Package: projectR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings projectR_1.2.0.tar.gz

StartedAt: 2020-04-15 04:46:51 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:51:55 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 304.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: projectR.Rcheck

Warnings: 1

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings projectR_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/projectR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘projectR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘projectR’ version ‘1.2.0’
* 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 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 ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
projectR-methods 52.106  0.091  52.643
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/projectR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL projectR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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                 120 
sparseOptimization   FALSE 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

Data Model: Dense, Normal
Sampler Type: Asynchronous
Loading Data...Done! (00:00:00)
Running on 1 out of 24 available threads
-- Equilibration Phase --
1000 of 50000, Atoms: 186(A), 164(P), ChiSq: 54024, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 220(A), 175(P), ChiSq: 41658, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 262(A), 182(P), ChiSq: 35238, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 283(A), 209(P), ChiSq: 34070, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 304(A), 214(P), ChiSq: 32860, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 289(A), 224(P), ChiSq: 32550, Time: 00:00:02 / 00:00:45
7000 of 50000, Atoms: 308(A), 218(P), ChiSq: 31939, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 308(A), 230(P), ChiSq: 31644, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 332(A), 235(P), ChiSq: 31530, Time: 00:00:03 / 00:00:43
10000 of 50000, Atoms: 337(A), 231(P), ChiSq: 31224, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 345(A), 225(P), ChiSq: 30945, Time: 00:00:04 / 00:00:46
12000 of 50000, Atoms: 360(A), 246(P), ChiSq: 30891, Time: 00:00:04 / 00:00:41
13000 of 50000, Atoms: 368(A), 240(P), ChiSq: 30812, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 371(A), 247(P), ChiSq: 30554, Time: 00:00:05 / 00:00:43
15000 of 50000, Atoms: 362(A), 267(P), ChiSq: 30592, Time: 00:00:05 / 00:00:40
16000 of 50000, Atoms: 384(A), 253(P), ChiSq: 30378, Time: 00:00:06 / 00:00:45
17000 of 50000, Atoms: 397(A), 263(P), ChiSq: 30386, Time: 00:00:06 / 00:00:42
18000 of 50000, Atoms: 393(A), 268(P), ChiSq: 30327, Time: 00:00:07 / 00:00:46
19000 of 50000, Atoms: 380(A), 261(P), ChiSq: 30299, Time: 00:00:07 / 00:00:43
20000 of 50000, Atoms: 376(A), 264(P), ChiSq: 30201, Time: 00:00:07 / 00:00:41
21000 of 50000, Atoms: 381(A), 268(P), ChiSq: 30167, Time: 00:00:08 / 00:00:44
22000 of 50000, Atoms: 392(A), 252(P), ChiSq: 30084, Time: 00:00:08 / 00:00:42
23000 of 50000, Atoms: 397(A), 252(P), ChiSq: 30030, Time: 00:00:09 / 00:00:45
24000 of 50000, Atoms: 394(A), 262(P), ChiSq: 30122, Time: 00:00:09 / 00:00:43
25000 of 50000, Atoms: 405(A), 250(P), ChiSq: 30066, Time: 00:00:10 / 00:00:46
26000 of 50000, Atoms: 427(A), 279(P), ChiSq: 30007, Time: 00:00:10 / 00:00:44
27000 of 50000, Atoms: 410(A), 259(P), ChiSq: 30002, Time: 00:00:11 / 00:00:46
28000 of 50000, Atoms: 418(A), 263(P), ChiSq: 29936, Time: 00:00:11 / 00:00:44
29000 of 50000, Atoms: 405(A), 250(P), ChiSq: 29949, Time: 00:00:12 / 00:00:46
30000 of 50000, Atoms: 414(A), 268(P), ChiSq: 29973, Time: 00:00:12 / 00:00:45
31000 of 50000, Atoms: 396(A), 255(P), ChiSq: 30077, Time: 00:00:13 / 00:00:47
32000 of 50000, Atoms: 424(A), 270(P), ChiSq: 30020, Time: 00:00:13 / 00:00:45
33000 of 50000, Atoms: 429(A), 245(P), ChiSq: 29987, Time: 00:00:13 / 00:00:44
34000 of 50000, Atoms: 414(A), 264(P), ChiSq: 29958, Time: 00:00:14 / 00:00:45
35000 of 50000, Atoms: 411(A), 255(P), ChiSq: 29992, Time: 00:00:14 / 00:00:44
36000 of 50000, Atoms: 430(A), 259(P), ChiSq: 29920, Time: 00:00:15 / 00:00:46
37000 of 50000, Atoms: 401(A), 269(P), ChiSq: 29973, Time: 00:00:15 / 00:00:44
38000 of 50000, Atoms: 422(A), 251(P), ChiSq: 29950, Time: 00:00:16 / 00:00:46
39000 of 50000, Atoms: 430(A), 257(P), ChiSq: 30003, Time: 00:00:16 / 00:00:45
40000 of 50000, Atoms: 433(A), 282(P), ChiSq: 29975, Time: 00:00:17 / 00:00:46
41000 of 50000, Atoms: 425(A), 259(P), ChiSq: 29965, Time: 00:00:17 / 00:00:45
42000 of 50000, Atoms: 395(A), 265(P), ChiSq: 29962, Time: 00:00:18 / 00:00:46
43000 of 50000, Atoms: 430(A), 256(P), ChiSq: 29949, Time: 00:00:18 / 00:00:45
44000 of 50000, Atoms: 431(A), 262(P), ChiSq: 29967, Time: 00:00:18 / 00:00:44
45000 of 50000, Atoms: 439(A), 260(P), ChiSq: 30002, Time: 00:00:19 / 00:00:45
46000 of 50000, Atoms: 464(A), 262(P), ChiSq: 29589, Time: 00:00:19 / 00:00:44
47000 of 50000, Atoms: 459(A), 258(P), ChiSq: 29399, Time: 00:00:20 / 00:00:45
48000 of 50000, Atoms: 504(A), 236(P), ChiSq: 28763, Time: 00:00:20 / 00:00:44
49000 of 50000, Atoms: 543(A), 228(P), ChiSq: 28339, Time: 00:00:21 / 00:00:45
50000 of 50000, Atoms: 557(A), 216(P), ChiSq: 28372, Time: 00:00:21 / 00:00:44
-- Sampling Phase --
1000 of 50000, Atoms: 553(A), 220(P), ChiSq: 28182, Time: 00:00:22 / 00:00:46
2000 of 50000, Atoms: 483(A), 239(P), ChiSq: 28220, Time: 00:00:22 / 00:00:45
3000 of 50000, Atoms: 498(A), 223(P), ChiSq: 28222, Time: 00:00:23 / 00:00:46
4000 of 50000, Atoms: 504(A), 236(P), ChiSq: 28183, Time: 00:00:23 / 00:00:45
5000 of 50000, Atoms: 493(A), 229(P), ChiSq: 28151, Time: 00:00:24 / 00:00:46
6000 of 50000, Atoms: 501(A), 219(P), ChiSq: 28179, Time: 00:00:24 / 00:00:45
7000 of 50000, Atoms: 499(A), 221(P), ChiSq: 28200, Time: 00:00:24 / 00:00:44
8000 of 50000, Atoms: 509(A), 227(P), ChiSq: 28248, Time: 00:00:25 / 00:00:45
9000 of 50000, Atoms: 486(A), 230(P), ChiSq: 28234, Time: 00:00:25 / 00:00:44
10000 of 50000, Atoms: 513(A), 214(P), ChiSq: 28177, Time: 00:00:26 / 00:00:45
11000 of 50000, Atoms: 527(A), 243(P), ChiSq: 28242, Time: 00:00:26 / 00:00:44
12000 of 50000, Atoms: 498(A), 227(P), ChiSq: 28162, Time: 00:00:27 / 00:00:45
13000 of 50000, Atoms: 483(A), 233(P), ChiSq: 28174, Time: 00:00:27 / 00:00:44
14000 of 50000, Atoms: 496(A), 241(P), ChiSq: 28208, Time: 00:00:28 / 00:00:45
15000 of 50000, Atoms: 482(A), 231(P), ChiSq: 28187, Time: 00:00:28 / 00:00:44
16000 of 50000, Atoms: 485(A), 227(P), ChiSq: 28168, Time: 00:00:29 / 00:00:45
17000 of 50000, Atoms: 482(A), 219(P), ChiSq: 28194, Time: 00:00:29 / 00:00:44
18000 of 50000, Atoms: 506(A), 215(P), ChiSq: 28243, Time: 00:00:30 / 00:00:45
19000 of 50000, Atoms: 505(A), 238(P), ChiSq: 28174, Time: 00:00:30 / 00:00:45
20000 of 50000, Atoms: 483(A), 227(P), ChiSq: 28185, Time: 00:00:31 / 00:00:45
21000 of 50000, Atoms: 495(A), 240(P), ChiSq: 28194, Time: 00:00:31 / 00:00:45
22000 of 50000, Atoms: 505(A), 211(P), ChiSq: 28251, Time: 00:00:32 / 00:00:45
23000 of 50000, Atoms: 501(A), 237(P), ChiSq: 28148, Time: 00:00:32 / 00:00:45
24000 of 50000, Atoms: 478(A), 226(P), ChiSq: 28203, Time: 00:00:33 / 00:00:45
25000 of 50000, Atoms: 508(A), 228(P), ChiSq: 28277, Time: 00:00:33 / 00:00:45
26000 of 50000, Atoms: 501(A), 240(P), ChiSq: 28255, Time: 00:00:34 / 00:00:45
27000 of 50000, Atoms: 501(A), 233(P), ChiSq: 28233, Time: 00:00:34 / 00:00:45
28000 of 50000, Atoms: 502(A), 224(P), ChiSq: 28201, Time: 00:00:35 / 00:00:45
29000 of 50000, Atoms: 488(A), 244(P), ChiSq: 28200, Time: 00:00:35 / 00:00:45
30000 of 50000, Atoms: 482(A), 237(P), ChiSq: 28223, Time: 00:00:36 / 00:00:45
31000 of 50000, Atoms: 501(A), 249(P), ChiSq: 28221, Time: 00:00:36 / 00:00:45
32000 of 50000, Atoms: 508(A), 241(P), ChiSq: 28178, Time: 00:00:37 / 00:00:45
33000 of 50000, Atoms: 488(A), 237(P), ChiSq: 28217, Time: 00:00:38 / 00:00:46
34000 of 50000, Atoms: 475(A), 246(P), ChiSq: 28216, Time: 00:00:38 / 00:00:46
35000 of 50000, Atoms: 495(A), 247(P), ChiSq: 28136, Time: 00:00:39 / 00:00:46
36000 of 50000, Atoms: 508(A), 224(P), ChiSq: 28212, Time: 00:00:39 / 00:00:46
37000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28324, Time: 00:00:40 / 00:00:46
38000 of 50000, Atoms: 503(A), 226(P), ChiSq: 28231, Time: 00:00:40 / 00:00:46
39000 of 50000, Atoms: 479(A), 233(P), ChiSq: 28220, Time: 00:00:41 / 00:00:46
40000 of 50000, Atoms: 502(A), 236(P), ChiSq: 28187, Time: 00:00:41 / 00:00:46
41000 of 50000, Atoms: 478(A), 237(P), ChiSq: 28187, Time: 00:00:42 / 00:00:46
42000 of 50000, Atoms: 483(A), 223(P), ChiSq: 28234, Time: 00:00:42 / 00:00:46
43000 of 50000, Atoms: 490(A), 230(P), ChiSq: 28283, Time: 00:00:43 / 00:00:46
44000 of 50000, Atoms: 500(A), 229(P), ChiSq: 28197, Time: 00:00:43 / 00:00:46
45000 of 50000, Atoms: 485(A), 228(P), ChiSq: 28290, Time: 00:00:44 / 00:00:46
46000 of 50000, Atoms: 504(A), 236(P), ChiSq: 28214, Time: 00:00:44 / 00:00:46
47000 of 50000, Atoms: 481(A), 233(P), ChiSq: 28240, Time: 00:00:45 / 00:00:46
48000 of 50000, Atoms: 491(A), 238(P), ChiSq: 28231, Time: 00:00:45 / 00:00:46
49000 of 50000, Atoms: 509(A), 241(P), ChiSq: 28209, Time: 00:00:46 / 00:00:46
50000 of 50000, Atoms: 484(A), 234(P), ChiSq: 28230, 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"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 56.443   0.697  57.456 

name	user	system	elapsed
auc_mat	0.101	0.003	0.105
cluster2pattern-methods	0.226	0.023	0.255
clusterPlotR-methods	0	0	0
correlateR	0.195	0.003	0.199
geneMatchR	0.031	0.023	0.054
intersectoR-methods	0.031	0.003	0.035
projectR-methods	52.106	0.091	52.643
rotatoR	0.006	0.000	0.006