| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-09-27 11:35:54 -0400 (Wed, 27 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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 | ||||
| Package 1566/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| projectR 1.16.0 (landing page) Genevieve Stein-O'Brien
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: projectR |
| Version: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2023-09-27 00:09:23 -0400 (Wed, 27 Sep 2023) |
| EndedAt: 2023-09-27 00:15:03 -0400 (Wed, 27 Sep 2023) |
| EllapsedTime: 339.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: projectR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/projectR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘projectR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘projectR’ version ‘1.16.0’
* 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 40.326 0.071 40.398
* 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.
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)
projectR.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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 3.20.0
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:
-- Standard Parameters --
nPatterns 5
nIterations 50000
seed 228
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: 224(A), 106(P), ChiSq: 52759, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 268(A), 135(P), ChiSq: 40730, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 312(A), 162(P), ChiSq: 35215, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 352(A), 174(P), ChiSq: 33529, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 324(A), 189(P), ChiSq: 32557, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 327(A), 197(P), ChiSq: 31922, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 353(A), 192(P), ChiSq: 31231, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 375(A), 204(P), ChiSq: 30273, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 406(A), 210(P), ChiSq: 29447, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 392(A), 199(P), ChiSq: 29238, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 415(A), 210(P), ChiSq: 29294, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 414(A), 231(P), ChiSq: 28972, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 428(A), 213(P), ChiSq: 28886, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 425(A), 228(P), ChiSq: 28927, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 432(A), 217(P), ChiSq: 28771, Time: 00:00:05 / 00:00:40
16000 of 50000, Atoms: 432(A), 219(P), ChiSq: 28752, Time: 00:00:05 / 00:00:37
17000 of 50000, Atoms: 436(A), 216(P), ChiSq: 28629, Time: 00:00:05 / 00:00:35
18000 of 50000, Atoms: 455(A), 225(P), ChiSq: 28587, Time: 00:00:06 / 00:00:39
19000 of 50000, Atoms: 437(A), 231(P), ChiSq: 28519, Time: 00:00:06 / 00:00:37
20000 of 50000, Atoms: 445(A), 238(P), ChiSq: 28444, Time: 00:00:06 / 00:00:35
21000 of 50000, Atoms: 435(A), 231(P), ChiSq: 28400, Time: 00:00:07 / 00:00:39
22000 of 50000, Atoms: 450(A), 229(P), ChiSq: 28298, Time: 00:00:07 / 00:00:37
23000 of 50000, Atoms: 453(A), 228(P), ChiSq: 28362, Time: 00:00:08 / 00:00:40
24000 of 50000, Atoms: 456(A), 230(P), ChiSq: 28295, Time: 00:00:08 / 00:00:38
25000 of 50000, Atoms: 474(A), 228(P), ChiSq: 28274, Time: 00:00:08 / 00:00:36
26000 of 50000, Atoms: 451(A), 241(P), ChiSq: 28171, Time: 00:00:09 / 00:00:39
27000 of 50000, Atoms: 463(A), 225(P), ChiSq: 28207, Time: 00:00:09 / 00:00:38
28000 of 50000, Atoms: 468(A), 236(P), ChiSq: 28204, Time: 00:00:10 / 00:00:40
29000 of 50000, Atoms: 466(A), 235(P), ChiSq: 28312, Time: 00:00:10 / 00:00:39
30000 of 50000, Atoms: 478(A), 231(P), ChiSq: 28145, Time: 00:00:10 / 00:00:37
31000 of 50000, Atoms: 471(A), 231(P), ChiSq: 28216, Time: 00:00:11 / 00:00:39
32000 of 50000, Atoms: 470(A), 231(P), ChiSq: 28296, Time: 00:00:11 / 00:00:38
33000 of 50000, Atoms: 466(A), 247(P), ChiSq: 28216, Time: 00:00:12 / 00:00:40
34000 of 50000, Atoms: 467(A), 233(P), ChiSq: 28244, Time: 00:00:12 / 00:00:39
35000 of 50000, Atoms: 466(A), 230(P), ChiSq: 28266, Time: 00:00:13 / 00:00:41
36000 of 50000, Atoms: 465(A), 224(P), ChiSq: 28193, Time: 00:00:13 / 00:00:39
37000 of 50000, Atoms: 477(A), 239(P), ChiSq: 28257, Time: 00:00:13 / 00:00:38
38000 of 50000, Atoms: 487(A), 236(P), ChiSq: 28340, Time: 00:00:14 / 00:00:40
39000 of 50000, Atoms: 459(A), 237(P), ChiSq: 28230, Time: 00:00:14 / 00:00:39
40000 of 50000, Atoms: 466(A), 231(P), ChiSq: 28291, Time: 00:00:15 / 00:00:41
41000 of 50000, Atoms: 480(A), 230(P), ChiSq: 28232, Time: 00:00:15 / 00:00:39
42000 of 50000, Atoms: 466(A), 221(P), ChiSq: 28242, Time: 00:00:15 / 00:00:38
43000 of 50000, Atoms: 461(A), 237(P), ChiSq: 28215, Time: 00:00:16 / 00:00:40
44000 of 50000, Atoms: 461(A), 230(P), ChiSq: 28193, Time: 00:00:16 / 00:00:39
45000 of 50000, Atoms: 478(A), 224(P), ChiSq: 28209, Time: 00:00:17 / 00:00:40
46000 of 50000, Atoms: 471(A), 241(P), ChiSq: 28238, Time: 00:00:17 / 00:00:39
47000 of 50000, Atoms: 449(A), 231(P), ChiSq: 28258, Time: 00:00:17 / 00:00:38
48000 of 50000, Atoms: 456(A), 229(P), ChiSq: 28291, Time: 00:00:18 / 00:00:40
49000 of 50000, Atoms: 469(A), 230(P), ChiSq: 28270, Time: 00:00:18 / 00:00:39
50000 of 50000, Atoms: 451(A), 228(P), ChiSq: 28236, Time: 00:00:19 / 00:00:40
-- Sampling Phase --
1000 of 50000, Atoms: 455(A), 222(P), ChiSq: 28193, Time: 00:00:19 / 00:00:39
2000 of 50000, Atoms: 458(A), 238(P), ChiSq: 28237, Time: 00:00:19 / 00:00:38
3000 of 50000, Atoms: 478(A), 232(P), ChiSq: 28248, Time: 00:00:20 / 00:00:40
4000 of 50000, Atoms: 463(A), 226(P), ChiSq: 28216, Time: 00:00:20 / 00:00:39
5000 of 50000, Atoms: 470(A), 232(P), ChiSq: 28320, Time: 00:00:21 / 00:00:40
6000 of 50000, Atoms: 465(A), 241(P), ChiSq: 28265, Time: 00:00:21 / 00:00:39
7000 of 50000, Atoms: 469(A), 237(P), ChiSq: 28290, Time: 00:00:21 / 00:00:38
8000 of 50000, Atoms: 461(A), 228(P), ChiSq: 28265, Time: 00:00:22 / 00:00:40
9000 of 50000, Atoms: 477(A), 237(P), ChiSq: 28280, Time: 00:00:22 / 00:00:39
10000 of 50000, Atoms: 464(A), 236(P), ChiSq: 28273, Time: 00:00:23 / 00:00:40
11000 of 50000, Atoms: 458(A), 221(P), ChiSq: 28215, Time: 00:00:23 / 00:00:39
12000 of 50000, Atoms: 460(A), 228(P), ChiSq: 28248, Time: 00:00:24 / 00:00:40
13000 of 50000, Atoms: 445(A), 240(P), ChiSq: 28243, Time: 00:00:24 / 00:00:39
14000 of 50000, Atoms: 469(A), 235(P), ChiSq: 28274, Time: 00:00:24 / 00:00:39
15000 of 50000, Atoms: 439(A), 234(P), ChiSq: 28227, Time: 00:00:25 / 00:00:40
16000 of 50000, Atoms: 463(A), 238(P), ChiSq: 28214, Time: 00:00:25 / 00:00:39
17000 of 50000, Atoms: 461(A), 238(P), ChiSq: 28171, Time: 00:00:26 / 00:00:40
18000 of 50000, Atoms: 458(A), 240(P), ChiSq: 28273, Time: 00:00:26 / 00:00:39
19000 of 50000, Atoms: 450(A), 220(P), ChiSq: 28230, Time: 00:00:26 / 00:00:39
20000 of 50000, Atoms: 470(A), 218(P), ChiSq: 28269, Time: 00:00:27 / 00:00:39
21000 of 50000, Atoms: 466(A), 229(P), ChiSq: 28239, Time: 00:00:27 / 00:00:39
22000 of 50000, Atoms: 465(A), 221(P), ChiSq: 28244, Time: 00:00:28 / 00:00:40
23000 of 50000, Atoms: 455(A), 234(P), ChiSq: 28226, Time: 00:00:28 / 00:00:39
24000 of 50000, Atoms: 471(A), 216(P), ChiSq: 28208, Time: 00:00:29 / 00:00:40
25000 of 50000, Atoms: 468(A), 234(P), ChiSq: 28206, Time: 00:00:29 / 00:00:39
26000 of 50000, Atoms: 465(A), 225(P), ChiSq: 28195, Time: 00:00:29 / 00:00:39
27000 of 50000, Atoms: 475(A), 236(P), ChiSq: 28322, Time: 00:00:30 / 00:00:39
28000 of 50000, Atoms: 462(A), 238(P), ChiSq: 28240, Time: 00:00:30 / 00:00:39
29000 of 50000, Atoms: 475(A), 226(P), ChiSq: 28281, Time: 00:00:31 / 00:00:40
30000 of 50000, Atoms: 460(A), 232(P), ChiSq: 28168, Time: 00:00:31 / 00:00:39
31000 of 50000, Atoms: 474(A), 222(P), ChiSq: 28179, Time: 00:00:32 / 00:00:40
32000 of 50000, Atoms: 448(A), 242(P), ChiSq: 28218, Time: 00:00:32 / 00:00:39
33000 of 50000, Atoms: 453(A), 240(P), ChiSq: 28222, Time: 00:00:32 / 00:00:39
34000 of 50000, Atoms: 467(A), 229(P), ChiSq: 28211, Time: 00:00:33 / 00:00:39
35000 of 50000, Atoms: 485(A), 240(P), ChiSq: 28238, Time: 00:00:33 / 00:00:39
36000 of 50000, Atoms: 462(A), 236(P), ChiSq: 28219, Time: 00:00:34 / 00:00:40
37000 of 50000, Atoms: 465(A), 235(P), ChiSq: 28252, Time: 00:00:34 / 00:00:39
38000 of 50000, Atoms: 466(A), 222(P), ChiSq: 28187, Time: 00:00:35 / 00:00:40
39000 of 50000, Atoms: 472(A), 245(P), ChiSq: 28312, Time: 00:00:35 / 00:00:39
40000 of 50000, Atoms: 467(A), 244(P), ChiSq: 28354, Time: 00:00:35 / 00:00:39
41000 of 50000, Atoms: 462(A), 225(P), ChiSq: 28185, Time: 00:00:36 / 00:00:39
42000 of 50000, Atoms: 486(A), 233(P), ChiSq: 28187, Time: 00:00:36 / 00:00:39
43000 of 50000, Atoms: 458(A), 237(P), ChiSq: 28219, Time: 00:00:37 / 00:00:40
44000 of 50000, Atoms: 448(A), 237(P), ChiSq: 28201, Time: 00:00:37 / 00:00:39
45000 of 50000, Atoms: 456(A), 230(P), ChiSq: 28251, Time: 00:00:37 / 00:00:39
46000 of 50000, Atoms: 463(A), 240(P), ChiSq: 28258, Time: 00:00:38 / 00:00:39
47000 of 50000, Atoms: 466(A), 245(P), ChiSq: 28262, Time: 00:00:38 / 00:00:39
48000 of 50000, Atoms: 457(A), 232(P), ChiSq: 28283, Time: 00:00:39 / 00:00:39
49000 of 50000, Atoms: 467(A), 227(P), ChiSq: 28255, Time: 00:00:39 / 00:00:39
50000 of 50000, Atoms: 460(A), 236(P), ChiSq: 28207, 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
50.938 0.676 51.603
projectR.Rcheck/projectR-Ex.timings
| name | user | system | elapsed | |
| alluvialMat | 1.268 | 0.080 | 1.348 | |
| aucMat | 0.056 | 0.020 | 0.076 | |
| cluster2pattern-methods | 0.107 | 0.035 | 0.143 | |
| clusterPlotR-methods | 0 | 0 | 0 | |
| correlateR | 0.121 | 0.027 | 0.149 | |
| geneMatchR | 0.008 | 0.040 | 0.048 | |
| intersectoR-methods | 0.018 | 0.004 | 0.023 | |
| projectR-methods | 40.326 | 0.071 | 40.398 | |
| rotatoR | 0.003 | 0.000 | 0.004 | |