Multiple platform build/check report for BioC 3.10 - CHECK report for projectR on tokay1

Package: projectR

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:projectR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings projectR_1.2.0.tar.gz

StartedAt: 2020-04-15 05:41:00 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:47:02 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 362.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: projectR.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:projectR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings projectR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/projectR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'projectR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'projectR' version '1.2.0'
* 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 ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'geneMatchR':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
projectR-methods 37.39      0   42.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
projectR-methods 27.27      0   27.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/projectR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/projectR_1.2.0.tar.gz && rm -rf projectR.buildbin-libdir && mkdir projectR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=projectR.buildbin-libdir projectR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL projectR_1.2.0.zip && rm projectR_1.2.0.tar.gz projectR_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  861k  100  861k    0     0  5901k      0 --:--:-- --:--:-- --:--:-- 6063k

install for i386

* 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
  converting help for package 'projectR'
    finding HTML links ... done
    AP.RNAseq6l3c3t                         html  
    auc_mat                                 html  
    cluster2pattern-methods                 html  
    clusterPlotR-methods                    html  
    correlateR-class                        html  
    correlateR                              html  
    geneMatchR                              html  
    initialize-correlateR-method            html  
    initialize-rotatoR-method               html  
    intersectoR-methods                     html  
    map.ESepiGen4c1l                        html  
    map.RNAseq6l3c3t                        html  
    p.ESepiGen4c1l                          html  
    p.RNAseq6l3c3t                          html  
    pd.ESepiGen4c1l                         html  
    pd.RNAseq6l3c3t                         html  
    projectR-methods                        html  
    rotatoR-class                           html  
    rotatoR                                 html  
** 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

install for x64

* installing *source* package 'projectR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'projectR' as projectR_1.2.0.zip
* DONE (projectR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'projectR' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 3.6.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 800 
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: 175(A), 108(P), ChiSq: 55715, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 262(A), 144(P), ChiSq: 38355, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 297(A), 142(P), ChiSq: 34804, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 315(A), 176(P), ChiSq: 32998, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 324(A), 182(P), ChiSq: 32031, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 328(A), 182(P), ChiSq: 31551, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 377(A), 200(P), ChiSq: 30019, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 404(A), 197(P), ChiSq: 29791, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 400(A), 200(P), ChiSq: 29580, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 406(A), 203(P), ChiSq: 29432, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 396(A), 212(P), ChiSq: 29284, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 418(A), 215(P), ChiSq: 28953, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 412(A), 198(P), ChiSq: 28987, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 432(A), 208(P), ChiSq: 28803, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 436(A), 208(P), ChiSq: 28679, Time: 00:00:04 / 00:00:32
16000 of 50000, Atoms: 428(A), 209(P), ChiSq: 28776, Time: 00:00:05 / 00:00:37
17000 of 50000, Atoms: 431(A), 211(P), ChiSq: 28608, Time: 00:00:05 / 00:00:35
18000 of 50000, Atoms: 441(A), 230(P), ChiSq: 28459, Time: 00:00:06 / 00:00:39
19000 of 50000, Atoms: 436(A), 231(P), ChiSq: 28492, Time: 00:00:06 / 00:00:37
20000 of 50000, Atoms: 461(A), 230(P), ChiSq: 28376, Time: 00:00:06 / 00:00:35
21000 of 50000, Atoms: 450(A), 215(P), ChiSq: 28469, Time: 00:00:07 / 00:00:39
22000 of 50000, Atoms: 452(A), 232(P), ChiSq: 28311, Time: 00:00:07 / 00:00:37
23000 of 50000, Atoms: 452(A), 231(P), ChiSq: 28321, Time: 00:00:07 / 00:00:35
24000 of 50000, Atoms: 440(A), 227(P), ChiSq: 28245, Time: 00:00:08 / 00:00:38
25000 of 50000, Atoms: 462(A), 224(P), ChiSq: 28242, Time: 00:00:08 / 00:00:36
26000 of 50000, Atoms: 481(A), 230(P), ChiSq: 28238, Time: 00:00:09 / 00:00:39
27000 of 50000, Atoms: 462(A), 228(P), ChiSq: 28274, Time: 00:00:09 / 00:00:38
28000 of 50000, Atoms: 459(A), 234(P), ChiSq: 28280, Time: 00:00:09 / 00:00:36
29000 of 50000, Atoms: 471(A), 226(P), ChiSq: 28293, Time: 00:00:10 / 00:00:39
30000 of 50000, Atoms: 450(A), 222(P), ChiSq: 28248, Time: 00:00:10 / 00:00:37
31000 of 50000, Atoms: 467(A), 234(P), ChiSq: 28270, Time: 00:00:11 / 00:00:39
32000 of 50000, Atoms: 481(A), 225(P), ChiSq: 28235, Time: 00:00:11 / 00:00:38
33000 of 50000, Atoms: 453(A), 222(P), ChiSq: 28203, Time: 00:00:11 / 00:00:37
34000 of 50000, Atoms: 466(A), 231(P), ChiSq: 28261, Time: 00:00:12 / 00:00:39
35000 of 50000, Atoms: 490(A), 216(P), ChiSq: 28212, Time: 00:00:12 / 00:00:38
36000 of 50000, Atoms: 470(A), 222(P), ChiSq: 28235, Time: 00:00:13 / 00:00:39
37000 of 50000, Atoms: 466(A), 234(P), ChiSq: 28206, Time: 00:00:13 / 00:00:38
38000 of 50000, Atoms: 478(A), 227(P), ChiSq: 28274, Time: 00:00:13 / 00:00:37
39000 of 50000, Atoms: 458(A), 238(P), ChiSq: 28283, Time: 00:00:14 / 00:00:39
40000 of 50000, Atoms: 468(A), 229(P), ChiSq: 28221, Time: 00:00:14 / 00:00:38
41000 of 50000, Atoms: 473(A), 231(P), ChiSq: 28304, Time: 00:00:14 / 00:00:37
42000 of 50000, Atoms: 445(A), 233(P), ChiSq: 28320, Time: 00:00:15 / 00:00:38
43000 of 50000, Atoms: 467(A), 223(P), ChiSq: 28261, Time: 00:00:15 / 00:00:37
44000 of 50000, Atoms: 462(A), 217(P), ChiSq: 28173, Time: 00:00:16 / 00:00:39
45000 of 50000, Atoms: 490(A), 233(P), ChiSq: 28217, Time: 00:00:16 / 00:00:38
46000 of 50000, Atoms: 451(A), 233(P), ChiSq: 28234, Time: 00:00:16 / 00:00:37
47000 of 50000, Atoms: 454(A), 223(P), ChiSq: 28214, Time: 00:00:17 / 00:00:38
48000 of 50000, Atoms: 463(A), 229(P), ChiSq: 28256, Time: 00:00:17 / 00:00:38
49000 of 50000, Atoms: 465(A), 231(P), ChiSq: 28273, Time: 00:00:18 / 00:00:39
50000 of 50000, Atoms: 486(A), 229(P), ChiSq: 28162, Time: 00:00:18 / 00:00:38
-- Sampling Phase --
1000 of 50000, Atoms: 452(A), 233(P), ChiSq: 28152, Time: 00:00:18 / 00:00:37
2000 of 50000, Atoms: 454(A), 235(P), ChiSq: 28240, Time: 00:00:19 / 00:00:38
3000 of 50000, Atoms: 465(A), 231(P), ChiSq: 28217, Time: 00:00:19 / 00:00:38
4000 of 50000, Atoms: 464(A), 216(P), ChiSq: 28259, Time: 00:00:20 / 00:00:39
5000 of 50000, Atoms: 472(A), 230(P), ChiSq: 28245, Time: 00:00:20 / 00:00:38
6000 of 50000, Atoms: 464(A), 235(P), ChiSq: 28173, Time: 00:00:20 / 00:00:37
7000 of 50000, Atoms: 460(A), 219(P), ChiSq: 28277, Time: 00:00:21 / 00:00:38
8000 of 50000, Atoms: 454(A), 226(P), ChiSq: 28260, Time: 00:00:21 / 00:00:38
9000 of 50000, Atoms: 479(A), 228(P), ChiSq: 28295, Time: 00:00:22 / 00:00:39
10000 of 50000, Atoms: 487(A), 223(P), ChiSq: 28273, Time: 00:00:22 / 00:00:38
11000 of 50000, Atoms: 466(A), 214(P), ChiSq: 28182, Time: 00:00:23 / 00:00:39
12000 of 50000, Atoms: 473(A), 229(P), ChiSq: 28286, Time: 00:00:23 / 00:00:38
13000 of 50000, Atoms: 469(A), 214(P), ChiSq: 28223, Time: 00:00:23 / 00:00:38
14000 of 50000, Atoms: 456(A), 226(P), ChiSq: 28169, Time: 00:00:24 / 00:00:39
15000 of 50000, Atoms: 456(A), 227(P), ChiSq: 28192, Time: 00:00:24 / 00:00:38
16000 of 50000, Atoms: 476(A), 232(P), ChiSq: 28286, Time: 00:00:25 / 00:00:39
17000 of 50000, Atoms: 482(A), 222(P), ChiSq: 28175, Time: 00:00:25 / 00:00:38
18000 of 50000, Atoms: 474(A), 220(P), ChiSq: 28283, Time: 00:00:25 / 00:00:38
19000 of 50000, Atoms: 456(A), 223(P), ChiSq: 28234, Time: 00:00:26 / 00:00:39
20000 of 50000, Atoms: 478(A), 234(P), ChiSq: 28231, Time: 00:00:26 / 00:00:38
21000 of 50000, Atoms: 476(A), 231(P), ChiSq: 28253, Time: 00:00:27 / 00:00:39
22000 of 50000, Atoms: 456(A), 225(P), ChiSq: 28237, Time: 00:00:27 / 00:00:38
23000 of 50000, Atoms: 460(A), 233(P), ChiSq: 28193, Time: 00:00:27 / 00:00:38
24000 of 50000, Atoms: 464(A), 222(P), ChiSq: 28302, Time: 00:00:28 / 00:00:38
25000 of 50000, Atoms: 461(A), 235(P), ChiSq: 28266, Time: 00:00:28 / 00:00:38
26000 of 50000, Atoms: 447(A), 233(P), ChiSq: 28270, Time: 00:00:29 / 00:00:39
27000 of 50000, Atoms: 459(A), 228(P), ChiSq: 28213, Time: 00:00:29 / 00:00:38
28000 of 50000, Atoms: 448(A), 225(P), ChiSq: 28248, Time: 00:00:29 / 00:00:38
29000 of 50000, Atoms: 469(A), 226(P), ChiSq: 28243, Time: 00:00:30 / 00:00:38
30000 of 50000, Atoms: 471(A), 235(P), ChiSq: 28301, Time: 00:00:30 / 00:00:38
31000 of 50000, Atoms: 477(A), 220(P), ChiSq: 28175, Time: 00:00:31 / 00:00:39
32000 of 50000, Atoms: 467(A), 223(P), ChiSq: 28213, Time: 00:00:31 / 00:00:38
33000 of 50000, Atoms: 480(A), 218(P), ChiSq: 28248, Time: 00:00:31 / 00:00:38
34000 of 50000, Atoms: 463(A), 235(P), ChiSq: 28236, Time: 00:00:32 / 00:00:38
35000 of 50000, Atoms: 460(A), 216(P), ChiSq: 28247, Time: 00:00:32 / 00:00:38
36000 of 50000, Atoms: 468(A), 220(P), ChiSq: 28235, Time: 00:00:33 / 00:00:38
37000 of 50000, Atoms: 479(A), 227(P), ChiSq: 28210, Time: 00:00:33 / 00:00:38
38000 of 50000, Atoms: 454(A), 230(P), ChiSq: 28269, Time: 00:00:33 / 00:00:37
39000 of 50000, Atoms: 464(A), 242(P), ChiSq: 28196, Time: 00:00:34 / 00:00:38
40000 of 50000, Atoms: 451(A), 234(P), ChiSq: 28279, Time: 00:00:34 / 00:00:38
41000 of 50000, Atoms: 454(A), 227(P), ChiSq: 28286, Time: 00:00:35 / 00:00:38
42000 of 50000, Atoms: 464(A), 230(P), ChiSq: 28220, Time: 00:00:35 / 00:00:38
43000 of 50000, Atoms: 466(A), 244(P), ChiSq: 28257, Time: 00:00:35 / 00:00:37
44000 of 50000, Atoms: 460(A), 232(P), ChiSq: 28196, Time: 00:00:36 / 00:00:38
45000 of 50000, Atoms: 474(A), 232(P), ChiSq: 28226, Time: 00:00:36 / 00:00:38
46000 of 50000, Atoms: 472(A), 223(P), ChiSq: 28199, Time: 00:00:37 / 00:00:38
47000 of 50000, Atoms: 472(A), 225(P), ChiSq: 28314, Time: 00:00:37 / 00:00:38
48000 of 50000, Atoms: 451(A), 233(P), ChiSq: 28227, Time: 00:00:37 / 00:00:37
49000 of 50000, Atoms: 457(A), 227(P), ChiSq: 28229, Time: 00:00:38 / 00:00:38
50000 of 50000, Atoms: 468(A), 211(P), ChiSq: 28253, Time: 00:00:38 / 00:00:38
[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"
== testthat results  ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  45.01    0.56   45.56


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 3.6.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 675 
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: 186(A), 151(P), ChiSq: 50569, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 225(A), 176(P), ChiSq: 39777, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 252(A), 183(P), ChiSq: 35476, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 278(A), 199(P), ChiSq: 33494, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 279(A), 212(P), ChiSq: 32655, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 310(A), 202(P), ChiSq: 32107, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 315(A), 197(P), ChiSq: 31546, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 322(A), 210(P), ChiSq: 31467, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 324(A), 211(P), ChiSq: 31396, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 328(A), 222(P), ChiSq: 30943, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 338(A), 218(P), ChiSq: 30911, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 340(A), 227(P), ChiSq: 30758, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 350(A), 228(P), ChiSq: 30673, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 360(A), 221(P), ChiSq: 30586, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 352(A), 228(P), ChiSq: 30640, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 376(A), 238(P), ChiSq: 30492, Time: 00:00:03 / 00:00:22
17000 of 50000, Atoms: 370(A), 230(P), ChiSq: 30390, Time: 00:00:04 / 00:00:28
18000 of 50000, Atoms: 375(A), 254(P), ChiSq: 30289, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 371(A), 234(P), ChiSq: 30261, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 387(A), 244(P), ChiSq: 30197, Time: 00:00:05 / 00:00:29
21000 of 50000, Atoms: 381(A), 257(P), ChiSq: 30089, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 398(A), 237(P), ChiSq: 30029, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 398(A), 252(P), ChiSq: 30086, Time: 00:00:05 / 00:00:25
24000 of 50000, Atoms: 407(A), 254(P), ChiSq: 30028, Time: 00:00:06 / 00:00:28
25000 of 50000, Atoms: 389(A), 252(P), ChiSq: 30053, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 408(A), 259(P), ChiSq: 29972, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 407(A), 245(P), ChiSq: 29996, Time: 00:00:07 / 00:00:29
28000 of 50000, Atoms: 387(A), 250(P), ChiSq: 29933, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 383(A), 250(P), ChiSq: 30042, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 411(A), 242(P), ChiSq: 29952, Time: 00:00:07 / 00:00:26
31000 of 50000, Atoms: 388(A), 246(P), ChiSq: 29954, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 418(A), 254(P), ChiSq: 30010, Time: 00:00:08 / 00:00:28
33000 of 50000, Atoms: 404(A), 250(P), ChiSq: 30003, Time: 00:00:08 / 00:00:27
34000 of 50000, Atoms: 406(A), 253(P), ChiSq: 29995, Time: 00:00:08 / 00:00:26
35000 of 50000, Atoms: 395(A), 252(P), ChiSq: 29956, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 400(A), 236(P), ChiSq: 29982, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 413(A), 256(P), ChiSq: 29961, Time: 00:00:09 / 00:00:26
38000 of 50000, Atoms: 410(A), 257(P), ChiSq: 29914, Time: 00:00:09 / 00:00:26
39000 of 50000, Atoms: 407(A), 258(P), ChiSq: 29994, Time: 00:00:10 / 00:00:28
40000 of 50000, Atoms: 404(A), 265(P), ChiSq: 29979, Time: 00:00:10 / 00:00:27
41000 of 50000, Atoms: 392(A), 260(P), ChiSq: 30060, Time: 00:00:10 / 00:00:26
42000 of 50000, Atoms: 405(A), 257(P), ChiSq: 29971, Time: 00:00:11 / 00:00:28
43000 of 50000, Atoms: 398(A), 252(P), ChiSq: 29968, Time: 00:00:11 / 00:00:27
44000 of 50000, Atoms: 400(A), 261(P), ChiSq: 29954, Time: 00:00:11 / 00:00:27
45000 of 50000, Atoms: 394(A), 266(P), ChiSq: 30080, Time: 00:00:12 / 00:00:28
46000 of 50000, Atoms: 393(A), 263(P), ChiSq: 29993, Time: 00:00:12 / 00:00:28
47000 of 50000, Atoms: 391(A), 242(P), ChiSq: 30030, Time: 00:00:12 / 00:00:27
48000 of 50000, Atoms: 391(A), 242(P), ChiSq: 30017, Time: 00:00:12 / 00:00:26
49000 of 50000, Atoms: 395(A), 263(P), ChiSq: 29980, Time: 00:00:13 / 00:00:28
50000 of 50000, Atoms: 417(A), 256(P), ChiSq: 29968, Time: 00:00:13 / 00:00:27
-- Sampling Phase --
1000 of 50000, Atoms: 406(A), 244(P), ChiSq: 29977, Time: 00:00:13 / 00:00:27
2000 of 50000, Atoms: 415(A), 249(P), ChiSq: 29993, Time: 00:00:14 / 00:00:28
3000 of 50000, Atoms: 409(A), 250(P), ChiSq: 29967, Time: 00:00:14 / 00:00:28
4000 of 50000, Atoms: 415(A), 247(P), ChiSq: 29990, Time: 00:00:14 / 00:00:27
5000 of 50000, Atoms: 398(A), 256(P), ChiSq: 30042, Time: 00:00:14 / 00:00:26
6000 of 50000, Atoms: 402(A), 257(P), ChiSq: 29959, Time: 00:00:15 / 00:00:28
7000 of 50000, Atoms: 419(A), 252(P), ChiSq: 29967, Time: 00:00:15 / 00:00:27
8000 of 50000, Atoms: 390(A), 250(P), ChiSq: 29978, Time: 00:00:15 / 00:00:27
9000 of 50000, Atoms: 407(A), 251(P), ChiSq: 29977, Time: 00:00:16 / 00:00:28
10000 of 50000, Atoms: 396(A), 246(P), ChiSq: 29999, Time: 00:00:16 / 00:00:28
11000 of 50000, Atoms: 413(A), 260(P), ChiSq: 29987, Time: 00:00:16 / 00:00:27
12000 of 50000, Atoms: 411(A), 258(P), ChiSq: 30019, Time: 00:00:17 / 00:00:28
13000 of 50000, Atoms: 391(A), 253(P), ChiSq: 30019, Time: 00:00:17 / 00:00:28
14000 of 50000, Atoms: 410(A), 248(P), ChiSq: 29996, Time: 00:00:17 / 00:00:27
15000 of 50000, Atoms: 418(A), 259(P), ChiSq: 29948, Time: 00:00:17 / 00:00:27
16000 of 50000, Atoms: 400(A), 242(P), ChiSq: 30000, Time: 00:00:18 / 00:00:28
17000 of 50000, Atoms: 400(A), 242(P), ChiSq: 29950, Time: 00:00:18 / 00:00:27
18000 of 50000, Atoms: 403(A), 252(P), ChiSq: 29988, Time: 00:00:18 / 00:00:27
19000 of 50000, Atoms: 413(A), 256(P), ChiSq: 29989, Time: 00:00:19 / 00:00:28
20000 of 50000, Atoms: 397(A), 254(P), ChiSq: 30057, Time: 00:00:19 / 00:00:28
21000 of 50000, Atoms: 389(A), 242(P), ChiSq: 29976, Time: 00:00:19 / 00:00:27
22000 of 50000, Atoms: 413(A), 248(P), ChiSq: 29955, Time: 00:00:20 / 00:00:28
23000 of 50000, Atoms: 427(A), 257(P), ChiSq: 29981, Time: 00:00:20 / 00:00:28
24000 of 50000, Atoms: 405(A), 256(P), ChiSq: 29983, Time: 00:00:20 / 00:00:27
25000 of 50000, Atoms: 415(A), 240(P), ChiSq: 30016, Time: 00:00:21 / 00:00:28
26000 of 50000, Atoms: 404(A), 243(P), ChiSq: 29913, Time: 00:00:21 / 00:00:28
27000 of 50000, Atoms: 395(A), 247(P), ChiSq: 29968, Time: 00:00:22 / 00:00:29
28000 of 50000, Atoms: 409(A), 246(P), ChiSq: 29991, Time: 00:00:22 / 00:00:28
29000 of 50000, Atoms: 400(A), 243(P), ChiSq: 29992, Time: 00:00:22 / 00:00:28
30000 of 50000, Atoms: 394(A), 249(P), ChiSq: 29970, Time: 00:00:22 / 00:00:28
31000 of 50000, Atoms: 410(A), 257(P), ChiSq: 29965, Time: 00:00:23 / 00:00:28
32000 of 50000, Atoms: 400(A), 261(P), ChiSq: 29972, Time: 00:00:23 / 00:00:28
33000 of 50000, Atoms: 411(A), 259(P), ChiSq: 29963, Time: 00:00:23 / 00:00:28
34000 of 50000, Atoms: 397(A), 249(P), ChiSq: 29988, Time: 00:00:24 / 00:00:29
35000 of 50000, Atoms: 399(A), 261(P), ChiSq: 29984, Time: 00:00:24 / 00:00:28
36000 of 50000, Atoms: 412(A), 243(P), ChiSq: 29945, Time: 00:00:24 / 00:00:28
37000 of 50000, Atoms: 428(A), 244(P), ChiSq: 29953, Time: 00:00:24 / 00:00:27
38000 of 50000, Atoms: 410(A), 247(P), ChiSq: 29969, Time: 00:00:25 / 00:00:28
39000 of 50000, Atoms: 403(A), 257(P), ChiSq: 29944, Time: 00:00:25 / 00:00:28
40000 of 50000, Atoms: 387(A), 260(P), ChiSq: 29980, Time: 00:00:25 / 00:00:28
41000 of 50000, Atoms: 392(A), 247(P), ChiSq: 29948, Time: 00:00:25 / 00:00:27
42000 of 50000, Atoms: 404(A), 257(P), ChiSq: 29982, Time: 00:00:26 / 00:00:28
43000 of 50000, Atoms: 393(A), 253(P), ChiSq: 29933, Time: 00:00:26 / 00:00:28
44000 of 50000, Atoms: 418(A), 240(P), ChiSq: 29942, Time: 00:00:27 / 00:00:28
45000 of 50000, Atoms: 405(A), 249(P), ChiSq: 29917, Time: 00:00:27 / 00:00:28
46000 of 50000, Atoms: 404(A), 242(P), ChiSq: 29917, Time: 00:00:27 / 00:00:28
47000 of 50000, Atoms: 393(A), 247(P), ChiSq: 29971, Time: 00:00:27 / 00:00:27
48000 of 50000, Atoms: 419(A), 240(P), ChiSq: 29933, Time: 00:00:28 / 00:00:28
49000 of 50000, Atoms: 406(A), 261(P), ChiSq: 29964, Time: 00:00:28 / 00:00:28
50000 of 50000, Atoms: 399(A), 251(P), ChiSq: 29970, Time: 00:00:29 / 00:00:29
[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"
== testthat results  ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  39.29    0.56   39.84

name	user	system	elapsed
auc_mat	0.06	0.00	0.06
cluster2pattern-methods	0.13	0.00	0.13
clusterPlotR-methods	0	0	0
correlateR	0.09	0.00	0.09
geneMatchR	0.02	0.02	0.03
intersectoR-methods	0.00	0.01	0.01
projectR-methods	37.39	0.00	42.29
rotatoR	0.02	0.00	0.01

name	user	system	elapsed
auc_mat	0.04	0.02	0.07
cluster2pattern-methods	0.11	0.00	0.11
clusterPlotR-methods	0	0	0
correlateR	0.11	0.00	0.11
geneMatchR	0.03	0.00	0.03
intersectoR-methods	0.01	0.00	0.02
projectR-methods	27.27	0.00	27.26
rotatoR	0	0	0

CHECK report for projectR on tokay1

Summary

Command output

Installation output

Tests output

Example timings