Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:08:34 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for projectR on machv2


To the developers/maintainers of the projectR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/projectR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1467/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
projectR 1.10.0  (landing page)
Genevieve Stein-O'Brien
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/projectR
git_branch: RELEASE_3_14
git_last_commit: 36c5ad2
git_last_commit_date: 2021-10-26 12:50:23 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: projectR
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings projectR_1.10.0.tar.gz
StartedAt: 2022-01-25 16:39:38 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 16:45:24 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 346.1 seconds
RetCode: 0
Status:   OK  
CheckDir: projectR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:projectR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings projectR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/projectR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.10.0’
* 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 ... 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 41.122  0.098  41.254
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/projectR.Rcheck/00check.log’
for details.



Installation output

projectR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 3.14.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 128 
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: 232(A), 126(P), ChiSq: 48862, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 276(A), 140(P), ChiSq: 38416, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 283(A), 165(P), ChiSq: 34884, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 298(A), 182(P), ChiSq: 32738, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 325(A), 176(P), ChiSq: 31915, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 371(A), 182(P), ChiSq: 30696, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 383(A), 196(P), ChiSq: 30217, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 376(A), 214(P), ChiSq: 30027, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 407(A), 195(P), ChiSq: 29480, Time: 00:00:03 / 00:00:43
10000 of 50000, Atoms: 424(A), 215(P), ChiSq: 29562, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 412(A), 203(P), ChiSq: 29278, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 412(A), 214(P), ChiSq: 28992, Time: 00:00:04 / 00:00:41
13000 of 50000, Atoms: 401(A), 222(P), ChiSq: 29206, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 409(A), 204(P), ChiSq: 28864, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 426(A), 221(P), ChiSq: 28864, Time: 00:00:05 / 00:00:40
16000 of 50000, Atoms: 436(A), 217(P), ChiSq: 28619, Time: 00:00:05 / 00:00:37
17000 of 50000, Atoms: 437(A), 227(P), ChiSq: 28455, Time: 00:00:06 / 00:00:42
18000 of 50000, Atoms: 450(A), 230(P), ChiSq: 28553, Time: 00:00:06 / 00:00:39
19000 of 50000, Atoms: 425(A), 221(P), ChiSq: 28528, Time: 00:00:06 / 00:00:37
20000 of 50000, Atoms: 449(A), 214(P), ChiSq: 28443, Time: 00:00:07 / 00:00:41
21000 of 50000, Atoms: 445(A), 235(P), ChiSq: 28399, Time: 00:00:07 / 00:00:39
22000 of 50000, Atoms: 443(A), 239(P), ChiSq: 28383, Time: 00:00:08 / 00:00:42
23000 of 50000, Atoms: 456(A), 226(P), ChiSq: 28330, Time: 00:00:08 / 00:00:40
24000 of 50000, Atoms: 465(A), 224(P), ChiSq: 28278, Time: 00:00:08 / 00:00:38
25000 of 50000, Atoms: 497(A), 241(P), ChiSq: 28218, Time: 00:00:09 / 00:00:41
26000 of 50000, Atoms: 447(A), 226(P), ChiSq: 28210, Time: 00:00:09 / 00:00:39
27000 of 50000, Atoms: 461(A), 232(P), ChiSq: 28295, Time: 00:00:10 / 00:00:42
28000 of 50000, Atoms: 473(A), 230(P), ChiSq: 28210, Time: 00:00:10 / 00:00:40
29000 of 50000, Atoms: 466(A), 229(P), ChiSq: 28146, Time: 00:00:10 / 00:00:39
30000 of 50000, Atoms: 468(A), 227(P), ChiSq: 28222, Time: 00:00:11 / 00:00:41
31000 of 50000, Atoms: 448(A), 235(P), ChiSq: 28256, Time: 00:00:11 / 00:00:39
32000 of 50000, Atoms: 476(A), 228(P), ChiSq: 28180, Time: 00:00:11 / 00:00:38
33000 of 50000, Atoms: 469(A), 238(P), ChiSq: 28227, Time: 00:00:12 / 00:00:40
34000 of 50000, Atoms: 465(A), 230(P), ChiSq: 28174, Time: 00:00:12 / 00:00:39
35000 of 50000, Atoms: 462(A), 229(P), ChiSq: 28237, Time: 00:00:13 / 00:00:41
36000 of 50000, Atoms: 463(A), 227(P), ChiSq: 28288, Time: 00:00:13 / 00:00:39
37000 of 50000, Atoms: 465(A), 236(P), ChiSq: 28261, Time: 00:00:13 / 00:00:38
38000 of 50000, Atoms: 458(A), 246(P), ChiSq: 28200, Time: 00:00:14 / 00:00:40
39000 of 50000, Atoms: 492(A), 228(P), ChiSq: 28194, Time: 00:00:14 / 00:00:39
40000 of 50000, Atoms: 472(A), 244(P), ChiSq: 28178, Time: 00:00:15 / 00:00:41
41000 of 50000, Atoms: 462(A), 236(P), ChiSq: 28128, Time: 00:00:15 / 00:00:39
42000 of 50000, Atoms: 457(A), 234(P), ChiSq: 28210, Time: 00:00:16 / 00:00:41
43000 of 50000, Atoms: 471(A), 220(P), ChiSq: 28261, Time: 00:00:16 / 00:00:40
44000 of 50000, Atoms: 478(A), 235(P), ChiSq: 28173, Time: 00:00:16 / 00:00:39
45000 of 50000, Atoms: 481(A), 233(P), ChiSq: 28182, Time: 00:00:17 / 00:00:40
46000 of 50000, Atoms: 466(A), 239(P), ChiSq: 28253, Time: 00:00:17 / 00:00:39
47000 of 50000, Atoms: 479(A), 244(P), ChiSq: 28244, Time: 00:00:18 / 00:00:41
48000 of 50000, Atoms: 472(A), 234(P), ChiSq: 28277, Time: 00:00:18 / 00:00:40
49000 of 50000, Atoms: 468(A), 236(P), ChiSq: 28173, Time: 00:00:18 / 00:00:39
50000 of 50000, Atoms: 464(A), 233(P), ChiSq: 28261, Time: 00:00:19 / 00:00:40
-- Sampling Phase --
1000 of 50000, Atoms: 472(A), 220(P), ChiSq: 28210, Time: 00:00:19 / 00:00:39
2000 of 50000, Atoms: 477(A), 223(P), ChiSq: 28191, Time: 00:00:20 / 00:00:41
3000 of 50000, Atoms: 488(A), 232(P), ChiSq: 28263, Time: 00:00:20 / 00:00:40
4000 of 50000, Atoms: 462(A), 237(P), ChiSq: 28200, Time: 00:00:20 / 00:00:39
5000 of 50000, Atoms: 466(A), 217(P), ChiSq: 28265, Time: 00:00:21 / 00:00:40
6000 of 50000, Atoms: 469(A), 230(P), ChiSq: 28198, Time: 00:00:21 / 00:00:39
7000 of 50000, Atoms: 466(A), 228(P), ChiSq: 28239, Time: 00:00:22 / 00:00:40
8000 of 50000, Atoms: 462(A), 226(P), ChiSq: 28228, Time: 00:00:22 / 00:00:40
9000 of 50000, Atoms: 474(A), 239(P), ChiSq: 28294, Time: 00:00:23 / 00:00:41
10000 of 50000, Atoms: 466(A), 235(P), ChiSq: 28208, Time: 00:00:23 / 00:00:40
11000 of 50000, Atoms: 468(A), 244(P), ChiSq: 28244, Time: 00:00:23 / 00:00:39
12000 of 50000, Atoms: 466(A), 246(P), ChiSq: 28283, Time: 00:00:24 / 00:00:40
13000 of 50000, Atoms: 460(A), 224(P), ChiSq: 28240, Time: 00:00:24 / 00:00:39
14000 of 50000, Atoms: 451(A), 214(P), ChiSq: 28273, Time: 00:00:25 / 00:00:40
15000 of 50000, Atoms: 479(A), 230(P), ChiSq: 28159, Time: 00:00:25 / 00:00:40
16000 of 50000, Atoms: 472(A), 229(P), ChiSq: 28168, Time: 00:00:25 / 00:00:39
17000 of 50000, Atoms: 467(A), 232(P), ChiSq: 28279, Time: 00:00:26 / 00:00:40
18000 of 50000, Atoms: 475(A), 240(P), ChiSq: 28234, Time: 00:00:26 / 00:00:39
19000 of 50000, Atoms: 463(A), 239(P), ChiSq: 28312, Time: 00:00:27 / 00:00:40
20000 of 50000, Atoms: 470(A), 240(P), ChiSq: 28229, Time: 00:00:27 / 00:00:39
21000 of 50000, Atoms: 473(A), 237(P), ChiSq: 28274, Time: 00:00:28 / 00:00:40
22000 of 50000, Atoms: 470(A), 237(P), ChiSq: 28280, Time: 00:00:28 / 00:00:40
23000 of 50000, Atoms: 476(A), 231(P), ChiSq: 28272, Time: 00:00:28 / 00:00:39
24000 of 50000, Atoms: 482(A), 235(P), ChiSq: 28234, Time: 00:00:29 / 00:00:40
25000 of 50000, Atoms: 470(A), 239(P), ChiSq: 28202, Time: 00:00:29 / 00:00:39
26000 of 50000, Atoms: 473(A), 233(P), ChiSq: 28245, Time: 00:00:30 / 00:00:40
27000 of 50000, Atoms: 470(A), 236(P), ChiSq: 28259, Time: 00:00:30 / 00:00:39
28000 of 50000, Atoms: 484(A), 233(P), ChiSq: 28234, Time: 00:00:31 / 00:00:40
29000 of 50000, Atoms: 465(A), 241(P), ChiSq: 28383, Time: 00:00:31 / 00:00:40
30000 of 50000, Atoms: 475(A), 231(P), ChiSq: 28224, Time: 00:00:31 / 00:00:39
31000 of 50000, Atoms: 488(A), 238(P), ChiSq: 28211, Time: 00:00:32 / 00:00:40
32000 of 50000, Atoms: 460(A), 230(P), ChiSq: 28293, Time: 00:00:32 / 00:00:39
33000 of 50000, Atoms: 454(A), 227(P), ChiSq: 28239, Time: 00:00:33 / 00:00:40
34000 of 50000, Atoms: 469(A), 235(P), ChiSq: 28273, Time: 00:00:33 / 00:00:39
35000 of 50000, Atoms: 457(A), 227(P), ChiSq: 28170, Time: 00:00:34 / 00:00:40
36000 of 50000, Atoms: 476(A), 243(P), ChiSq: 28217, Time: 00:00:34 / 00:00:40
37000 of 50000, Atoms: 487(A), 232(P), ChiSq: 28290, Time: 00:00:34 / 00:00:39
38000 of 50000, Atoms: 473(A), 226(P), ChiSq: 28230, Time: 00:00:35 / 00:00:40
39000 of 50000, Atoms: 471(A), 237(P), ChiSq: 28202, Time: 00:00:35 / 00:00:39
40000 of 50000, Atoms: 477(A), 236(P), ChiSq: 28244, Time: 00:00:35 / 00:00:39
41000 of 50000, Atoms: 460(A), 231(P), ChiSq: 28272, Time: 00:00:36 / 00:00:39
42000 of 50000, Atoms: 465(A), 236(P), ChiSq: 28253, Time: 00:00:36 / 00:00:39
43000 of 50000, Atoms: 480(A), 235(P), ChiSq: 28291, Time: 00:00:37 / 00:00:40
44000 of 50000, Atoms: 459(A), 225(P), ChiSq: 28207, Time: 00:00:37 / 00:00:39
45000 of 50000, Atoms: 467(A), 221(P), ChiSq: 28206, Time: 00:00:38 / 00:00:40
46000 of 50000, Atoms: 464(A), 230(P), ChiSq: 28210, Time: 00:00:38 / 00:00:39
47000 of 50000, Atoms: 466(A), 216(P), ChiSq: 28203, Time: 00:00:38 / 00:00:39
48000 of 50000, Atoms: 454(A), 229(P), ChiSq: 28219, Time: 00:00:39 / 00:00:39
49000 of 50000, Atoms: 463(A), 238(P), ChiSq: 28206, Time: 00:00:39 / 00:00:39
50000 of 50000, Atoms: 493(A), 224(P), ChiSq: 28270, Time: 00:00:40 / 00:00:40
[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 
 53.736   0.660  54.430 

Example timings

projectR.Rcheck/projectR-Ex.timings

nameusersystemelapsed
alluvialMat1.1550.0261.183
aucMat0.1090.0120.122
cluster2pattern-methods0.2470.0740.322
clusterPlotR-methods000
correlateR0.2580.0320.290
geneMatchR0.0260.0540.081
intersectoR-methods0.0410.0100.050
projectR-methods41.122 0.09841.254
rotatoR0.0070.0010.007