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CHECK report for projectR on celaya2

This page was generated on 2020-01-16 13:53:45 -0500 (Thu, 16 Jan 2020).

Package 1309/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
projectR 1.3.0
Genevieve Stein-O'Brien
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/projectR
Branch: master
Last Commit: 2b4473c
Last Changed Date: 2019-10-29 13:43:32 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: projectR
Version: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2020-01-16 07:42:01 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:48:49 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 408.2 seconds
RetCode: 0
Status:  OK 
CheckDir: projectR.Rcheck
Warnings: 0

Command output

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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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/projectR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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 ... 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 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 58.266  0.113  58.399
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/projectR.Rcheck/00check.log’
for details.

Installation output

projectR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

Tests output

projectR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 3.7.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 384 
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 23 available threads
-- Equilibration Phase --
1000 of 50000, Atoms: 185(A), 140(P), ChiSq: 51087, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 221(A), 189(P), ChiSq: 39717, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 268(A), 179(P), ChiSq: 34921, Time: 00:00:01 / 00:00:50
4000 of 50000, Atoms: 290(A), 195(P), ChiSq: 33481, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 302(A), 211(P), ChiSq: 32612, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 301(A), 208(P), ChiSq: 32176, Time: 00:00:02 / 00:00:45
7000 of 50000, Atoms: 329(A), 208(P), ChiSq: 31635, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 348(A), 216(P), ChiSq: 31350, Time: 00:00:03 / 00:00:49
9000 of 50000, Atoms: 342(A), 231(P), ChiSq: 31274, Time: 00:00:04 / 00:00:57
10000 of 50000, Atoms: 356(A), 218(P), ChiSq: 31074, Time: 00:00:04 / 00:00:51
11000 of 50000, Atoms: 358(A), 218(P), ChiSq: 30749, Time: 00:00:05 / 00:00:57
12000 of 50000, Atoms: 369(A), 223(P), ChiSq: 30766, Time: 00:00:05 / 00:00:52
13000 of 50000, Atoms: 385(A), 240(P), ChiSq: 30755, Time: 00:00:06 / 00:00:57
14000 of 50000, Atoms: 378(A), 253(P), ChiSq: 30561, Time: 00:00:06 / 00:00:52
15000 of 50000, Atoms: 386(A), 252(P), ChiSq: 30526, Time: 00:00:07 / 00:00:56
16000 of 50000, Atoms: 377(A), 259(P), ChiSq: 30455, Time: 00:00:07 / 00:00:52
17000 of 50000, Atoms: 385(A), 286(P), ChiSq: 30259, Time: 00:00:08 / 00:00:56
18000 of 50000, Atoms: 402(A), 264(P), ChiSq: 30230, Time: 00:00:08 / 00:00:53
19000 of 50000, Atoms: 388(A), 256(P), ChiSq: 30204, Time: 00:00:09 / 00:00:56
20000 of 50000, Atoms: 417(A), 270(P), ChiSq: 30183, Time: 00:00:10 / 00:00:59
21000 of 50000, Atoms: 400(A), 262(P), ChiSq: 30162, Time: 00:00:10 / 00:00:55
22000 of 50000, Atoms: 391(A), 280(P), ChiSq: 30132, Time: 00:00:11 / 00:00:58
23000 of 50000, Atoms: 423(A), 285(P), ChiSq: 30018, Time: 00:00:11 / 00:00:55
24000 of 50000, Atoms: 409(A), 277(P), ChiSq: 29956, Time: 00:00:12 / 00:00:57
25000 of 50000, Atoms: 424(A), 288(P), ChiSq: 30002, Time: 00:00:13 / 00:00:59
26000 of 50000, Atoms: 413(A), 278(P), ChiSq: 29968, Time: 00:00:13 / 00:00:57
27000 of 50000, Atoms: 422(A), 291(P), ChiSq: 29960, Time: 00:00:14 / 00:00:59
28000 of 50000, Atoms: 435(A), 283(P), ChiSq: 29919, Time: 00:00:14 / 00:00:56
29000 of 50000, Atoms: 445(A), 285(P), ChiSq: 29902, Time: 00:00:15 / 00:00:58
30000 of 50000, Atoms: 433(A), 266(P), ChiSq: 29978, Time: 00:00:16 / 00:01:00
31000 of 50000, Atoms: 420(A), 276(P), ChiSq: 29985, Time: 00:00:16 / 00:00:58
32000 of 50000, Atoms: 425(A), 277(P), ChiSq: 29957, Time: 00:00:17 / 00:00:59
33000 of 50000, Atoms: 454(A), 271(P), ChiSq: 29944, Time: 00:00:18 / 00:01:00
34000 of 50000, Atoms: 430(A), 267(P), ChiSq: 29937, Time: 00:00:18 / 00:00:58
35000 of 50000, Atoms: 427(A), 260(P), ChiSq: 29963, Time: 00:00:19 / 00:01:00
36000 of 50000, Atoms: 429(A), 266(P), ChiSq: 30014, Time: 00:00:19 / 00:00:58
37000 of 50000, Atoms: 434(A), 265(P), ChiSq: 29973, Time: 00:00:20 / 00:00:59
38000 of 50000, Atoms: 414(A), 253(P), ChiSq: 29971, Time: 00:00:20 / 00:00:57
39000 of 50000, Atoms: 422(A), 275(P), ChiSq: 30000, Time: 00:00:21 / 00:00:59
40000 of 50000, Atoms: 435(A), 265(P), ChiSq: 29902, Time: 00:00:22 / 00:01:00
41000 of 50000, Atoms: 426(A), 270(P), ChiSq: 29989, Time: 00:00:22 / 00:00:58
42000 of 50000, Atoms: 450(A), 271(P), ChiSq: 29927, Time: 00:00:23 / 00:00:59
43000 of 50000, Atoms: 440(A), 264(P), ChiSq: 29940, Time: 00:00:24 / 00:01:00
44000 of 50000, Atoms: 407(A), 250(P), ChiSq: 30021, Time: 00:00:24 / 00:00:59
45000 of 50000, Atoms: 415(A), 247(P), ChiSq: 29960, Time: 00:00:25 / 00:01:00
46000 of 50000, Atoms: 425(A), 266(P), ChiSq: 29999, Time: 00:00:25 / 00:00:58
47000 of 50000, Atoms: 434(A), 271(P), ChiSq: 29968, Time: 00:00:26 / 00:00:59
48000 of 50000, Atoms: 426(A), 273(P), ChiSq: 29999, Time: 00:00:27 / 00:01:00
49000 of 50000, Atoms: 426(A), 258(P), ChiSq: 29996, Time: 00:00:27 / 00:00:59
50000 of 50000, Atoms: 429(A), 240(P), ChiSq: 29967, Time: 00:00:28 / 00:00:59
-- Sampling Phase --
1000 of 50000, Atoms: 438(A), 260(P), ChiSq: 29953, Time: 00:00:28 / 00:00:58
2000 of 50000, Atoms: 441(A), 250(P), ChiSq: 29951, Time: 00:00:29 / 00:00:59
3000 of 50000, Atoms: 428(A), 265(P), ChiSq: 29938, Time: 00:00:30 / 00:01:00
4000 of 50000, Atoms: 437(A), 279(P), ChiSq: 29953, Time: 00:00:30 / 00:00:59
5000 of 50000, Atoms: 416(A), 248(P), ChiSq: 29996, Time: 00:00:31 / 00:00:59
6000 of 50000, Atoms: 410(A), 256(P), ChiSq: 30022, Time: 00:00:31 / 00:00:58
7000 of 50000, Atoms: 444(A), 258(P), ChiSq: 29915, Time: 00:00:32 / 00:00:59
8000 of 50000, Atoms: 429(A), 246(P), ChiSq: 29972, Time: 00:00:33 / 00:01:00
9000 of 50000, Atoms: 424(A), 258(P), ChiSq: 29978, Time: 00:00:33 / 00:00:58
10000 of 50000, Atoms: 421(A), 261(P), ChiSq: 30004, Time: 00:00:34 / 00:00:59
11000 of 50000, Atoms: 423(A), 259(P), ChiSq: 30040, Time: 00:00:35 / 00:01:00
12000 of 50000, Atoms: 426(A), 260(P), ChiSq: 30016, Time: 00:00:35 / 00:00:59
13000 of 50000, Atoms: 420(A), 253(P), ChiSq: 29929, Time: 00:00:36 / 00:00:59
14000 of 50000, Atoms: 413(A), 258(P), ChiSq: 30043, Time: 00:00:37 / 00:01:00
15000 of 50000, Atoms: 428(A), 261(P), ChiSq: 29947, Time: 00:00:37 / 00:00:59
16000 of 50000, Atoms: 432(A), 259(P), ChiSq: 29917, Time: 00:00:38 / 00:00:59
17000 of 50000, Atoms: 417(A), 256(P), ChiSq: 30035, Time: 00:00:38 / 00:00:58
18000 of 50000, Atoms: 445(A), 257(P), ChiSq: 29935, Time: 00:00:39 / 00:00:59
19000 of 50000, Atoms: 406(A), 268(P), ChiSq: 30045, Time: 00:00:39 / 00:00:58
20000 of 50000, Atoms: 424(A), 248(P), ChiSq: 30069, Time: 00:00:40 / 00:00:59
21000 of 50000, Atoms: 415(A), 258(P), ChiSq: 30004, Time: 00:00:41 / 00:00:59
22000 of 50000, Atoms: 441(A), 246(P), ChiSq: 29918, Time: 00:00:41 / 00:00:58
23000 of 50000, Atoms: 415(A), 271(P), ChiSq: 30094, Time: 00:00:42 / 00:00:59
24000 of 50000, Atoms: 427(A), 256(P), ChiSq: 29966, Time: 00:00:42 / 00:00:58
25000 of 50000, Atoms: 412(A), 253(P), ChiSq: 30023, Time: 00:00:43 / 00:00:58
26000 of 50000, Atoms: 420(A), 256(P), ChiSq: 30010, Time: 00:00:44 / 00:00:59
27000 of 50000, Atoms: 419(A), 266(P), ChiSq: 29955, Time: 00:00:44 / 00:00:58
28000 of 50000, Atoms: 431(A), 264(P), ChiSq: 29941, Time: 00:00:45 / 00:00:59
29000 of 50000, Atoms: 407(A), 263(P), ChiSq: 29941, Time: 00:00:45 / 00:00:58
30000 of 50000, Atoms: 424(A), 277(P), ChiSq: 30032, Time: 00:00:46 / 00:00:58
31000 of 50000, Atoms: 411(A), 254(P), ChiSq: 29996, Time: 00:00:47 / 00:00:59
32000 of 50000, Atoms: 413(A), 248(P), ChiSq: 29976, Time: 00:00:47 / 00:00:58
33000 of 50000, Atoms: 429(A), 260(P), ChiSq: 30026, Time: 00:00:48 / 00:00:58
34000 of 50000, Atoms: 394(A), 254(P), ChiSq: 30015, Time: 00:00:48 / 00:00:58
35000 of 50000, Atoms: 411(A), 266(P), ChiSq: 29892, Time: 00:00:49 / 00:00:58
36000 of 50000, Atoms: 423(A), 267(P), ChiSq: 30032, Time: 00:00:50 / 00:00:58
37000 of 50000, Atoms: 417(A), 278(P), ChiSq: 29979, Time: 00:00:50 / 00:00:58
38000 of 50000, Atoms: 436(A), 268(P), ChiSq: 30022, Time: 00:00:51 / 00:00:58
39000 of 50000, Atoms: 422(A), 262(P), ChiSq: 29973, Time: 00:00:51 / 00:00:57
40000 of 50000, Atoms: 415(A), 253(P), ChiSq: 29967, Time: 00:00:52 / 00:00:58
41000 of 50000, Atoms: 425(A), 268(P), ChiSq: 29967, Time: 00:00:52 / 00:00:57
42000 of 50000, Atoms: 423(A), 263(P), ChiSq: 29992, Time: 00:00:53 / 00:00:58
43000 of 50000, Atoms: 424(A), 274(P), ChiSq: 29990, Time: 00:00:54 / 00:00:58
44000 of 50000, Atoms: 399(A), 261(P), ChiSq: 30003, Time: 00:00:54 / 00:00:57
45000 of 50000, Atoms: 437(A), 259(P), ChiSq: 29986, Time: 00:00:55 / 00:00:58
46000 of 50000, Atoms: 422(A), 275(P), ChiSq: 29954, Time: 00:00:55 / 00:00:57
47000 of 50000, Atoms: 413(A), 263(P), ChiSq: 29916, Time: 00:00:56 / 00:00:57
48000 of 50000, Atoms: 425(A), 263(P), ChiSq: 29951, Time: 00:00:57 / 00:00:58
49000 of 50000, Atoms: 414(A), 270(P), ChiSq: 29981, Time: 00:00:57 / 00:00:57
50000 of 50000, Atoms: 403(A), 262(P), ChiSq: 29981, Time: 00:00:58 / 00:00:58
[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 
 71.966   1.201  73.139

Example timings

projectR.Rcheck/projectR-Ex.timings

nameusersystemelapsed
auc_mat0.1080.0040.111
cluster2pattern-methods0.3090.0520.361
clusterPlotR-methods000
correlateR0.9340.0050.939
geneMatchR0.0580.0610.119
intersectoR-methods0.0540.0080.062
projectR-methods58.266 0.11358.399
rotatoR0.0060.0010.007