| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:38 -0400 (Mon, 16 Oct 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" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 2023-10-16 00:02:06 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 00:07:47 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 341.1 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 39.399 0.039 39.439
* 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 593
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: 186(A), 156(P), ChiSq: 49350, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 224(A), 182(P), ChiSq: 38120, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 256(A), 195(P), ChiSq: 35208, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 279(A), 201(P), ChiSq: 33843, Time: 00:00:01 / 00:00:36
5000 of 50000, Atoms: 287(A), 222(P), ChiSq: 32948, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 297(A), 209(P), ChiSq: 32206, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 305(A), 220(P), ChiSq: 31972, Time: 00:00:02 / 00:00:38
8000 of 50000, Atoms: 306(A), 217(P), ChiSq: 31704, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 318(A), 229(P), ChiSq: 31266, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 333(A), 225(P), ChiSq: 31237, Time: 00:00:03 / 00:00:38
11000 of 50000, Atoms: 338(A), 256(P), ChiSq: 30926, Time: 00:00:03 / 00:00:34
12000 of 50000, Atoms: 345(A), 228(P), ChiSq: 30877, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 340(A), 233(P), ChiSq: 30621, Time: 00:00:04 / 00:00:38
14000 of 50000, Atoms: 331(A), 239(P), ChiSq: 30665, Time: 00:00:04 / 00:00:35
15000 of 50000, Atoms: 346(A), 245(P), ChiSq: 30423, Time: 00:00:04 / 00:00:32
16000 of 50000, Atoms: 369(A), 241(P), ChiSq: 30345, Time: 00:00:05 / 00:00:37
17000 of 50000, Atoms: 366(A), 249(P), ChiSq: 30377, Time: 00:00:05 / 00:00:35
18000 of 50000, Atoms: 368(A), 237(P), ChiSq: 30274, Time: 00:00:06 / 00:00:39
19000 of 50000, Atoms: 382(A), 239(P), ChiSq: 30213, Time: 00:00:06 / 00:00:37
20000 of 50000, Atoms: 387(A), 261(P), ChiSq: 30168, Time: 00:00:06 / 00:00:35
21000 of 50000, Atoms: 375(A), 246(P), ChiSq: 30109, Time: 00:00:07 / 00:00:39
22000 of 50000, Atoms: 396(A), 239(P), ChiSq: 30024, Time: 00:00:07 / 00:00:37
23000 of 50000, Atoms: 412(A), 254(P), ChiSq: 30094, Time: 00:00:07 / 00:00:35
24000 of 50000, Atoms: 405(A), 255(P), ChiSq: 29984, Time: 00:00:08 / 00:00:38
25000 of 50000, Atoms: 417(A), 257(P), ChiSq: 29952, Time: 00:00:08 / 00:00:36
26000 of 50000, Atoms: 403(A), 255(P), ChiSq: 29932, Time: 00:00:09 / 00:00:39
27000 of 50000, Atoms: 389(A), 243(P), ChiSq: 30073, Time: 00:00:09 / 00:00:38
28000 of 50000, Atoms: 382(A), 268(P), ChiSq: 29953, Time: 00:00:09 / 00:00:36
29000 of 50000, Atoms: 414(A), 271(P), ChiSq: 30044, Time: 00:00:10 / 00:00:39
30000 of 50000, Atoms: 408(A), 256(P), ChiSq: 29983, Time: 00:00:10 / 00:00:37
31000 of 50000, Atoms: 421(A), 272(P), ChiSq: 29927, Time: 00:00:11 / 00:00:39
32000 of 50000, Atoms: 405(A), 260(P), ChiSq: 30023, Time: 00:00:11 / 00:00:38
33000 of 50000, Atoms: 405(A), 247(P), ChiSq: 29993, Time: 00:00:11 / 00:00:37
34000 of 50000, Atoms: 397(A), 239(P), ChiSq: 30015, Time: 00:00:12 / 00:00:39
35000 of 50000, Atoms: 402(A), 251(P), ChiSq: 29990, Time: 00:00:12 / 00:00:38
36000 of 50000, Atoms: 431(A), 269(P), ChiSq: 29972, Time: 00:00:12 / 00:00:36
37000 of 50000, Atoms: 421(A), 255(P), ChiSq: 29921, Time: 00:00:13 / 00:00:38
38000 of 50000, Atoms: 422(A), 253(P), ChiSq: 30001, Time: 00:00:13 / 00:00:37
39000 of 50000, Atoms: 428(A), 255(P), ChiSq: 29915, Time: 00:00:14 / 00:00:39
40000 of 50000, Atoms: 418(A), 252(P), ChiSq: 29999, Time: 00:00:14 / 00:00:38
41000 of 50000, Atoms: 402(A), 261(P), ChiSq: 29969, Time: 00:00:14 / 00:00:37
42000 of 50000, Atoms: 405(A), 257(P), ChiSq: 30002, Time: 00:00:15 / 00:00:38
43000 of 50000, Atoms: 411(A), 247(P), ChiSq: 30006, Time: 00:00:15 / 00:00:37
44000 of 50000, Atoms: 413(A), 263(P), ChiSq: 29968, Time: 00:00:16 / 00:00:39
45000 of 50000, Atoms: 390(A), 254(P), ChiSq: 29953, Time: 00:00:16 / 00:00:38
46000 of 50000, Atoms: 403(A), 250(P), ChiSq: 29971, Time: 00:00:16 / 00:00:37
47000 of 50000, Atoms: 415(A), 270(P), ChiSq: 29908, Time: 00:00:17 / 00:00:38
48000 of 50000, Atoms: 413(A), 254(P), ChiSq: 29992, Time: 00:00:17 / 00:00:38
49000 of 50000, Atoms: 418(A), 253(P), ChiSq: 29982, Time: 00:00:18 / 00:00:39
50000 of 50000, Atoms: 392(A), 270(P), ChiSq: 29960, Time: 00:00:18 / 00:00:38
-- Sampling Phase --
1000 of 50000, Atoms: 411(A), 259(P), ChiSq: 29955, Time: 00:00:18 / 00:00:37
2000 of 50000, Atoms: 379(A), 253(P), ChiSq: 29999, Time: 00:00:19 / 00:00:38
3000 of 50000, Atoms: 412(A), 264(P), ChiSq: 29934, Time: 00:00:19 / 00:00:38
4000 of 50000, Atoms: 404(A), 259(P), ChiSq: 29909, Time: 00:00:20 / 00:00:39
5000 of 50000, Atoms: 419(A), 268(P), ChiSq: 29978, Time: 00:00:20 / 00:00:38
6000 of 50000, Atoms: 411(A), 258(P), ChiSq: 29887, Time: 00:00:20 / 00:00:37
7000 of 50000, Atoms: 427(A), 252(P), ChiSq: 29560, Time: 00:00:21 / 00:00:38
8000 of 50000, Atoms: 444(A), 245(P), ChiSq: 29467, Time: 00:00:21 / 00:00:38
9000 of 50000, Atoms: 462(A), 252(P), ChiSq: 29425, Time: 00:00:22 / 00:00:39
10000 of 50000, Atoms: 499(A), 236(P), ChiSq: 29006, Time: 00:00:22 / 00:00:38
11000 of 50000, Atoms: 495(A), 229(P), ChiSq: 28503, Time: 00:00:23 / 00:00:39
12000 of 50000, Atoms: 499(A), 229(P), ChiSq: 28281, Time: 00:00:23 / 00:00:38
13000 of 50000, Atoms: 517(A), 218(P), ChiSq: 28182, Time: 00:00:23 / 00:00:38
14000 of 50000, Atoms: 490(A), 237(P), ChiSq: 28149, Time: 00:00:24 / 00:00:39
15000 of 50000, Atoms: 484(A), 223(P), ChiSq: 28162, Time: 00:00:24 / 00:00:38
16000 of 50000, Atoms: 481(A), 238(P), ChiSq: 28239, Time: 00:00:25 / 00:00:39
17000 of 50000, Atoms: 481(A), 241(P), ChiSq: 28213, Time: 00:00:25 / 00:00:38
18000 of 50000, Atoms: 472(A), 227(P), ChiSq: 28200, Time: 00:00:26 / 00:00:39
19000 of 50000, Atoms: 473(A), 232(P), ChiSq: 28225, Time: 00:00:26 / 00:00:39
20000 of 50000, Atoms: 467(A), 242(P), ChiSq: 28212, Time: 00:00:26 / 00:00:38
21000 of 50000, Atoms: 460(A), 234(P), ChiSq: 28183, Time: 00:00:27 / 00:00:39
22000 of 50000, Atoms: 471(A), 233(P), ChiSq: 28191, Time: 00:00:27 / 00:00:38
23000 of 50000, Atoms: 480(A), 233(P), ChiSq: 28231, Time: 00:00:28 / 00:00:39
24000 of 50000, Atoms: 475(A), 235(P), ChiSq: 28153, Time: 00:00:28 / 00:00:38
25000 of 50000, Atoms: 479(A), 235(P), ChiSq: 28236, Time: 00:00:28 / 00:00:38
26000 of 50000, Atoms: 482(A), 231(P), ChiSq: 28259, Time: 00:00:29 / 00:00:39
27000 of 50000, Atoms: 450(A), 248(P), ChiSq: 28205, Time: 00:00:29 / 00:00:38
28000 of 50000, Atoms: 448(A), 241(P), ChiSq: 28220, Time: 00:00:30 / 00:00:39
29000 of 50000, Atoms: 461(A), 238(P), ChiSq: 28210, Time: 00:00:30 / 00:00:38
30000 of 50000, Atoms: 465(A), 239(P), ChiSq: 28224, Time: 00:00:31 / 00:00:39
31000 of 50000, Atoms: 463(A), 237(P), ChiSq: 28228, Time: 00:00:31 / 00:00:39
32000 of 50000, Atoms: 469(A), 245(P), ChiSq: 28236, Time: 00:00:31 / 00:00:38
33000 of 50000, Atoms: 499(A), 236(P), ChiSq: 28129, Time: 00:00:32 / 00:00:39
34000 of 50000, Atoms: 485(A), 236(P), ChiSq: 28190, Time: 00:00:32 / 00:00:38
35000 of 50000, Atoms: 470(A), 223(P), ChiSq: 28197, Time: 00:00:33 / 00:00:39
36000 of 50000, Atoms: 478(A), 245(P), ChiSq: 28244, Time: 00:00:33 / 00:00:38
37000 of 50000, Atoms: 466(A), 236(P), ChiSq: 28182, Time: 00:00:34 / 00:00:39
38000 of 50000, Atoms: 471(A), 234(P), ChiSq: 28217, Time: 00:00:34 / 00:00:39
39000 of 50000, Atoms: 468(A), 237(P), ChiSq: 28152, Time: 00:00:34 / 00:00:38
40000 of 50000, Atoms: 462(A), 240(P), ChiSq: 28213, Time: 00:00:35 / 00:00:39
41000 of 50000, Atoms: 457(A), 236(P), ChiSq: 28226, Time: 00:00:35 / 00:00:38
42000 of 50000, Atoms: 485(A), 234(P), ChiSq: 28188, Time: 00:00:36 / 00:00:39
43000 of 50000, Atoms: 446(A), 242(P), ChiSq: 28245, Time: 00:00:36 / 00:00:38
44000 of 50000, Atoms: 481(A), 235(P), ChiSq: 28238, Time: 00:00:36 / 00:00:38
45000 of 50000, Atoms: 491(A), 239(P), ChiSq: 28191, Time: 00:00:37 / 00:00:39
46000 of 50000, Atoms: 481(A), 234(P), ChiSq: 28161, Time: 00:00:37 / 00:00:38
47000 of 50000, Atoms: 456(A), 235(P), ChiSq: 28314, Time: 00:00:38 / 00:00:39
48000 of 50000, Atoms: 478(A), 237(P), ChiSq: 28286, Time: 00:00:38 / 00:00:38
49000 of 50000, Atoms: 483(A), 219(P), ChiSq: 28253, Time: 00:00:39 / 00:00:39
50000 of 50000, Atoms: 456(A), 238(P), ChiSq: 28276, Time: 00:00:39 / 00:00:39
[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
50.671 0.678 51.336
projectR.Rcheck/projectR-Ex.timings
| name | user | system | elapsed | |
| alluvialMat | 1.298 | 0.052 | 1.350 | |
| aucMat | 0.065 | 0.008 | 0.073 | |
| cluster2pattern-methods | 0.105 | 0.040 | 0.145 | |
| clusterPlotR-methods | 0 | 0 | 0 | |
| correlateR | 0.126 | 0.020 | 0.146 | |
| geneMatchR | 0.020 | 0.028 | 0.048 | |
| intersectoR-methods | 0.019 | 0.005 | 0.022 | |
| projectR-methods | 39.399 | 0.039 | 39.439 | |
| rotatoR | 0.004 | 0.001 | 0.004 | |