Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:40 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1551/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
projectR 1.15.0  (landing page)
Genevieve Stein-O'Brien
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/projectR
git_branch: devel
git_last_commit: 4186eb9
git_last_commit_date: 2022-11-01 11:19:29 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: projectR
Version: 1.15.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings projectR_1.15.0.tar.gz
StartedAt: 2023-04-12 08:30:53 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 08:37:19 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 386.0 seconds
RetCode: 0
Status:   OK  
CheckDir: projectR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings projectR_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/projectR.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘projectR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘projectR’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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 40.574  0.087  40.662
* 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 ...
  ‘projectR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/projectR.Rcheck/00check.log’
for details.



Installation output

projectR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL projectR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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 3.19.1 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 32 
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: 201(A), 132(P), ChiSq: 49236, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 249(A), 149(P), ChiSq: 39010, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 257(A), 158(P), ChiSq: 36303, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 283(A), 177(P), ChiSq: 34071, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 294(A), 176(P), ChiSq: 33389, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 327(A), 186(P), ChiSq: 32458, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 325(A), 190(P), ChiSq: 32190, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 334(A), 185(P), ChiSq: 31613, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 377(A), 185(P), ChiSq: 31059, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 383(A), 205(P), ChiSq: 30756, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 375(A), 197(P), ChiSq: 30575, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 385(A), 197(P), ChiSq: 30383, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 389(A), 208(P), ChiSq: 30209, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 400(A), 219(P), ChiSq: 30267, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 402(A), 198(P), ChiSq: 30065, Time: 00:00:04 / 00:00:32
16000 of 50000, Atoms: 406(A), 215(P), ChiSq: 29834, Time: 00:00:05 / 00:00:37
17000 of 50000, Atoms: 390(A), 235(P), ChiSq: 29720, Time: 00:00:05 / 00:00:35
18000 of 50000, Atoms: 456(A), 235(P), ChiSq: 29435, Time: 00:00:06 / 00:00:39
19000 of 50000, Atoms: 477(A), 225(P), ChiSq: 29080, Time: 00:00:06 / 00:00:37
20000 of 50000, Atoms: 468(A), 230(P), ChiSq: 28664, Time: 00:00:07 / 00:00:41
21000 of 50000, Atoms: 469(A), 224(P), ChiSq: 28591, Time: 00:00:07 / 00:00:39
22000 of 50000, Atoms: 462(A), 219(P), ChiSq: 28325, Time: 00:00:07 / 00:00:37
23000 of 50000, Atoms: 463(A), 248(P), ChiSq: 28300, Time: 00:00:08 / 00:00:40
24000 of 50000, Atoms: 473(A), 238(P), ChiSq: 28252, Time: 00:00:08 / 00:00:38
25000 of 50000, Atoms: 464(A), 233(P), ChiSq: 28142, Time: 00:00:09 / 00:00:41
26000 of 50000, Atoms: 452(A), 244(P), ChiSq: 28174, Time: 00:00:09 / 00:00:39
27000 of 50000, Atoms: 460(A), 241(P), ChiSq: 28215, Time: 00:00:09 / 00:00:38
28000 of 50000, Atoms: 483(A), 235(P), ChiSq: 28171, Time: 00:00:10 / 00:00:40
29000 of 50000, Atoms: 495(A), 241(P), ChiSq: 28235, Time: 00:00:10 / 00:00:39
30000 of 50000, Atoms: 477(A), 234(P), ChiSq: 28169, Time: 00:00:11 / 00:00:41
31000 of 50000, Atoms: 466(A), 234(P), ChiSq: 28211, Time: 00:00:11 / 00:00:39
32000 of 50000, Atoms: 486(A), 233(P), ChiSq: 28161, Time: 00:00:12 / 00:00:42
33000 of 50000, Atoms: 477(A), 220(P), ChiSq: 28219, Time: 00:00:12 / 00:00:40
34000 of 50000, Atoms: 471(A), 238(P), ChiSq: 28181, Time: 00:00:12 / 00:00:39
35000 of 50000, Atoms: 473(A), 233(P), ChiSq: 28246, Time: 00:00:13 / 00:00:41
36000 of 50000, Atoms: 470(A), 239(P), ChiSq: 28204, Time: 00:00:13 / 00:00:39
37000 of 50000, Atoms: 453(A), 238(P), ChiSq: 28285, Time: 00:00:14 / 00:00:41
38000 of 50000, Atoms: 465(A), 240(P), ChiSq: 28202, Time: 00:00:14 / 00:00:40
39000 of 50000, Atoms: 486(A), 232(P), ChiSq: 28207, Time: 00:00:14 / 00:00:39
40000 of 50000, Atoms: 475(A), 239(P), ChiSq: 28190, Time: 00:00:15 / 00:00:41
41000 of 50000, Atoms: 479(A), 237(P), ChiSq: 28165, Time: 00:00:15 / 00:00:39
42000 of 50000, Atoms: 465(A), 249(P), ChiSq: 28221, Time: 00:00:16 / 00:00:41
43000 of 50000, Atoms: 493(A), 240(P), ChiSq: 28211, Time: 00:00:16 / 00:00:40
44000 of 50000, Atoms: 475(A), 235(P), ChiSq: 28187, Time: 00:00:16 / 00:00:39
45000 of 50000, Atoms: 491(A), 237(P), ChiSq: 28209, Time: 00:00:17 / 00:00:40
46000 of 50000, Atoms: 479(A), 227(P), ChiSq: 28218, Time: 00:00:17 / 00:00:39
47000 of 50000, Atoms: 480(A), 238(P), ChiSq: 28215, Time: 00:00:18 / 00:00:41
48000 of 50000, Atoms: 470(A), 234(P), ChiSq: 28272, Time: 00:00:18 / 00:00:40
49000 of 50000, Atoms: 484(A), 236(P), ChiSq: 28161, Time: 00:00:18 / 00:00:39
50000 of 50000, Atoms: 473(A), 215(P), ChiSq: 28249, Time: 00:00:19 / 00:00:40
-- Sampling Phase --
1000 of 50000, Atoms: 487(A), 234(P), ChiSq: 28289, Time: 00:00:19 / 00:00:39
2000 of 50000, Atoms: 463(A), 243(P), ChiSq: 28212, Time: 00:00:20 / 00:00:41
3000 of 50000, Atoms: 442(A), 250(P), ChiSq: 28260, Time: 00:00:20 / 00:00:40
4000 of 50000, Atoms: 485(A), 232(P), ChiSq: 28165, Time: 00:00:21 / 00:00:41
5000 of 50000, Atoms: 473(A), 233(P), ChiSq: 28153, Time: 00:00:21 / 00:00:40
6000 of 50000, Atoms: 452(A), 251(P), ChiSq: 28290, Time: 00:00:21 / 00:00:39
7000 of 50000, Atoms: 468(A), 233(P), ChiSq: 28204, Time: 00:00:22 / 00:00:40
8000 of 50000, Atoms: 483(A), 244(P), ChiSq: 28180, Time: 00:00:22 / 00:00:40
9000 of 50000, Atoms: 475(A), 235(P), ChiSq: 28248, Time: 00:00:23 / 00:00:41
10000 of 50000, Atoms: 471(A), 237(P), ChiSq: 28220, Time: 00:00:23 / 00:00:40
11000 of 50000, Atoms: 469(A), 231(P), ChiSq: 28159, Time: 00:00:24 / 00:00:41
12000 of 50000, Atoms: 477(A), 233(P), ChiSq: 28221, Time: 00:00:24 / 00:00:40
13000 of 50000, Atoms: 476(A), 242(P), ChiSq: 28172, Time: 00:00:24 / 00:00:39
14000 of 50000, Atoms: 465(A), 230(P), ChiSq: 28251, Time: 00:00:25 / 00:00:40
15000 of 50000, Atoms: 484(A), 247(P), ChiSq: 28265, Time: 00:00:25 / 00:00:40
16000 of 50000, Atoms: 473(A), 231(P), ChiSq: 28187, Time: 00:00:26 / 00:00:41
17000 of 50000, Atoms: 493(A), 229(P), ChiSq: 28212, Time: 00:00:26 / 00:00:40
18000 of 50000, Atoms: 490(A), 239(P), ChiSq: 28213, Time: 00:00:27 / 00:00:41
19000 of 50000, Atoms: 473(A), 246(P), ChiSq: 28207, Time: 00:00:27 / 00:00:40
20000 of 50000, Atoms: 476(A), 225(P), ChiSq: 28201, Time: 00:00:27 / 00:00:39
21000 of 50000, Atoms: 481(A), 233(P), ChiSq: 28188, Time: 00:00:28 / 00:00:40
22000 of 50000, Atoms: 459(A), 243(P), ChiSq: 28232, Time: 00:00:28 / 00:00:40
23000 of 50000, Atoms: 479(A), 236(P), ChiSq: 28222, Time: 00:00:29 / 00:00:40
24000 of 50000, Atoms: 473(A), 222(P), ChiSq: 28235, Time: 00:00:29 / 00:00:40
25000 of 50000, Atoms: 459(A), 226(P), ChiSq: 28188, Time: 00:00:30 / 00:00:41
26000 of 50000, Atoms: 469(A), 244(P), ChiSq: 28153, Time: 00:00:30 / 00:00:40
27000 of 50000, Atoms: 462(A), 231(P), ChiSq: 28220, Time: 00:00:30 / 00:00:39
28000 of 50000, Atoms: 489(A), 232(P), ChiSq: 28201, Time: 00:00:31 / 00:00:40
29000 of 50000, Atoms: 450(A), 239(P), ChiSq: 28188, Time: 00:00:31 / 00:00:40
30000 of 50000, Atoms: 470(A), 246(P), ChiSq: 28213, Time: 00:00:32 / 00:00:40
31000 of 50000, Atoms: 480(A), 231(P), ChiSq: 28127, Time: 00:00:32 / 00:00:40
32000 of 50000, Atoms: 479(A), 240(P), ChiSq: 28227, Time: 00:00:32 / 00:00:39
33000 of 50000, Atoms: 474(A), 246(P), ChiSq: 28227, Time: 00:00:33 / 00:00:40
34000 of 50000, Atoms: 469(A), 241(P), ChiSq: 28190, Time: 00:00:33 / 00:00:39
35000 of 50000, Atoms: 462(A), 231(P), ChiSq: 28175, Time: 00:00:34 / 00:00:40
36000 of 50000, Atoms: 478(A), 251(P), ChiSq: 28207, Time: 00:00:34 / 00:00:40
37000 of 50000, Atoms: 461(A), 237(P), ChiSq: 28234, Time: 00:00:35 / 00:00:40
38000 of 50000, Atoms: 472(A), 240(P), ChiSq: 28199, Time: 00:00:35 / 00:00:40
39000 of 50000, Atoms: 471(A), 234(P), ChiSq: 28212, Time: 00:00:35 / 00:00:39
40000 of 50000, Atoms: 438(A), 239(P), ChiSq: 28181, Time: 00:00:36 / 00:00:40
41000 of 50000, Atoms: 460(A), 224(P), ChiSq: 28151, Time: 00:00:36 / 00:00:39
42000 of 50000, Atoms: 459(A), 243(P), ChiSq: 28203, Time: 00:00:37 / 00:00:40
43000 of 50000, Atoms: 466(A), 232(P), ChiSq: 28161, Time: 00:00:37 / 00:00:40
44000 of 50000, Atoms: 461(A), 236(P), ChiSq: 28215, Time: 00:00:38 / 00:00:40
45000 of 50000, Atoms: 474(A), 228(P), ChiSq: 28141, Time: 00:00:38 / 00:00:40
46000 of 50000, Atoms: 474(A), 223(P), ChiSq: 28198, Time: 00:00:38 / 00:00:39
47000 of 50000, Atoms: 463(A), 233(P), ChiSq: 28225, Time: 00:00:39 / 00:00:40
48000 of 50000, Atoms: 469(A), 233(P), ChiSq: 28188, Time: 00:00:39 / 00:00:39
49000 of 50000, Atoms: 471(A), 241(P), ChiSq: 28187, Time: 00:00:40 / 00:00:40
50000 of 50000, Atoms: 477(A), 228(P), ChiSq: 28193, 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 
 53.129   1.149  54.265 

Example timings

projectR.Rcheck/projectR-Ex.timings

nameusersystemelapsed
alluvialMat1.7820.0561.839
aucMat0.0670.0000.067
cluster2pattern-methods0.1040.0120.116
clusterPlotR-methods000
correlateR0.0790.0320.110
geneMatchR0.0160.0030.020
intersectoR-methods0.0200.0040.024
projectR-methods40.574 0.08740.662
rotatoR0.0040.0000.004