17 / 00:00:24
24000 of 50000, Atoms: 410(A), 251(P), ChiSq: 29928, Time: 00:00:17 / 00:00:23
25000 of 50000, Atoms: 400(A), 267(P), ChiSq: 29999, Time: 00:00:17 / 00:00:23
26000 of 50000, Atoms: 418(A), 256(P), ChiSq: 29965, Time: 00:00:17 / 00:00:22
27000 of 50000, Atoms: 373(A), 270(P), ChiSq: 29957, Time: 00:00:18 / 00:00:23
28000 of 50000, Atoms: 407(A), 245(P), ChiSq: 30029, Time: 00:00:18 / 00:00:23
29000 of 50000, Atoms: 405(A), 241(P), ChiSq: 29971, Time: 00:00:18 / 00:00:23
30000 of 50000, Atoms: 407(A), 259(P), ChiSq: 29984, Time: 00:00:18 / 00:00:22
31000 of 50000, Atoms: 412(A), 253(P), ChiSq: 29974, Time: 00:00:19 / 00:00:23
32000 of 50000, Atoms: 387(A), 267(P), ChiSq: 29926, Time: 00:00:19 / 00:00:23
33000 of 50000, Atoms: 396(A), 262(P), ChiSq: 29968, Time: 00:00:19 / 00:00:23
34000 of 50000, Atoms: 404(A), 250(P), ChiSq: 29983, Time: 00:00:19 / 00:00:23
35000 of 50000, Atoms: 415(A), 241(P), ChiSq: 29995, Time: 00:00:20 / 00:00:23
36000 of 50000, Atoms: 414(A), 256(P), ChiSq: 29969, Time: 00:00:20 / 00:00:23
37000 of 50000, Atoms: 399(A), 272(P), ChiSq: 29948, Time: 00:00:20 / 00:00:23
38000 of 50000, Atoms: 408(A), 272(P), ChiSq: 30022, Time: 00:00:20 / 00:00:23
39000 of 50000, Atoms: 426(A), 255(P), ChiSq: 29927, Time: 00:00:21 / 00:00:23
40000 of 50000, Atoms: 432(A), 265(P), ChiSq: 29984, Time: 00:00:21 / 00:00:23
41000 of 50000, Atoms: 405(A), 245(P), ChiSq: 30039, Time: 00:00:21 / 00:00:23
42000 of 50000, Atoms: 403(A), 255(P), ChiSq: 30003, Time: 00:00:21 / 00:00:23
43000 of 50000, Atoms: 410(A), 261(P), ChiSq: 29975, Time: 00:00:22 / 00:00:23
44000 of 50000, Atoms: 420(A), 274(P), ChiSq: 29964, Time: 00:00:22 / 00:00:23
45000 of 50000, Atoms: 416(A), 251(P), ChiSq: 29960, Time: 00:00:22 / 00:00:23
46000 of 50000, Atoms: 409(A), 252(P), ChiSq: 29950, Time: 00:00:22 / 00:00:23
47000 of 50000, Atoms: 399(A), 252(P), ChiSq: 29999, Time: 00:00:23 / 00:00:23
48000 of 50000, Atoms: 422(A), 267(P), ChiSq: 29913, Time: 00:00:23 / 00:00:23
49000 of 50000, Atoms: 401(A), 276(P), ChiSq: 29999, Time: 00:00:23 / 00:00:23
50000 of 50000, Atoms: 409(A), 266(P), ChiSq: 30013, Time: 00:00:23 / 00:00:23
[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 
  30.95    0.56   31.51