Hao Chen
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/uSORT |
| Branch: RELEASE_3_8 |
| Last Commit: 2b2c850 |
| Last Changed Date: 2019-01-04 13:53:06 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:07 -0400 (Sat, 13 Apr 2019).
| Package 1614/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| uSORT 1.8.1 Hao Chen
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: uSORT |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:uSORT.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings uSORT_1.8.1.tar.gz |
| StartedAt: 2019-04-13 06:07:54 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:12:31 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 277.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: uSORT.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:uSORT.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings uSORT_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/uSORT.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'C:/Users/biocbuild/bbs-3.8-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sWanderlust 19.52 0.22 19.73
autoSPIN 13.90 0.03 13.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sWanderlust 17.83 0.16 17.99
autoSPIN 11.45 0.06 11.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/uSORT.Rcheck/00check.log'
for details.
uSORT.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/uSORT_1.8.1.tar.gz && rm -rf uSORT.buildbin-libdir && mkdir uSORT.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=uSORT.buildbin-libdir uSORT_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL uSORT_1.8.1.zip && rm uSORT_1.8.1.tar.gz uSORT_1.8.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1641k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1641k 100 1641k 0 0 29.2M 0 --:--:-- --:--:-- --:--:-- 30.8M
install for i386
* 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
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
In R CMD INSTALL
install for x64
* installing *source* package 'uSORT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'uSORT' as uSORT_1.8.1.zip
* DONE (uSORT)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'uSORT' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
uSORT.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 0.02 seconds
Randomly Select waypoints...
Flock waypoints...
Iteratively realign trajectory:
Running iterations... 1
Correlation with previous iteration: 0.999465
Running iterations... 2
Correlation with previous iteration: 0.999529
Running iterations... 3
Correlation with previous iteration: 0.998748
Running iterations... 4
Correlation with previous iteration: 0.999147
Running iterations... 5
Correlation with previous iteration: 1
Wanderlust Sorting Done!
RUNIT TEST PROTOCOL -- Sat Apr 13 06:12:15 2019
***********************************************
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
4.14 0.23 4.37
|
uSORT.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 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 -- Sat Apr 13 06:12:21 2019
***********************************************
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
5.04 0.26 5.29
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uSORT.Rcheck/examples_i386/uSORT-Ex.timings
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uSORT.Rcheck/examples_x64/uSORT-Ex.timings
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