| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:47:54 -0400 (Tue, 09 Apr 2019).
| Package 211/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.7.7 Helena L. Crowell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: CATALYST |
| Version: 1.7.7 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CATALYST_1.7.7.tar.gz |
| StartedAt: 2019-04-08 23:13:59 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:23:03 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 543.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CATALYST.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CATALYST_1.7.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.7.7’
* 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 ‘CATALYST’ 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 ... OK
* 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
plotClusterHeatmap,daFrame : <anonymous>: no visible binding for global
variable ‘cluster_id’
Undefined global functions or variables:
cluster_id
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runDR 30.261 0.052 30.421
plotYields 24.365 0.084 12.581
plotDiffHeatmap 17.861 0.119 12.415
plotClusterExprs 17.195 0.068 17.277
plotMedExprs 12.016 0.012 12.032
applyCutoffs 11.738 0.000 11.739
plotClusterHeatmap 11.702 0.012 11.714
plotMahal 11.335 0.000 11.352
dbFrame-methods 11.218 0.008 11.229
outFCS 10.440 0.004 10.445
estCutoffs 10.138 0.032 9.230
plotAbundances 9.717 0.024 9.747
assignPrelim 9.521 0.004 9.540
normCytof 9.342 0.024 9.371
plotEvents 9.235 0.008 9.253
outFrames 8.589 0.000 8.591
compCytof 8.244 0.000 8.246
daFrame-methods 7.811 0.011 7.838
mergeClusters 7.760 0.004 7.809
plotDR 6.631 0.372 7.006
computeSpillmat 6.632 0.004 6.637
plotSpillmat 6.509 0.005 6.513
cluster 6.413 0.004 6.419
extractClusters 6.189 0.008 6.200
plotCodes 6.165 0.008 6.174
adaptSpillmat 5.680 0.124 5.804
filter 5.769 0.012 5.783
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
invokeRestart("muffleWarning")
})
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43)
Error: testthat unit tests failed
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck/00check.log’
for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘CATALYST’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘filter’ in package ‘CATALYST’ ** 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 (CATALYST)
CATALYST.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(CATALYST)
Attaching package: 'CATALYST'
The following object is masked from 'package:stats':
filter
>
> test_check("CATALYST")
── 1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#4
unused argument (use_dimred = "MDS")
1: expect_warning(runDR(y, "PCA", i, use_dimred = "MDS")) at testthat/test_runDR.R:43
2: quasi_capture(enquo(object), capture_warnings, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, warning = function(condition) {
out$push(condition)
invokeRestart("muffleWarning")
})
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43)
Error: testthat unit tests failed
Execution halted
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| adaptSpillmat | 5.680 | 0.124 | 5.804 | |
| applyCutoffs | 11.738 | 0.000 | 11.739 | |
| assignPrelim | 9.521 | 0.004 | 9.540 | |
| cluster | 6.413 | 0.004 | 6.419 | |
| compCytof | 8.244 | 0.000 | 8.246 | |
| computeSpillmat | 6.632 | 0.004 | 6.637 | |
| concatFCS | 0.07 | 0.00 | 0.07 | |
| daFrame-class | 0.662 | 0.000 | 0.662 | |
| daFrame-methods | 7.811 | 0.011 | 7.838 | |
| data | 0.009 | 0.000 | 0.009 | |
| dbFrame-methods | 11.218 | 0.008 | 11.229 | |
| estCutoffs | 10.138 | 0.032 | 9.230 | |
| extractClusters | 6.189 | 0.008 | 6.200 | |
| filter | 5.769 | 0.012 | 5.783 | |
| guessPanel | 0.027 | 0.000 | 0.026 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 7.760 | 0.004 | 7.809 | |
| normCytof | 9.342 | 0.024 | 9.371 | |
| outFCS | 10.440 | 0.004 | 10.445 | |
| outFrames | 8.589 | 0.000 | 8.591 | |
| plotAbundances | 9.717 | 0.024 | 9.747 | |
| plotClusterExprs | 17.195 | 0.068 | 17.277 | |
| plotClusterHeatmap | 11.702 | 0.012 | 11.714 | |
| plotCodes | 6.165 | 0.008 | 6.174 | |
| plotCounts | 0.56 | 0.00 | 0.56 | |
| plotDR | 6.631 | 0.372 | 7.006 | |
| plotDiffHeatmap | 17.861 | 0.119 | 12.415 | |
| plotEvents | 9.235 | 0.008 | 9.253 | |
| plotExprHeatmap | 1.392 | 0.000 | 1.392 | |
| plotExprs | 4.841 | 0.008 | 4.849 | |
| plotMDS | 0.733 | 0.000 | 0.735 | |
| plotMahal | 11.335 | 0.000 | 11.352 | |
| plotMedExprs | 12.016 | 0.012 | 12.032 | |
| plotNRS | 0.939 | 0.000 | 0.938 | |
| plotSpillmat | 6.509 | 0.005 | 6.513 | |
| plotYields | 24.365 | 0.084 | 12.581 | |
| runDR | 30.261 | 0.052 | 30.421 | |