Hao Chen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/uSORT |
| Branch: RELEASE_3_7 |
| Last Commit: c2f7b0a |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:29:26 -0400 (Wed, 17 Oct 2018).
| Package 1528/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| uSORT 1.6.0 Hao Chen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: uSORT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:uSORT.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings uSORT_1.6.0.tar.gz |
| StartedAt: 2018-10-16 04:23:16 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 04:25:30 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 134.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: uSORT.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:uSORT.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings uSORT_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/uSORT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘uSORT/DESCRIPTION’ ... OK
* this is package ‘uSORT’ version ‘1.6.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘uSORT’ can be installed ... WARNING
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/biocbuild/bbs-3.7-bioc/meat/uSORT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sWanderlust 23.404 0.736 24.192
autoSPIN 11.956 0.152 12.085
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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 WARNING
See
‘/home/biocbuild/bbs-3.7-bioc/meat/uSORT.Rcheck/00check.log’
for details.
uSORT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL uSORT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘uSORT’ ... ** R ** inst ** byte-compile and prepare package for lazy loading Note: break used in wrong context: no loop is visible ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (uSORT)
uSORT.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.
> BiocGenerics:::testPackage("uSORT")
No starting point specified, the first row will be used!
Building lNN graph...
lNN computed in: 0 seconds
Randomly Select waypoints...
Flock waypoints...
Iteratively realign trajectory:
Running iterations... 1
Correlation with previous iteration: 0.999438
Running iterations... 2
Correlation with previous iteration: 0.999519
Running iterations... 3
Correlation with previous iteration: 0.998746
Running iterations... 4
Correlation with previous iteration: 0.999146
Running iterations... 5
Correlation with previous iteration: 1
Wanderlust Sorting Done!
RUNIT TEST PROTOCOL -- Tue Oct 16 04:25:28 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
uSORT RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.692 0.324 5.095
uSORT.Rcheck/uSORT-Ex.timings
| name | user | system | elapsed | |
| Rwanderlust | 1.024 | 0.040 | 1.060 | |
| SPIN | 0.092 | 0.004 | 0.094 | |
| STS_sortingcost | 0.012 | 0.004 | 0.017 | |
| autoSPIN | 11.956 | 0.152 | 12.085 | |
| driving_force_gene_selection | 0.000 | 0.000 | 0.001 | |
| elbow_detection | 0.004 | 0.000 | 0.004 | |
| monocle_wrapper | 0.004 | 0.000 | 0.002 | |
| neighborhood_sortingcost | 0.028 | 0.004 | 0.035 | |
| pca_gene_selection | 2.596 | 0.108 | 2.728 | |
| sWanderlust | 23.404 | 0.736 | 24.192 | |
| uSORT | 0.004 | 0.000 | 0.003 | |
| uSORT_GUI | 0.000 | 0.000 | 0.001 | |
| uSORT_preProcess | 1.556 | 0.080 | 1.632 | |
| uSORT_sorting_wrapper | 2.032 | 0.048 | 2.076 | |
| uSORT_write_results | 0.004 | 0.000 | 0.002 | |