Hao Chen
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/uSORT |
| git_branch: master |
| git_last_commit: 82fa06f |
| git_last_commit_date: 2021-10-26 12:30:07 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:57 -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 uSORT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/uSORT.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 2040/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| uSORT 1.21.0 (landing page) Hao Chen
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: uSORT |
| Version: 1.21.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:uSORT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings uSORT_1.21.0.tar.gz |
| StartedAt: 2022-03-17 20:34:13 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:36:36 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 143.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: uSORT.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:uSORT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings uSORT_1.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/uSORT.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 'uSORT/DESCRIPTION' ... OK
* this is package 'uSORT' version '1.21.0'
* 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 whether package 'uSORT' can be installed ... WARNING
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See 'D:/biocbuild/bbs-3.15-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 ... NOTE
mcesApply1: no visible global function definition for 'clusterEvalQ'
mcesApply1: no visible global function definition for 'parRapply'
mcesApply1: no visible global function definition for 'parCapply'
Undefined global functions or variables:
clusterEvalQ parCapply parRapply
* 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 (user + system) or elapsed time > 5s
user system elapsed
sWanderlust 15.55 0.61 16.25
autoSPIN 11.51 0.96 12.50
* 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, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/uSORT.Rcheck/00check.log'
for details.
uSORT.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL uSORT
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'uSORT' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parRapply' when loading 'uSORT'
Note: break used in wrong context: no loop is visible
** help
*** installing help indices
converting help for package 'uSORT'
finding HTML links ... done
EXP_to_CellDataSet html
Rwanderlust html
SPIN html
STS_sorting html
STS_sorting_wrapper html
STS_sortingcost html
autoSPIN html
clusterGenes1 html
compareModels1 html
diff_test_helper1 html
differentialGeneTest1 html
distance.function html
driving_force_gene_selection html
elbow_detection html
fluidigmSC_analyzeGeneDetection html
fluidigmSC_identifyExpOutliers html
fluidigmSC_isElementIgnoreCase html
fluidigmSC_readLinearExp html
fluidigmSC_removeGenesByLinearExpForAllType
html
fluidigmSC_removeGenesByLinearExpForAllType_log2
html
monocle_wrapper html
neighborhood_sorting html
neighborhood_sorting_wrapper html
neighborhood_sortingcost html
pca_gene_selection html
sWanderlust html
scattering_quantification_per_gene html
sorting_method_parameter_GUI html
summed_local_variance html
summed_local_variance_cyclical html
summed_local_variance_linear html
trajectory_landmarks html
uSORT html
uSORT_GUI html
uSORT_parameters_GUI html
uSORT_preProcess html
uSORT_sorting_wrapper html
uSORT_write_results html
variability_per_gene html
wanderlust_wrapper html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parRapply' when loading 'uSORT'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parRapply' when loading 'uSORT'
** testing if installed package keeps a record of temporary installation path
* DONE (uSORT)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'GeneGeneInteR' is missing or broken
done
uSORT.Rcheck/tests/runTests.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.
> BiocGenerics:::testPackage("uSORT")
No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parRapply' when loading '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: 0.985372
Running iterations... 2
Correlation with previous iteration: 0.99972
Running iterations... 3
Correlation with previous iteration: 0.999971
Wanderlust Sorting Done!
RUNIT TEST PROTOCOL -- Thu Mar 17 20:36:28 2022
***********************************************
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
3.43 0.32 3.75
uSORT.Rcheck/uSORT-Ex.timings
| name | user | system | elapsed | |
| Rwanderlust | 0.61 | 0.03 | 0.64 | |
| SPIN | 0.05 | 0.00 | 0.04 | |
| STS_sortingcost | 0.00 | 0.01 | 0.01 | |
| autoSPIN | 11.51 | 0.96 | 12.50 | |
| driving_force_gene_selection | 0 | 0 | 0 | |
| elbow_detection | 0 | 0 | 0 | |
| monocle_wrapper | 0 | 0 | 0 | |
| neighborhood_sortingcost | 0.05 | 0.00 | 0.05 | |
| pca_gene_selection | 2.76 | 0.33 | 3.10 | |
| sWanderlust | 15.55 | 0.61 | 16.25 | |
| uSORT | 0 | 0 | 0 | |
| uSORT_GUI | 0 | 0 | 0 | |
| uSORT_preProcess | 1.91 | 0.20 | 2.10 | |
| uSORT_sorting_wrapper | 2.54 | 0.22 | 2.77 | |
| uSORT_write_results | 0 | 0 | 0 | |