Genevieve Stein-O'Brien
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/projectR |
| Branch: RELEASE_3_9 |
| Last Commit: 69a67dd |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:43:48 -0400 (Wed, 16 Oct 2019).
| Package 1259/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| projectR 1.0.0 Genevieve Stein-O'Brien
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: projectR |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:projectR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings projectR_1.0.0.tar.gz |
| StartedAt: 2019-10-16 06:09:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:14:21 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 280.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: projectR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:projectR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings projectR_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/projectR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'projectR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'projectR' version '1.0.0'
* 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 ... 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 whether package 'projectR' 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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
projectR-methods 5.13 0 5.13
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/projectR.Rcheck/00check.log'
for details.
projectR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/projectR_1.0.0.tar.gz && rm -rf projectR.buildbin-libdir && mkdir projectR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=projectR.buildbin-libdir projectR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL projectR_1.0.0.zip && rm projectR_1.0.0.tar.gz projectR_1.0.0.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
100 859k 100 859k 0 0 12.4M 0 --:--:-- --:--:-- --:--:-- 13.7M
install for i386
* installing *source* package 'projectR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'projectR'
finding HTML links ... done
AP.RNAseq6l3c3t html
auc_mat html
cluster2pattern-methods html
clusterPlotR-methods html
correlateR-class html
correlateR html
geneMatchR html
initialize-correlateR-method html
initialize-rotatoR-method html
intersectoR-methods html
map.ESepiGen4c1l html
map.RNAseq6l3c3t html
p.ESepiGen4c1l html
p.RNAseq6l3c3t html
pd.ESepiGen4c1l html
pd.RNAseq6l3c3t html
projectR-methods html
rotatoR-class html
rotatoR html
** 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
install for x64
* installing *source* package 'projectR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'projectR' as projectR_1.0.0.zip
* DONE (projectR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'projectR' successfully unpacked and MD5 sums checked
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projectR.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> library(testthat)
> library(projectR)
>
> test_check("projectR")
This is CoGAPS version 3.4.1
Running Standard CoGAPS on 108 genes and 54 samples with parameters:
-- Standard Parameters --
nPatterns 5
nIterations 5000
seed 241
singleCell FALSE
sparseOptimization FALSE
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
Loading Data...Done! (00:00:00)
-- Equilibration Phase --
2500 of 5000, Atoms: 521(242), ChiSq: 28226, Time: 00:00:01 / 00:00:04
5000 of 5000, Atoms: 482(237), ChiSq: 28179, Time: 00:00:02 / 00:00:04
-- Sampling Phase --
2500 of 5000, Atoms: 489(240), ChiSq: 28193, Time: 00:00:04 / 00:00:05
5000 of 5000, Atoms: 473(255), ChiSq: 28236, Time: 00:00:05 / 00:00:05
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
== testthat results ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.59 0.68 13.25
|
projectR.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> library(testthat)
> library(projectR)
>
> test_check("projectR")
This is CoGAPS version 3.4.1
Running Standard CoGAPS on 108 genes and 54 samples with parameters:
-- Standard Parameters --
nPatterns 5
nIterations 5000
seed 850
singleCell FALSE
sparseOptimization FALSE
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
Loading Data...Done! (00:00:00)
-- Equilibration Phase --
2500 of 5000, Atoms: 488(237), ChiSq: 29023, Time: 00:00:00 / 00:00:00
5000 of 5000, Atoms: 510(220), ChiSq: 28467, Time: 00:00:01 / 00:00:02
-- Sampling Phase --
2500 of 5000, Atoms: 488(250), ChiSq: 28264, Time: 00:00:02 / 00:00:02
5000 of 5000, Atoms: 488(243), ChiSq: 28213, Time: 00:00:03 / 00:00:03
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
== testthat results ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.06 0.53 14.57
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projectR.Rcheck/examples_i386/projectR-Ex.timings
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projectR.Rcheck/examples_x64/projectR-Ex.timings
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