Helena L. Crowell
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: RELEASE_3_8 |
| Last Commit: 88805f2 |
| Last Changed Date: 2019-03-21 07:35:25 -0400 (Thu, 21 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:44 -0400 (Tue, 16 Apr 2019).
| Package 204/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.6.7 Helena L. Crowell
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CATALYST |
| Version: 1.6.7 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CATALYST_1.6.7.tar.gz |
| StartedAt: 2019-04-15 22:41:53 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:51:08 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 554.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CATALYST_1.6.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CATALYST.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.6.7’
* 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 ... OK
* 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
plotYields 33.956 0.096 19.415
runDR 29.432 1.772 29.975
plotDiffHeatmap 21.100 0.048 14.103
plotClusterHeatmap 21.064 0.028 21.107
plotClusterExprs 17.296 0.036 17.355
plotMedExprs 14.916 0.004 14.968
plotMahal 13.828 0.000 13.861
outFCS 12.972 0.004 12.992
estCutoffs 11.740 0.036 10.795
outFrames 11.272 0.000 11.281
normCytof 11.248 0.012 11.276
plotEvents 11.048 0.000 11.074
dbFrame-methods 11.000 0.004 11.027
applyCutoffs 9.264 0.000 9.298
plotSpillmat 8.812 0.012 8.874
plotAbundances 8.696 0.012 8.722
assignPrelim 8.504 0.000 8.509
adaptSpillmat 7.484 0.084 7.606
computeSpillmat 6.964 0.000 6.973
plotCodes 6.956 0.000 6.968
plotDR 6.772 0.012 6.808
compCytof 6.592 0.020 6.622
filter 6.564 0.000 6.570
mergeClusters 6.216 0.000 6.228
cluster 5.468 0.004 5.480
daFrame-methods 5.452 0.008 5.464
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/CATALYST.Rcheck/00check.log’
for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘CATALYST’ ... ** 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 * DONE (CATALYST)
CATALYST.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 86 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
28.372 0.512 28.926
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| adaptSpillmat | 7.484 | 0.084 | 7.606 | |
| applyCutoffs | 9.264 | 0.000 | 9.298 | |
| assignPrelim | 8.504 | 0.000 | 8.509 | |
| cluster | 5.468 | 0.004 | 5.480 | |
| compCytof | 6.592 | 0.020 | 6.622 | |
| computeSpillmat | 6.964 | 0.000 | 6.973 | |
| concatFCS | 0.044 | 0.004 | 0.048 | |
| daFrame-class | 0.572 | 0.000 | 0.573 | |
| daFrame-methods | 5.452 | 0.008 | 5.464 | |
| data | 0.012 | 0.000 | 0.009 | |
| dbFrame-methods | 11.000 | 0.004 | 11.027 | |
| estCutoffs | 11.740 | 0.036 | 10.795 | |
| extractClusters | 4.540 | 0.004 | 4.550 | |
| filter | 6.564 | 0.000 | 6.570 | |
| guessPanel | 0.020 | 0.000 | 0.021 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 6.216 | 0.000 | 6.228 | |
| normCytof | 11.248 | 0.012 | 11.276 | |
| outFCS | 12.972 | 0.004 | 12.992 | |
| outFrames | 11.272 | 0.000 | 11.281 | |
| plotAbundances | 8.696 | 0.012 | 8.722 | |
| plotClusterExprs | 17.296 | 0.036 | 17.355 | |
| plotClusterHeatmap | 21.064 | 0.028 | 21.107 | |
| plotCodes | 6.956 | 0.000 | 6.968 | |
| plotCounts | 0.672 | 0.000 | 0.672 | |
| plotDR | 6.772 | 0.012 | 6.808 | |
| plotDiffHeatmap | 21.100 | 0.048 | 14.103 | |
| plotEvents | 11.048 | 0.000 | 11.074 | |
| plotExprHeatmap | 1.384 | 0.000 | 1.385 | |
| plotExprs | 4.148 | 0.004 | 4.156 | |
| plotMDS | 0.964 | 0.000 | 0.965 | |
| plotMahal | 13.828 | 0.000 | 13.861 | |
| plotMedExprs | 14.916 | 0.004 | 14.968 | |
| plotNRS | 1.568 | 0.000 | 1.572 | |
| plotSpillmat | 8.812 | 0.012 | 8.874 | |
| plotYields | 33.956 | 0.096 | 19.415 | |
| runDR | 29.432 | 1.772 | 29.975 | |