##############################################################################
##############################################################################
###
### 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 28.59   0.01   28.63
* 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                 519 
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: 207(A), 119(P), ChiSq: 53432, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 232(A), 153(P), ChiSq: 39011, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 280(A), 159(P), ChiSq: 35143, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 293(A), 173(P), ChiSq: 33984, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 302(A), 183(P), ChiSq: 33061, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 320(A), 197(P), ChiSq: 32456, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 333(A), 203(P), ChiSq: 31949, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 356(A), 204(P), ChiSq: 31459, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 353(A), 200(P), ChiSq: 31194, Time: 00:00:01 / 00:00:14
10000 of 50000, Atoms: 348(A), 200(P), ChiSq: 31105, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 353(A), 212(P), ChiSq: 31047, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 366(A), 211(P), ChiSq: 30832, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 374(A), 223(P), ChiSq: 30578, Time: 00:00:02 / 00:00:19
14000 of 50000, Atoms: 368(A), 219(P), ChiSq: 30629, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 377(A), 232(P), ChiSq: 30531, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 385(A), 222(P), ChiSq: 30418, Time: 00:00:03 / 00:00:22
17000 of 50000, Atoms: 385(A), 230(P), ChiSq: 30282, Time: 00:00:03 / 00:00:21
18000 of 50000, Atoms: 392(A), 234(P), ChiSq: 30320, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 395(A), 225(P), ChiSq: 30195, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 407(A), 221(P), ChiSq: 30226, Time: 00:00:04 / 00:00:23
21000 of 50000, Atoms: 407(A), 233(P), ChiSq: 30057, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 424(A), 230(P), ChiSq: 30062, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 406(A), 249(P), ChiSq: 29977, Time: 00:00:05 / 00:00:25
24000 of 50000, Atoms: 427(A), 243(P), ChiSq: 29925, Time: 00:00:06 / 00:00:28
25000 of 50000, Atoms: 426(A), 239(P), ChiSq: 30050, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 461(A), 245(P), ChiSq: 29588, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 478(A), 240(P), ChiSq: 28660, Time: 00:00:06 / 00:00:25
28000 of 50000, Atoms: 492(A), 223(P), ChiSq: 28243, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 533(A), 210(P), ChiSq: 28152, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 464(A), 231(P), ChiSq: 28249, Time: 00:00:07 / 00:00:26
31000 of 50000, Atoms: 493(A), 230(P), ChiSq: 28261, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 474(A), 219(P), ChiSq: 28223, Time: 00:00:08 / 00:00:28
33000 of 50000, Atoms: 471(A), 220(P), ChiSq: 28248, Time: 00:00:08 / 00:00:27
34000 of 50000, Atoms: 468(A), 239(P), ChiSq: 28149, Time: 00:00:08 / 00:00:26
35000 of 50000, Atoms: 466(A), 234(P), ChiSq: 28110, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 480(A), 237(P), ChiSq: 28153, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 465(A), 241(P), ChiSq: 28221, Time: 00:00:09 / 00:00:26
38000 of 50000, Atoms: 487(A), 237(P), ChiSq: 28264, Time: 00:00:10 / 00:00:28
39000 of 50000, Atoms: 494(A), 235(P), ChiSq: 28162, Time: 00:00:10 / 00:00:28
40000 of 50000, Atoms: 446(A), 254(P), ChiSq: 28168, Time: 00:00:10 / 00:00:27
41000 of 50000, Atoms: 466(A), 238(P), ChiSq: 28251, Time: 00:00:10 / 00:00:26
42000 of 50000, Atoms: 466(A), 244(P), ChiSq: 28204, Time: 00:00:11 / 00:00:28
43000 of 50000, Atoms: 470(A), 247(P), ChiSq: 28204, Time: 00:00:11 / 00:00:27
44000 of 50000, Atoms: 451(A), 250(P), ChiSq: 28228, Time: 00:00:11 / 00:00:27
45000 of 50000, Atoms: 464(A), 238(P), ChiSq: 28265, Time: 00:00:12 / 00:00:28
46000 of 50000, Atoms: 475(A), 233(P), ChiSq: 28224, Time: 00:00:12 / 00:00:28
47000 of 50000, Atoms: 460(A), 227(P), ChiSq: 28217, Time: 00:00:12 / 00:00:27
48000 of 50000, Atoms: 467(A), 242(P), ChiSq: 28129, Time: 00:00:13 / 00:00:29
49000 of 50000, Atoms: 472(A), 230(P), ChiSq: 28203, Time: 00:00:13 / 00:00:28
50000 of 50000, Atoms: 472(A), 238(P), ChiSq: 28252, Time: 00:00:13 / 00:00:27
-- Sampling Phase --
1000 of 50000, Atoms: 477(A), 235(P), ChiSq: 28195, Time: 00:00:13 / 00:00:27
2000 of 50000, Atoms: 473(A), 234(P), ChiSq: 28307, Time: 00:00:14 / 00:00:28
3000 of 50000, Atoms: 460(A), 237(P), ChiSq: 28156, Time: 00:00:14 / 00:00:28
4000 of 50000, Atoms: 471(A), 243(P), ChiSq: 28112, Time: 00:00:14 / 00:00:27
5000 of 50000, Atoms: 473(A), 235(P), ChiSq: 28160, Time: 00:00:15 / 00:00:28
6000 of 50000, Atoms: 493(A), 232(P), ChiSq: 28183, Time: 00:00:15 / 00:00:28
7000 of 50000, Atoms: 471(A), 235(P), ChiSq: 28219, Time: 00:00:15 / 00:00:27
8000 of 50000, Atoms: 476(A), 251(P), ChiSq: 28143, Time: 00:00:15 / 00:00:27
9000 of 50000, Atoms: 454(A), 240(P), ChiSq: 28198, Time: 00:00:16 / 00:00:28
10000 of 50000, Atoms: 489(A), 241(P), ChiSq: 28149, Time: 00:00:16 / 00:00:28
11000 of 50000, Atoms: 471(A), 243(P), ChiSq: 28141, Time: 00:00:16 / 00:00:27
12000 of 50000, Atoms: 471(A), 232(P), ChiSq: 28122, Time: 00:00:17 / 00:00:28
13000 of 50000, Atoms: 470(A), 239(P), ChiSq: 28151, Time: 00:00:17 / 00:00:28
14000 of 50000, Atoms: 482(A), 247(P), ChiSq: 28187, Time: 00:00:17 / 00:00:27
15000 of 50000, Atoms: 458(A), 235(P), ChiSq: 28258, Time: 00:00:18 / 00:00:28
16000 of 50000, Atoms: 474(A), 257(P), ChiSq: 28155, Time: 00:00:18 / 00:00:28
17000 of 50000, Atoms: 461(A), 236(P), ChiSq: 28229, Time: 00:00:18 / 00:00:27
18000 of 50000, Atoms: 465(A), 244(P), ChiSq: 28194, Time: 00:00:19 / 00:00:29
19000 of 50000, Atoms: 467(A), 239(P), ChiSq: 28227, Time: 00:00:19 / 00:00:28
20000 of 50000, Atoms: 473(A), 242(P), ChiSq: 28187, Time: 00:00:19 / 00:00:28
21000 of 50000, Atoms: 474(A), 227(P), ChiSq: 28173, Time: 00:00:19 / 00:00:27
22000 of 50000, Atoms: 487(A), 239(P), ChiSq: 28131, Time: 00:00:20 / 00:00:28
23000 of 50000, Atoms: 459(A), 242(P), ChiSq: 28235, Time: 00:00:20 / 00:00:28
24000 of 50000, Atoms: 485(A), 226(P), ChiSq: 28231, Time: 00:00:20 / 00:00:27
25000 of 50000, Atoms: 473(A), 245(P), ChiSq: 28144, Time: 00:00:21 / 00:00:28
26000 of 50000, Atoms: 469(A), 241(P), ChiSq: 28202, Time: 00:00:21 / 00:00:28
27000 of 50000, Atoms: 481(A), 226(P), ChiSq: 28168, Time: 00:00:21 / 00:00:27
28000 of 50000, Atoms: 473(A), 227(P), ChiSq: 28170, Time: 00:00:22 / 00:00:28
29000 of 50000, Atoms: 457(A), 229(P), ChiSq: 28148, Time: 00:00:22 / 00:00:28
30000 of 50000, Atoms: 461(A), 230(P), ChiSq: 28147, Time: 00:00:22 / 00:00:28
31000 of 50000, Atoms: 483(A), 233(P), ChiSq: 28189, Time: 00:00:22 / 00:00:27
32000 of 50000, Atoms: 483(A), 237(P), ChiSq: 28204, Time: 00:00:23 / 00:00:28
33000 of 50000, Atoms: 465(A), 233(P), ChiSq: 28221, Time: 00:00:23 / 00:00:28
34000 of 50000, Atoms: 466(A), 240(P), ChiSq: 28199, Time: 00:00:23 / 00:00:27
35000 of 50000, Atoms: 477(A), 243(P), ChiSq: 28220, Time: 00:00:24 / 00:00:28
36000 of 50000, Atoms: 482(A), 246(P), ChiSq: 28193, Time: 00:00:24 / 00:00:28
37000 of 50000, Atoms: 464(A), 213(P), ChiSq: 28223, Time: 00:00:24 / 00:00:27
38000 of 50000, Atoms: 459(A), 238(P), ChiSq: 28263, Time: 00:00:25 / 00:00:28
39000 of 50000, Atoms: 466(A), 237(P), ChiSq: 28236, Time: 00:00:25 / 00:00:28
40000 of 50000, Atoms: 471(A), 229(P), ChiSq: 28189, Time: 00:00:25 / 00:00:28
41000 of 50000, Atoms: 472(A), 238(P), ChiSq: 28189, Time: 00:00:25 / 00:00:27
42000 of 50000, Atoms: 483(A), 238(P), ChiSq: 28213, Time: 00:00:26 / 00:00:28
43000 of 50000, Atoms: 475(A), 239(P), ChiSq: 28231, Time: 00:00:26 / 00:00:28
44000 of 50000, Atoms: 474(A), 232(P), ChiSq: 28172, Time: 00:00:26 / 00:00:27
45000 of 50000, Atoms: 472(A), 246(P), ChiSq: 28164, Time: 00:00:27 / 00:00:28
46000 of 50000, Atoms: 479(A), 233(P), ChiSq: 28195, Time: 00:00:27 / 00:00:28
47000 of 50000, Atoms: 463(A), 235(P), ChiSq: 28228, Time: 00:00:27 / 00:00:27
48000 of 50000, Atoms: 464(A), 243(P), ChiSq: 28165, Time: 00:00:28 / 00:00:28
49000 of 50000, Atoms: 450(A), 241(P), ChiSq: 28220, Time: 00:00:28 / 00:00:28
50000 of 50000, Atoms: 466(A), 235(P), ChiSq: 28241, Time: 00:00:28 / 00:00:28
[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 
  38.92    0.70   39.57