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).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R 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 |
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. |
Package 1551/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
projectR 1.15.0 (landing page) Genevieve Stein-O'Brien
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
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 |
############################################################################## ############################################################################## ### ### 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.
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 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
projectR.Rcheck/projectR-Ex.timings
name | user | system | elapsed | |
alluvialMat | 1.782 | 0.056 | 1.839 | |
aucMat | 0.067 | 0.000 | 0.067 | |
cluster2pattern-methods | 0.104 | 0.012 | 0.116 | |
clusterPlotR-methods | 0 | 0 | 0 | |
correlateR | 0.079 | 0.032 | 0.110 | |
geneMatchR | 0.016 | 0.003 | 0.020 | |
intersectoR-methods | 0.020 | 0.004 | 0.024 | |
projectR-methods | 40.574 | 0.087 | 40.662 | |
rotatoR | 0.004 | 0.000 | 0.004 | |