| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:21 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1474/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| projectR 1.11.0 (landing page) Genevieve Stein-O'Brien
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: projectR |
| Version: 1.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:projectR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings projectR_1.11.0.tar.gz |
| StartedAt: 2022-03-17 19:55:48 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:59:19 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 210.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: projectR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:projectR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings projectR_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/projectR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'projectR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'projectR' version '1.11.0'
* 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 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 28.51 0 28.51
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/projectR.Rcheck/00check.log'
for details.
projectR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL projectR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'projectR'
finding HTML links ... done
AP.RNAseq6l3c3t html
alluvialMat html
aucMat html
cluster2pattern-methods html
clusterPlotR-methods html
correlateR-class html
correlateR html
geneMatchR html
initialize-correlateR-method html
initialize-rotatoR-method html
intersectoR-methods html
map.ESepiGen4c1l html
map.RNAseq6l3c3t html
p.ESepiGen4c1l html
p.RNAseq6l3c3t html
pd.ESepiGen4c1l html
pd.RNAseq6l3c3t html
projectR-methods html
rotatoR-class html
rotatoR html
** 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)
Making 'packages.html' ... done
projectR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 3.15.2
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:
-- Standard Parameters --
nPatterns 5
nIterations 50000
seed 310
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: 205(A), 158(P), ChiSq: 47816, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 235(A), 179(P), ChiSq: 37281, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 258(A), 187(P), ChiSq: 36171, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 279(A), 186(P), ChiSq: 34169, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 281(A), 204(P), ChiSq: 33094, Time: 00:00:01 / 00:00:27
6000 of 50000, Atoms: 304(A), 187(P), ChiSq: 32283, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 317(A), 209(P), ChiSq: 31672, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 349(A), 207(P), ChiSq: 31600, Time: 00:00:02 / 00:00:32
9000 of 50000, Atoms: 333(A), 202(P), ChiSq: 31460, Time: 00:00:02 / 00:00:28
10000 of 50000, Atoms: 352(A), 202(P), ChiSq: 31151, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 401(A), 212(P), ChiSq: 30414, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 390(A), 220(P), ChiSq: 30094, Time: 00:00:03 / 00:00:31
13000 of 50000, Atoms: 420(A), 216(P), ChiSq: 30012, Time: 00:00:03 / 00:00:28
14000 of 50000, Atoms: 438(A), 222(P), ChiSq: 29886, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 442(A), 213(P), ChiSq: 29651, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 461(A), 225(P), ChiSq: 28949, Time: 00:00:04 / 00:00:30
17000 of 50000, Atoms: 465(A), 215(P), ChiSq: 28919, Time: 00:00:04 / 00:00:28
18000 of 50000, Atoms: 434(A), 233(P), ChiSq: 28533, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 459(A), 224(P), ChiSq: 28383, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 447(A), 217(P), ChiSq: 28520, Time: 00:00:05 / 00:00:29
21000 of 50000, Atoms: 428(A), 227(P), ChiSq: 28364, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 430(A), 221(P), ChiSq: 28317, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 467(A), 223(P), ChiSq: 28230, Time: 00:00:05 / 00:00:25
24000 of 50000, Atoms: 458(A), 237(P), ChiSq: 28233, Time: 00:00:06 / 00:00:28
25000 of 50000, Atoms: 464(A), 225(P), ChiSq: 28221, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 476(A), 227(P), ChiSq: 28249, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 468(A), 223(P), ChiSq: 28251, Time: 00:00:07 / 00:00:29
28000 of 50000, Atoms: 490(A), 224(P), ChiSq: 28222, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 462(A), 245(P), ChiSq: 28212, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 472(A), 233(P), ChiSq: 28220, Time: 00:00:08 / 00:00:30
31000 of 50000, Atoms: 488(A), 231(P), ChiSq: 28260, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 470(A), 247(P), ChiSq: 28215, Time: 00:00:08 / 00:00:28
33000 of 50000, Atoms: 474(A), 247(P), ChiSq: 28141, Time: 00:00:09 / 00:00:30
34000 of 50000, Atoms: 477(A), 226(P), ChiSq: 28243, Time: 00:00:09 / 00:00:29
35000 of 50000, Atoms: 463(A), 242(P), ChiSq: 28262, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 462(A), 234(P), ChiSq: 28213, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 458(A), 233(P), ChiSq: 28166, Time: 00:00:10 / 00:00:29
38000 of 50000, Atoms: 461(A), 226(P), ChiSq: 28287, Time: 00:00:10 / 00:00:28
39000 of 50000, Atoms: 441(A), 224(P), ChiSq: 28253, Time: 00:00:10 / 00:00:28
40000 of 50000, Atoms: 467(A), 225(P), ChiSq: 28269, Time: 00:00:11 / 00:00:30
41000 of 50000, Atoms: 473(A), 248(P), ChiSq: 28254, Time: 00:00:11 / 00:00:29
42000 of 50000, Atoms: 478(A), 233(P), ChiSq: 28190, Time: 00:00:11 / 00:00:28
43000 of 50000, Atoms: 461(A), 249(P), ChiSq: 28215, Time: 00:00:11 / 00:00:27
44000 of 50000, Atoms: 450(A), 227(P), ChiSq: 28183, Time: 00:00:12 / 00:00:29
45000 of 50000, Atoms: 454(A), 230(P), ChiSq: 28276, Time: 00:00:12 / 00:00:28
46000 of 50000, Atoms: 465(A), 224(P), ChiSq: 28271, Time: 00:00:12 / 00:00:28
47000 of 50000, Atoms: 457(A), 229(P), ChiSq: 28129, Time: 00:00:12 / 00:00:27
48000 of 50000, Atoms: 478(A), 229(P), ChiSq: 28159, Time: 00:00:13 / 00:00:29
49000 of 50000, Atoms: 452(A), 229(P), ChiSq: 28293, Time: 00:00:13 / 00:00:28
50000 of 50000, Atoms: 471(A), 225(P), ChiSq: 28208, Time: 00:00:13 / 00:00:27
-- Sampling Phase --
1000 of 50000, Atoms: 472(A), 233(P), ChiSq: 28172, Time: 00:00:14 / 00:00:29
2000 of 50000, Atoms: 446(A), 227(P), ChiSq: 28221, Time: 00:00:14 / 00:00:28
3000 of 50000, Atoms: 461(A), 225(P), ChiSq: 28225, Time: 00:00:14 / 00:00:28
4000 of 50000, Atoms: 462(A), 243(P), ChiSq: 28204, Time: 00:00:14 / 00:00:27
5000 of 50000, Atoms: 451(A), 244(P), ChiSq: 28238, Time: 00:00:15 / 00:00:28
6000 of 50000, Atoms: 473(A), 226(P), ChiSq: 28223, Time: 00:00:15 / 00:00:28
7000 of 50000, Atoms: 485(A), 243(P), ChiSq: 28209, Time: 00:00:15 / 00:00:27
8000 of 50000, Atoms: 461(A), 244(P), ChiSq: 28202, Time: 00:00:16 / 00:00:29
9000 of 50000, Atoms: 458(A), 235(P), ChiSq: 28142, Time: 00:00:16 / 00:00:28
10000 of 50000, Atoms: 465(A), 221(P), ChiSq: 28198, Time: 00:00:16 / 00:00:28
11000 of 50000, Atoms: 497(A), 218(P), ChiSq: 28176, Time: 00:00:16 / 00:00:27
12000 of 50000, Atoms: 464(A), 222(P), ChiSq: 28131, Time: 00:00:17 / 00:00:28
13000 of 50000, Atoms: 459(A), 236(P), ChiSq: 28197, Time: 00:00:17 / 00:00:28
14000 of 50000, Atoms: 471(A), 235(P), ChiSq: 28160, Time: 00:00:17 / 00:00:27
15000 of 50000, Atoms: 462(A), 235(P), ChiSq: 28214, Time: 00:00:17 / 00:00:27
16000 of 50000, Atoms: 460(A), 243(P), ChiSq: 28210, Time: 00:00:18 / 00:00:28
17000 of 50000, Atoms: 457(A), 224(P), ChiSq: 28174, Time: 00:00:18 / 00:00:27
18000 of 50000, Atoms: 452(A), 225(P), ChiSq: 28283, Time: 00:00:18 / 00:00:27
19000 of 50000, Atoms: 473(A), 229(P), ChiSq: 28219, Time: 00:00:19 / 00:00:28
20000 of 50000, Atoms: 458(A), 233(P), ChiSq: 28160, Time: 00:00:19 / 00:00:28
21000 of 50000, Atoms: 460(A), 236(P), ChiSq: 28238, Time: 00:00:19 / 00:00:27
22000 of 50000, Atoms: 451(A), 235(P), ChiSq: 28272, Time: 00:00:19 / 00:00:27
23000 of 50000, Atoms: 474(A), 227(P), ChiSq: 28221, Time: 00:00:20 / 00:00:28
24000 of 50000, Atoms: 470(A), 230(P), ChiSq: 28161, Time: 00:00:20 / 00:00:27
25000 of 50000, Atoms: 478(A), 249(P), ChiSq: 28244, Time: 00:00:20 / 00:00:27
26000 of 50000, Atoms: 452(A), 241(P), ChiSq: 28212, Time: 00:00:21 / 00:00:28
27000 of 50000, Atoms: 482(A), 243(P), ChiSq: 28143, Time: 00:00:21 / 00:00:27
28000 of 50000, Atoms: 476(A), 236(P), ChiSq: 28171, Time: 00:00:21 / 00:00:27
29000 of 50000, Atoms: 450(A), 225(P), ChiSq: 28194, Time: 00:00:21 / 00:00:27
30000 of 50000, Atoms: 458(A), 243(P), ChiSq: 28177, Time: 00:00:22 / 00:00:28
31000 of 50000, Atoms: 467(A), 236(P), ChiSq: 28177, Time: 00:00:22 / 00:00:27
32000 of 50000, Atoms: 485(A), 239(P), ChiSq: 28183, Time: 00:00:22 / 00:00:27
33000 of 50000, Atoms: 498(A), 232(P), ChiSq: 28209, Time: 00:00:22 / 00:00:26
34000 of 50000, Atoms: 462(A), 236(P), ChiSq: 28163, Time: 00:00:23 / 00:00:27
35000 of 50000, Atoms: 486(A), 228(P), ChiSq: 28132, Time: 00:00:23 / 00:00:27
36000 of 50000, Atoms: 462(A), 237(P), ChiSq: 28213, Time: 00:00:23 / 00:00:27
37000 of 50000, Atoms: 462(A), 233(P), ChiSq: 28222, Time: 00:00:24 / 00:00:27
38000 of 50000, Atoms: 478(A), 232(P), ChiSq: 28146, Time: 00:00:24 / 00:00:27
39000 of 50000, Atoms: 463(A), 232(P), ChiSq: 28251, Time: 00:00:24 / 00:00:27
40000 of 50000, Atoms: 459(A), 243(P), ChiSq: 28239, Time: 00:00:25 / 00:00:28
41000 of 50000, Atoms: 472(A), 230(P), ChiSq: 28206, Time: 00:00:25 / 00:00:27
42000 of 50000, Atoms: 468(A), 223(P), ChiSq: 28202, Time: 00:00:26 / 00:00:28
43000 of 50000, Atoms: 489(A), 247(P), ChiSq: 28261, Time: 00:00:26 / 00:00:28
44000 of 50000, Atoms: 476(A), 247(P), ChiSq: 28290, Time: 00:00:26 / 00:00:27
45000 of 50000, Atoms: 458(A), 237(P), ChiSq: 28171, Time: 00:00:27 / 00:00:28
46000 of 50000, Atoms: 470(A), 232(P), ChiSq: 28236, Time: 00:00:27 / 00:00:28
47000 of 50000, Atoms: 460(A), 231(P), ChiSq: 28189, Time: 00:00:28 / 00:00:28
48000 of 50000, Atoms: 484(A), 245(P), ChiSq: 28186, Time: 00:00:28 / 00:00:28
49000 of 50000, Atoms: 462(A), 244(P), ChiSq: 28204, Time: 00:00:28 / 00:00:28
50000 of 50000, Atoms: 487(A), 244(P), ChiSq: 28235, 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
37.23 0.40 37.62
projectR.Rcheck/projectR-Ex.timings
| name | user | system | elapsed | |
| alluvialMat | 0.44 | 0.02 | 0.45 | |
| aucMat | 0.06 | 0.00 | 0.06 | |
| cluster2pattern-methods | 0.14 | 0.01 | 0.16 | |
| clusterPlotR-methods | 0 | 0 | 0 | |
| correlateR | 0.16 | 0.02 | 0.17 | |
| geneMatchR | 0.56 | 0.01 | 0.58 | |
| intersectoR-methods | 0.01 | 0.00 | 0.01 | |
| projectR-methods | 28.51 | 0.00 | 28.51 | |
| rotatoR | 0 | 0 | 0 | |