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CHECK report for projectR on malbec1

This page was generated on 2020-04-15 12:15:26 -0400 (Wed, 15 Apr 2020).

Package 1312/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
projectR 1.2.0
Genevieve Stein-O'Brien
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/projectR
Branch: RELEASE_3_10
Last Commit: 0e1bca2
Last Changed Date: 2019-10-29 13:11:33 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: projectR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings projectR_1.2.0.tar.gz
StartedAt: 2020-04-15 06:23:34 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:29:11 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 337.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: projectR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings projectR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/projectR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
projectR-methods 64.492   2.12   80.57
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/projectR.Rcheck/00check.log’
for details.

Installation output

projectR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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)

Tests output

projectR.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 20 available threads
-- Equilibration Phase --
1000 of 50000, Atoms: 204(A), 142(P), ChiSq: 48684, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 241(A), 159(P), ChiSq: 37372, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 290(A), 170(P), ChiSq: 34898, Time: 00:00:01 / 00:00:50
4000 of 50000, Atoms: 278(A), 176(P), ChiSq: 33758, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 315(A), 184(P), ChiSq: 32518, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 354(A), 182(P), ChiSq: 31129, Time: 00:00:02 / 00:00:45
7000 of 50000, Atoms: 372(A), 204(P), ChiSq: 30567, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 378(A), 198(P), ChiSq: 30100, Time: 00:00:03 / 00:00:49
9000 of 50000, Atoms: 380(A), 202(P), ChiSq: 29829, Time: 00:00:03 / 00:00:43
10000 of 50000, Atoms: 401(A), 197(P), ChiSq: 29455, Time: 00:00:04 / 00:00:51
11000 of 50000, Atoms: 407(A), 200(P), ChiSq: 29162, Time: 00:00:04 / 00:00:46
12000 of 50000, Atoms: 459(A), 204(P), ChiSq: 29016, Time: 00:00:05 / 00:00:52
13000 of 50000, Atoms: 416(A), 214(P), ChiSq: 28966, Time: 00:00:05 / 00:00:47
14000 of 50000, Atoms: 447(A), 222(P), ChiSq: 28938, Time: 00:00:06 / 00:00:52
15000 of 50000, Atoms: 455(A), 227(P), ChiSq: 28693, Time: 00:00:06 / 00:00:48
16000 of 50000, Atoms: 464(A), 219(P), ChiSq: 28683, Time: 00:00:07 / 00:00:52
17000 of 50000, Atoms: 452(A), 213(P), ChiSq: 28657, Time: 00:00:08 / 00:00:56
18000 of 50000, Atoms: 473(A), 228(P), ChiSq: 28454, Time: 00:00:08 / 00:00:53
19000 of 50000, Atoms: 480(A), 239(P), ChiSq: 28446, Time: 00:00:09 / 00:00:56
20000 of 50000, Atoms: 466(A), 232(P), ChiSq: 28409, Time: 00:00:10 / 00:00:59
21000 of 50000, Atoms: 467(A), 229(P), ChiSq: 28480, Time: 00:00:10 / 00:00:55
22000 of 50000, Atoms: 469(A), 231(P), ChiSq: 28276, Time: 00:00:11 / 00:00:58
23000 of 50000, Atoms: 484(A), 239(P), ChiSq: 28350, Time: 00:00:12 / 00:01:00
24000 of 50000, Atoms: 496(A), 232(P), ChiSq: 28280, Time: 00:00:12 / 00:00:57
25000 of 50000, Atoms: 481(A), 223(P), ChiSq: 28253, Time: 00:00:13 / 00:00:59
26000 of 50000, Atoms: 494(A), 218(P), ChiSq: 28269, Time: 00:00:13 / 00:00:57
27000 of 50000, Atoms: 497(A), 233(P), ChiSq: 28222, Time: 00:00:14 / 00:00:59
28000 of 50000, Atoms: 512(A), 230(P), ChiSq: 28243, Time: 00:00:15 / 00:01:00
29000 of 50000, Atoms: 480(A), 228(P), ChiSq: 28277, Time: 00:00:15 / 00:00:58
30000 of 50000, Atoms: 498(A), 231(P), ChiSq: 28174, Time: 00:00:16 / 00:01:00
31000 of 50000, Atoms: 481(A), 237(P), ChiSq: 28269, Time: 00:00:16 / 00:00:58
32000 of 50000, Atoms: 491(A), 236(P), ChiSq: 28231, Time: 00:00:17 / 00:00:59
33000 of 50000, Atoms: 485(A), 219(P), ChiSq: 28277, Time: 00:00:17 / 00:00:57
34000 of 50000, Atoms: 498(A), 221(P), ChiSq: 28235, Time: 00:00:18 / 00:00:58
35000 of 50000, Atoms: 513(A), 224(P), ChiSq: 28179, Time: 00:00:18 / 00:00:57
36000 of 50000, Atoms: 470(A), 245(P), ChiSq: 28230, Time: 00:00:19 / 00:00:58
37000 of 50000, Atoms: 489(A), 244(P), ChiSq: 28203, Time: 00:00:19 / 00:00:56
38000 of 50000, Atoms: 484(A), 217(P), ChiSq: 28258, Time: 00:00:20 / 00:00:57
39000 of 50000, Atoms: 501(A), 233(P), ChiSq: 28207, Time: 00:00:20 / 00:00:56
40000 of 50000, Atoms: 488(A), 230(P), ChiSq: 28247, Time: 00:00:21 / 00:00:57
41000 of 50000, Atoms: 502(A), 225(P), ChiSq: 28251, Time: 00:00:21 / 00:00:55
42000 of 50000, Atoms: 507(A), 228(P), ChiSq: 28223, Time: 00:00:22 / 00:00:57
43000 of 50000, Atoms: 498(A), 227(P), ChiSq: 28276, Time: 00:00:23 / 00:00:58
44000 of 50000, Atoms: 509(A), 217(P), ChiSq: 28292, Time: 00:00:23 / 00:00:56
45000 of 50000, Atoms: 483(A), 223(P), ChiSq: 28284, Time: 00:00:24 / 00:00:57
46000 of 50000, Atoms: 475(A), 238(P), ChiSq: 28257, Time: 00:00:24 / 00:00:56
47000 of 50000, Atoms: 474(A), 231(P), ChiSq: 28265, Time: 00:00:25 / 00:00:57
48000 of 50000, Atoms: 480(A), 234(P), ChiSq: 28238, Time: 00:00:26 / 00:00:58
49000 of 50000, Atoms: 491(A), 242(P), ChiSq: 28241, Time: 00:00:26 / 00:00:56
50000 of 50000, Atoms: 493(A), 224(P), ChiSq: 28265, Time: 00:00:27 / 00:00:57
-- Sampling Phase --
1000 of 50000, Atoms: 495(A), 228(P), ChiSq: 28276, Time: 00:00:28 / 00:00:58
2000 of 50000, Atoms: 490(A), 221(P), ChiSq: 28215, Time: 00:00:28 / 00:00:57
3000 of 50000, Atoms: 495(A), 228(P), ChiSq: 28273, Time: 00:00:29 / 00:00:58
4000 of 50000, Atoms: 492(A), 229(P), ChiSq: 28211, Time: 00:00:29 / 00:00:57
5000 of 50000, Atoms: 500(A), 220(P), ChiSq: 28301, Time: 00:00:30 / 00:00:57
6000 of 50000, Atoms: 491(A), 231(P), ChiSq: 28287, Time: 00:00:31 / 00:00:58
7000 of 50000, Atoms: 514(A), 217(P), ChiSq: 28270, Time: 00:00:31 / 00:00:57
8000 of 50000, Atoms: 507(A), 236(P), ChiSq: 28217, Time: 00:00:32 / 00:00:58
9000 of 50000, Atoms: 480(A), 252(P), ChiSq: 28218, Time: 00:00:33 / 00:00:58
10000 of 50000, Atoms: 485(A), 234(P), ChiSq: 28188, Time: 00:00:33 / 00:00:57
11000 of 50000, Atoms: 494(A), 242(P), ChiSq: 28253, Time: 00:00:34 / 00:00:58
12000 of 50000, Atoms: 484(A), 220(P), ChiSq: 28240, Time: 00:00:35 / 00:00:59
13000 of 50000, Atoms: 512(A), 223(P), ChiSq: 28282, Time: 00:00:35 / 00:00:58
14000 of 50000, Atoms: 498(A), 222(P), ChiSq: 28264, Time: 00:00:36 / 00:00:58
15000 of 50000, Atoms: 496(A), 237(P), ChiSq: 28266, Time: 00:00:36 / 00:00:57
16000 of 50000, Atoms: 487(A), 230(P), ChiSq: 28233, Time: 00:00:37 / 00:00:58
17000 of 50000, Atoms: 482(A), 209(P), ChiSq: 28295, Time: 00:00:38 / 00:00:58
18000 of 50000, Atoms: 513(A), 236(P), ChiSq: 28235, Time: 00:00:38 / 00:00:58
19000 of 50000, Atoms: 509(A), 237(P), ChiSq: 28256, Time: 00:00:39 / 00:00:58
20000 of 50000, Atoms: 480(A), 228(P), ChiSq: 28228, Time: 00:00:39 / 00:00:57
21000 of 50000, Atoms: 489(A), 236(P), ChiSq: 28275, Time: 00:00:40 / 00:00:58
22000 of 50000, Atoms: 483(A), 229(P), ChiSq: 28224, Time: 00:00:41 / 00:00:58
23000 of 50000, Atoms: 491(A), 233(P), ChiSq: 28238, Time: 00:00:41 / 00:00:57
24000 of 50000, Atoms: 486(A), 233(P), ChiSq: 28217, Time: 00:00:42 / 00:00:58
25000 of 50000, Atoms: 494(A), 235(P), ChiSq: 28265, Time: 00:00:43 / 00:00:58
26000 of 50000, Atoms: 474(A), 240(P), ChiSq: 28265, Time: 00:00:44 / 00:00:59
27000 of 50000, Atoms: 492(A), 224(P), ChiSq: 28177, Time: 00:00:44 / 00:00:58
28000 of 50000, Atoms: 509(A), 221(P), ChiSq: 28230, Time: 00:00:45 / 00:00:59
29000 of 50000, Atoms: 507(A), 227(P), ChiSq: 28202, Time: 00:00:45 / 00:00:58
30000 of 50000, Atoms: 482(A), 242(P), ChiSq: 28245, Time: 00:00:46 / 00:00:58
31000 of 50000, Atoms: 496(A), 236(P), ChiSq: 28234, Time: 00:00:47 / 00:00:59
32000 of 50000, Atoms: 499(A), 228(P), ChiSq: 28272, Time: 00:00:47 / 00:00:58
33000 of 50000, Atoms: 507(A), 230(P), ChiSq: 28210, Time: 00:00:48 / 00:00:58
34000 of 50000, Atoms: 483(A), 246(P), ChiSq: 28203, Time: 00:00:48 / 00:00:58
35000 of 50000, Atoms: 486(A), 235(P), ChiSq: 28221, Time: 00:00:49 / 00:00:58
36000 of 50000, Atoms: 479(A), 233(P), ChiSq: 28224, Time: 00:00:50 / 00:00:58
37000 of 50000, Atoms: 483(A), 233(P), ChiSq: 28227, Time: 00:00:50 / 00:00:58
38000 of 50000, Atoms: 484(A), 232(P), ChiSq: 28270, Time: 00:00:51 / 00:00:58
39000 of 50000, Atoms: 503(A), 227(P), ChiSq: 28308, Time: 00:00:51 / 00:00:57
40000 of 50000, Atoms: 491(A), 235(P), ChiSq: 28170, Time: 00:00:52 / 00:00:58
41000 of 50000, Atoms: 497(A), 233(P), ChiSq: 28234, Time: 00:00:53 / 00:00:58
42000 of 50000, Atoms: 501(A), 231(P), ChiSq: 28210, Time: 00:00:53 / 00:00:58
43000 of 50000, Atoms: 500(A), 234(P), ChiSq: 28289, Time: 00:00:54 / 00:00:58
44000 of 50000, Atoms: 495(A), 228(P), ChiSq: 28259, Time: 00:00:55 / 00:00:58
45000 of 50000, Atoms: 489(A), 238(P), ChiSq: 28260, Time: 00:00:55 / 00:00:58
46000 of 50000, Atoms: 477(A), 239(P), ChiSq: 28268, Time: 00:00:56 / 00:00:58
47000 of 50000, Atoms: 501(A), 219(P), ChiSq: 28247, Time: 00:00:57 / 00:00:58
48000 of 50000, Atoms: 488(A), 233(P), ChiSq: 28239, Time: 00:00:57 / 00:00:58
49000 of 50000, Atoms: 506(A), 238(P), ChiSq: 28307, Time: 00:00:58 / 00:00:58
50000 of 50000, Atoms: 501(A), 247(P), ChiSq: 28283, Time: 00:00:59 / 00:00:59
[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 
 65.600   2.320  68.067

Example timings

projectR.Rcheck/projectR-Ex.timings

nameusersystemelapsed
auc_mat0.1040.0000.103
cluster2pattern-methods0.1920.0040.196
clusterPlotR-methods000
correlateR0.1040.0000.107
geneMatchR0.0160.0080.023
intersectoR-methods0.0240.0000.024
projectR-methods64.492 2.12080.570
rotatoR0.0040.0000.004