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This page was generated on 2022-01-26 13:05:48 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings projectR_1.10.0.tar.gz
StartedAt: 2022-01-25 09:04:41 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 09:08:24 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 223.2 seconds
RetCode: 0
Status:   OK  
CheckDir: projectR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings projectR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/projectR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.10.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
projectR-methods 30.654  0.216   30.87
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/projectR.Rcheck/00check.log’
for details.



Installation output

projectR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 3.14.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 524 
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: 200(A), 142(P), ChiSq: 49158, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 219(A), 191(P), ChiSq: 38622, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 253(A), 194(P), ChiSq: 35327, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 267(A), 202(P), ChiSq: 33736, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 290(A), 221(P), ChiSq: 32554, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 283(A), 225(P), ChiSq: 32687, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 314(A), 212(P), ChiSq: 31884, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 308(A), 225(P), ChiSq: 31394, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 332(A), 231(P), ChiSq: 31154, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 326(A), 231(P), ChiSq: 31095, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 344(A), 234(P), ChiSq: 30896, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 340(A), 247(P), ChiSq: 30818, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 346(A), 241(P), ChiSq: 30801, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 333(A), 260(P), ChiSq: 30723, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 344(A), 238(P), ChiSq: 30602, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 375(A), 240(P), ChiSq: 30330, Time: 00:00:04 / 00:00:30
17000 of 50000, Atoms: 388(A), 242(P), ChiSq: 30329, Time: 00:00:04 / 00:00:28
18000 of 50000, Atoms: 380(A), 243(P), ChiSq: 30255, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 386(A), 249(P), ChiSq: 30232, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 403(A), 240(P), ChiSq: 30221, Time: 00:00:05 / 00:00:29
21000 of 50000, Atoms: 384(A), 250(P), ChiSq: 30160, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 362(A), 240(P), ChiSq: 30133, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 390(A), 250(P), ChiSq: 30061, Time: 00:00:06 / 00:00:30
24000 of 50000, Atoms: 377(A), 270(P), ChiSq: 30057, Time: 00:00:06 / 00:00:28
25000 of 50000, Atoms: 401(A), 243(P), ChiSq: 30016, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 430(A), 255(P), ChiSq: 29924, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 420(A), 251(P), ChiSq: 29958, Time: 00:00:07 / 00:00:29
28000 of 50000, Atoms: 393(A), 251(P), ChiSq: 29994, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 409(A), 281(P), ChiSq: 30002, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 400(A), 260(P), ChiSq: 29925, Time: 00:00:08 / 00:00:30
31000 of 50000, Atoms: 397(A), 255(P), ChiSq: 29974, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 406(A), 259(P), ChiSq: 29978, Time: 00:00:08 / 00:00:28
33000 of 50000, Atoms: 432(A), 267(P), ChiSq: 29967, Time: 00:00:08 / 00:00:27
34000 of 50000, Atoms: 414(A), 247(P), ChiSq: 29992, Time: 00:00:09 / 00:00:29
35000 of 50000, Atoms: 429(A), 254(P), ChiSq: 29954, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 397(A), 254(P), ChiSq: 29995, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 409(A), 246(P), ChiSq: 29964, Time: 00:00:10 / 00:00:29
38000 of 50000, Atoms: 409(A), 249(P), ChiSq: 29958, Time: 00:00:10 / 00:00:28
39000 of 50000, Atoms: 381(A), 255(P), ChiSq: 30013, Time: 00:00:10 / 00:00:28
40000 of 50000, Atoms: 397(A), 261(P), ChiSq: 30041, Time: 00:00:10 / 00:00:27
41000 of 50000, Atoms: 406(A), 253(P), ChiSq: 30002, Time: 00:00:11 / 00:00:29
42000 of 50000, Atoms: 403(A), 239(P), ChiSq: 29991, Time: 00:00:11 / 00:00:28
43000 of 50000, Atoms: 394(A), 263(P), ChiSq: 29951, Time: 00:00:11 / 00:00:27
44000 of 50000, Atoms: 395(A), 258(P), ChiSq: 29983, Time: 00:00:12 / 00:00:29
45000 of 50000, Atoms: 397(A), 256(P), ChiSq: 30016, Time: 00:00:12 / 00:00:28
46000 of 50000, Atoms: 401(A), 256(P), ChiSq: 29978, Time: 00:00:12 / 00:00:28
47000 of 50000, Atoms: 398(A), 263(P), ChiSq: 29967, Time: 00:00:12 / 00:00:27
48000 of 50000, Atoms: 412(A), 251(P), ChiSq: 30017, Time: 00:00:13 / 00:00:29
49000 of 50000, Atoms: 418(A), 245(P), ChiSq: 29953, Time: 00:00:13 / 00:00:28
50000 of 50000, Atoms: 411(A), 266(P), ChiSq: 29967, Time: 00:00:13 / 00:00:27
-- Sampling Phase --
1000 of 50000, Atoms: 403(A), 252(P), ChiSq: 29905, Time: 00:00:14 / 00:00:29
2000 of 50000, Atoms: 404(A), 253(P), ChiSq: 29993, Time: 00:00:14 / 00:00:28
3000 of 50000, Atoms: 424(A), 256(P), ChiSq: 29964, Time: 00:00:14 / 00:00:28
4000 of 50000, Atoms: 400(A), 257(P), ChiSq: 30004, Time: 00:00:15 / 00:00:29
5000 of 50000, Atoms: 384(A), 258(P), ChiSq: 29980, Time: 00:00:15 / 00:00:28
6000 of 50000, Atoms: 406(A), 259(P), ChiSq: 29939, Time: 00:00:15 / 00:00:28
7000 of 50000, Atoms: 408(A), 241(P), ChiSq: 30018, Time: 00:00:16 / 00:00:29
8000 of 50000, Atoms: 406(A), 254(P), ChiSq: 29957, Time: 00:00:16 / 00:00:29
9000 of 50000, Atoms: 405(A), 262(P), ChiSq: 30001, Time: 00:00:16 / 00:00:28
10000 of 50000, Atoms: 417(A), 266(P), ChiSq: 29923, Time: 00:00:17 / 00:00:29
11000 of 50000, Atoms: 403(A), 259(P), ChiSq: 29916, Time: 00:00:17 / 00:00:29
12000 of 50000, Atoms: 422(A), 257(P), ChiSq: 29986, Time: 00:00:17 / 00:00:28
13000 of 50000, Atoms: 407(A), 272(P), ChiSq: 29949, Time: 00:00:17 / 00:00:28
14000 of 50000, Atoms: 404(A), 251(P), ChiSq: 29972, Time: 00:00:18 / 00:00:29
15000 of 50000, Atoms: 407(A), 243(P), ChiSq: 29928, Time: 00:00:18 / 00:00:28
16000 of 50000, Atoms: 417(A), 254(P), ChiSq: 29935, Time: 00:00:18 / 00:00:28
17000 of 50000, Atoms: 409(A), 249(P), ChiSq: 30065, Time: 00:00:19 / 00:00:29
18000 of 50000, Atoms: 391(A), 251(P), ChiSq: 30011, Time: 00:00:19 / 00:00:29
19000 of 50000, Atoms: 412(A), 265(P), ChiSq: 29964, Time: 00:00:19 / 00:00:28
20000 of 50000, Atoms: 401(A), 266(P), ChiSq: 29935, Time: 00:00:20 / 00:00:29
21000 of 50000, Atoms: 409(A), 253(P), ChiSq: 30015, Time: 00:00:20 / 00:00:29
22000 of 50000, Atoms: 391(A), 258(P), ChiSq: 30013, Time: 00:00:20 / 00:00:28
23000 of 50000, Atoms: 410(A), 270(P), ChiSq: 29942, Time: 00:00:21 / 00:00:29
24000 of 50000, Atoms: 405(A), 248(P), ChiSq: 29999, Time: 00:00:21 / 00:00:29
25000 of 50000, Atoms: 405(A), 252(P), ChiSq: 30049, Time: 00:00:21 / 00:00:28
26000 of 50000, Atoms: 400(A), 251(P), ChiSq: 29987, Time: 00:00:22 / 00:00:29
27000 of 50000, Atoms: 412(A), 260(P), ChiSq: 29956, Time: 00:00:22 / 00:00:29
28000 of 50000, Atoms: 386(A), 270(P), ChiSq: 29954, Time: 00:00:22 / 00:00:28
29000 of 50000, Atoms: 410(A), 257(P), ChiSq: 29975, Time: 00:00:22 / 00:00:28
30000 of 50000, Atoms: 409(A), 249(P), ChiSq: 30015, Time: 00:00:23 / 00:00:29
31000 of 50000, Atoms: 409(A), 251(P), ChiSq: 29997, Time: 00:00:23 / 00:00:28
32000 of 50000, Atoms: 393(A), 263(P), ChiSq: 29979, Time: 00:00:23 / 00:00:28
33000 of 50000, Atoms: 403(A), 244(P), ChiSq: 29973, Time: 00:00:24 / 00:00:29
34000 of 50000, Atoms: 410(A), 268(P), ChiSq: 29974, Time: 00:00:24 / 00:00:29
35000 of 50000, Atoms: 397(A), 257(P), ChiSq: 29977, Time: 00:00:24 / 00:00:28
36000 of 50000, Atoms: 391(A), 267(P), ChiSq: 29986, Time: 00:00:25 / 00:00:29
37000 of 50000, Atoms: 410(A), 242(P), ChiSq: 29950, Time: 00:00:25 / 00:00:29
38000 of 50000, Atoms: 411(A), 252(P), ChiSq: 29956, Time: 00:00:25 / 00:00:28
39000 of 50000, Atoms: 400(A), 253(P), ChiSq: 30004, Time: 00:00:26 / 00:00:29
40000 of 50000, Atoms: 395(A), 254(P), ChiSq: 29957, Time: 00:00:26 / 00:00:29
41000 of 50000, Atoms: 424(A), 260(P), ChiSq: 29986, Time: 00:00:26 / 00:00:28
42000 of 50000, Atoms: 393(A), 254(P), ChiSq: 29973, Time: 00:00:27 / 00:00:29
43000 of 50000, Atoms: 397(A), 249(P), ChiSq: 29976, Time: 00:00:27 / 00:00:29
44000 of 50000, Atoms: 431(A), 251(P), ChiSq: 29952, Time: 00:00:27 / 00:00:28
45000 of 50000, Atoms: 415(A), 261(P), ChiSq: 29949, Time: 00:00:28 / 00:00:29
46000 of 50000, Atoms: 396(A), 277(P), ChiSq: 29966, Time: 00:00:28 / 00:00:29
47000 of 50000, Atoms: 388(A), 243(P), ChiSq: 29900, Time: 00:00:28 / 00:00:28
48000 of 50000, Atoms: 412(A), 260(P), ChiSq: 29964, Time: 00:00:28 / 00:00:28
49000 of 50000, Atoms: 413(A), 254(P), ChiSq: 30034, Time: 00:00:29 / 00:00:29
50000 of 50000, Atoms: 401(A), 266(P), ChiSq: 29981, 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"
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 24 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
 37.901   0.325  38.207 

Example timings

projectR.Rcheck/projectR-Ex.timings

nameusersystemelapsed
alluvialMat0.9640.0000.964
aucMat0.0550.0160.071
cluster2pattern-methods0.0900.0190.110
clusterPlotR-methods000
correlateR0.0800.0240.104
geneMatchR0.0100.0070.018
intersectoR-methods0.0210.0010.021
projectR-methods30.654 0.21630.870
rotatoR0.0040.0000.004